Effects of organic fertilizers on plant growth and the rhizosphere microbiome.

Application of organic fertilizers is an important strategy for sustainable agriculture. The biological source of organic fertilizers determines their specific functional characteristics, but few studies have systematically examined these functions or assessed their health risk to soil ecology. To fill this gap, we analyzed 16S rRNA gene amplicon sequencing data from 637 soil samples amended with plant- and animal-derived organic fertilizers (hereafter plant fertilizers and animal fertilizers). Results showed that animal fertilizers increased the diversity of soil microbiome, while plant fertilizers maintained the stability of soil microbial community. Microcosm experiments verified that plant fertilizers were beneficial to plant root development and increased carbon cycle pathways, while animal fertilizers enriched nitrogen cycle pathways. Compared with animal fertilizers, plant fertilizers harbored a lower abundance of risk factors such as antibiotic resistance genes and viruses. Consequently, plant fertilizers might be more suitable for long-term application in agriculture. This work provides a guide for organic fertilizer selection from the perspective of soil microecology and promotes sustainable development of organic agriculture.IMPORTANCEThis study provides valuable guidance for use of organic fertilizers in agricultural production from the perspective of the microbiome and ecological risk.

Maternal secretin ameliorates obesity by promoting white adipose tissue browning in offspring.

Our knowledge of the coordination of intergenerational inheritance and offspring metabolic reprogramming by gastrointestinal endocrine factors is largely unknown. Here, we showed that secretin (SCT), a brain-gut peptide, is downregulated by overnutrition in pregnant mice and women. More importantly, genetic loss of SCT in the maternal gut results in undesirable phenotypes developed in offspring including enhanced high-fat diet (HFD)-induced obesity and attenuated browning of inguinal white adipose tissue (iWAT). Mechanistically, loss of maternal SCT represses iWAT browning in offspring by a global change in genome methylation pattern through upregulation of DNMT1. SCT functions to facilitate ubiquitination and degradation of DNMT1 by activating AMPKα, which contributes to the observed alteration of DNMT1 in progeny. Lastly, we showed that SCT treatment during pregnancy can reduce the development of obesity and improve glucose tolerance and insulin resistance in offspring of HFD-fed females, suggesting that SCT may serve as a novel biomarker or a strategy for preventing metabolic diseases.

Lipid Metabolites as Potential Regulators of the Antibiotic Resistome in Tetramorium caespitum.

Antibiotic resistance genes (ARGs) are ancient but have become a modern critical threat to health. Gut microbiota, a dynamic reservoir for ARGs, transfer resistance between individuals. Surveillance of the antibiotic resistome in the gut during different host growth phases is critical to understanding the dynamics of the resistome in this ecosystem. Herein, we disentangled the ARG profiles and the dynamic mechanism of ARGs in the egg and adult phases of Tetramorium caespitum. Experimental results showed a remarkable difference in both gut microbiota and gut resistome with the development of T. caespitum. Meta-based metagenomic results of gut microbiota indicated the generalizability of gut antibiotic resistome dynamics during host development. By using Raman spectroscopy and metabolomics, the metabolic phenotype and metabolites indicated that the biotic phase significantly changed lipid metabolism as T. caespitum aged. Lipid metabolites were demonstrated as the main factor driving the enrichment of ARGs in T. caespitum. Cuminaldehyde, the antibacterial lipid metabolite that displayed a remarkable increase in the adult phase, was demonstrated to strongly induce ARG abundance. Our findings show that the gut resistome is host developmental stage-dependent and likely modulated by metabolites, offering novel insights into possible steps to reduce ARG dissemination in the soil food chain.

Effects of different assembly strategies on gene annotation in activated sludge.

Activated sludge comprises diverse bacteria, fungi, and other microorganisms, featuring a rich repertoire of genes involved in antibiotic resistance, pollutant degradation, and elemental cycling. In this regard, hybrid assembly technology can revolutionize metagenomics by detecting greater gene diversity in environmental samples. Nonetheless, the optimal utilization and comparability of genomic information between hybrid assembly and short- or long-read technology remain unclear. To address this gap, we compared the performance of the hybrid assembly, short- and long-read technologies, abundance and diversity of annotated genes, and taxonomic diversity by analysing 46, 161, and 45 activated sludge metagenomic datasets, respectively. The results revealed that hybrid assembly technology exhibited the best performance, generating the most contiguous and longest contigs but with a lower proportion of high-quality metagenome-assembled genomes than short-read technology. Compared with short- or long-read technologies, hybrid assembly technology can detect a greater diversity of microbiota and antibiotic resistance genes, as well as a wider range of potential hosts. However, this approach may yield lower gene abundance and pathogen detection. Our study revealed the specific advantages and disadvantages of hybrid assembly and short- and long-read applications in wastewater treatment plants, and our approach could serve as a blueprint to be extended to terrestrial environments.

Whole grains-derived functional ingredients against hyperglycemia: targeting hepatic glucose metabolism.

Type 2 diabetes mellitus (T2DM) is characterized by the dysregulation of glucose homeostasis, resulting in hyperglycemia. However, concerns have been raised about the safety and efficacy of current hypoglycemic drugs due to undesirable side effects. Increasing studies have shown that whole grains (WG) consumption is inversely associated with the risk of T2DM and its subsequent complications. Thus, dietary strategies involving functional components from the WG provide an intriguing approach to restoring and maintaining glucose homeostasis. This review provides a comprehensive understanding of the major functional components derived from WG and their positive effects on glucose homeostasis, demonstrates the underlying molecular mechanisms targeting hepatic glucose metabolism, and discusses the unclear aspects according to the latest viewpoints and current research. Improved glycemic response and insulin resistance were observed after consumption of WG-derived bioactive ingredients, which are involved in the integrated, multi-factorial, multi-targeted regulation of hepatic glucose metabolism. Promotion of glucose uptake, glycolysis, and glycogen synthesis pathways, while inhibition of gluconeogenesis, contributes to amelioration of abnormal hepatic glucose metabolism and insulin resistance by bioactive components. Hence, the development of WG-based functional food ingredients with potent hypoglycemic properties is necessary to manage insulin resistance and T2DM.

Antimicrobial Peptides in the Global Microbiome: Biosynthetic Genes and Resistance Determinants.

Antimicrobial peptides are a promising new class of antimicrobials that could address the antibiotic resistance crisis, which poses a major threat to human health. These peptides are present in all kingdoms of life, but especially in microorganisms, having multiple origins in diverse taxa. To date, there has been no global study on the diversity of antimicrobial peptides, the hosts in which these occur, and the potential for resistance to these agents. Here, we investigated the diversity and number of antimicrobial peptides in four main habitats (aquatic, terrestrial, human, and engineered) by analyzing 52,515 metagenome-assembled genomes. The number of antimicrobial peptides was higher in the human gut microbiome than in other habitats, and most hosts of antimicrobial peptides were habitat-specific. The relative abundance of genes that confer resistance to antimicrobial peptides varied between habitats and was generally low, except for the built environment and on human skin. The horizontal transfer of potential resistance genes among these habitats was probably constrained by ecological barriers. We systematically quantified the risk of each resistance determinant to human health and found that nearly half of them pose a threat, especially those that confer resistance to multiple AMPs and polymyxin B. Our results help identify the biosynthetic potential of antimicrobial peptides in the global microbiome, further identifying peptides with a low risk of developing resistance.

Effect of chlorpyrifos on freshwater microbial community and metabolic capacity of zebrafish.

Chlorpyrifos is a widely used organophosphorus insecticide because of its high efficiency and overall effectiveness, and it is commonly detected in aquatic ecosystems. However, at present, the impact of chlorpyrifos on the aquatic micro-ecological environment is still poorly understood. Here, we established aquatic microcosm systems treated with 0.2 and 2.0 µg/L chlorpyrifos, and employed omics biotechnology, including metagenomics and 16S rRNA gene sequencing, to investigate the effect of chlorpyrifos on the composition and functional potential of the aquatic and zebrafish intestinal microbiomes after 7 d and 14 d chlorpyrifos treatment. After 14 d chlorpyrifos treatment, the aquatic microbial community was adversely affected in terms of its composition, structure, and stability, while its diversity showed only a slight impact. Most functions, especially capacities for environmental information processing and metabolism, were destroyed by chlorpyrifos treatment for 14 d. We observed that chlorpyrifos increased the number of risky antibiotic resistance genes and aggravated the growth of human pathogens. Although no clear effects on the structure of the zebrafish intestinal microbial community were observed, chlorpyrifos treatment did alter the metabolic capacity of the zebrafish. Our study highlights the ecological risk of chlorpyrifos to the aquatic environment and provides a theoretical basis for the rational use of pesticides in agricultural production.

Cadmium induced a non-coding RNA microRNA535 mediates Cd accumulation in rice.

Identifying key regulators related to cadmium (Cd) tolerance and accumulation is the main factor for genetic engineering to improve plants for bioremediation and ensure crop food safety. MicroRNAs (miRNAs), as fine-tuning regulators of genes, participate in various abiotic stress processes. MiR535 is an ancient conserved non-coding small RNA in land plants, positively responding to Cd stress. We investigated the effects of knocking out (mir535) and overexpressing miR535 (mir535 and OE535) under Cd stress in rice plants in this study. The mir535 plants showed better Cd tolerance than wild type (WT), whereas the OE535 showed the opposite effect. Cd accumulated approximately 71.9% and 127% in the roots of mir535 and OE535 plants, respectively, compared to WT, after exposure to 2 µmol/L Cd. In brown rice, the total Cd accumulation of OE535 and mir535 was about 78% greater and 35% lower than WT. When growing in 2 mg/kg Cd of soil, the Cd concentration was significantly lower in mir535 and higher in OE535 than in the WT; afterward, we further revealed the most possible target gene SQUAMOSA promoter binding-like transcription factor 7(SPL7) and it negatively regulates Nramp5 expression, which in turn regulates Cd metabolism. Therefore, the CRISPR/Cas9 technology may be a valuable strategy for creating new rice varieties to ensure food safety.

The mechanism of different cyanobacterial responses to glyphosate.

Glyphosate, the most extensively used herbicide globally, has raised ecotoxicological concerns because it can be transported into the aquatic environment and cause adverse effects on the aquatic system. However, the functional mechanism of glyphosate on cyanobacteria are not completely disentangled. In this study, we selected six common cyanobacteria to evaluate glyphosate effects on cyanobacterial growth in monoculture experiment. Results showed that the growth of five tested cyanobacterial species were promoted under different degrees, and only Pseudanabaena was inhibited by glyphosate. In the phylogenetic tree based on gene sequences of 5-enol-pyruvylshikimate-3-phosphate synthase (EPSPS), a target for glyphosate, we found that the position of Pseudanabaena is the closest to plant, which was sensitive to glyphosate, thereby explaining the inhibitory effect of Pseudanabaena following glyphosate exposure. The primary degraded metabolites or analogs did not induce cyanobacterial growth, laterally demonstrating that glyphosate was used as a source of phosphorus to accelerate cyanobacterial growth because phosphorus levels increased in the medium of glyphosate treatment. Overall, this study provides a better understanding of the influence of glyphosate on the composition of aquatic microbiota and explains the mechanism of cyanobacterial response to glyphosate.

Composition identification and functional verification of bacterial community in disease-suppressive soils by machine learning.

It has been widely reported that probiotic consortia in the rhizosphere can enhance the plant resistance to pathogens. However, the general composition and functional profiles of bacterial community in soils which suppress multiple diseases for various plants remain largely unknown. Here, we combined metadata analysis with machine learning to identify the general patterns of bacterial-community composition in disease-suppressive soils. Disease-suppressive soils significantly enriched Firmicutes and Actinobacteria but showed a decrease in Proteobacteria and Bacteroidetes. Our machine-learning models accurately identified the disease-conducive and -suppressive soils with 54 biomarker genera, 28 of which were potentially beneficial. We further carried out a successive passaging experiment with the susceptible rps2 mutant of Arabidopsis thaliana invaded by Pseudomonas syringae pv. tomato DC3000 (avrRpt2) for functional verification of potential beneficial bacteria. The disease-suppressive ability of Kribbella, Nocardioides and Bacillus was confirmed, and they positively activated the pathogen-associated molecular patterns-triggered immunity pathway. Results also showed that chemical control by pesticides in agricultural production decreased the disease-suppressive ability of soil. This study provides a method for accurately predicting the occurrence of multiple diseases in soil and identified potential beneficial bacteria to guide a wide range of multiple-strain biological control strategies in agricultural management.

Development of a machine-learning model to identify the impacts of pesticides characteristics on soil microbial communities from high-throughput sequencing data.

High-throughput sequencing (HTS) of soil environmental DNA provides an advanced insight into the effects of pesticides on soil microbial systems. However, the association between the properties of the pesticide and its ecological impact remains methodically challenging. Risks associated with pesticide use can be minimized if pesticides with optimal structural traits were applied. For this purpose, we merged the 20 independent HTS studies, to reveal that pesticides significantly reduced beneficial bacteria associated with soil and plant immunity, enhanced the human pathogen and weaken the soil's ecological stability. Through the machine-learning approach, correlating these impacts with the physicochemical properties of the pesticides yielded a random forest model with good predictive capabilities. The models revealed that physical pesticide properties such as the dissociation constant (pKa), the molecular weight and water solubility, determined the ecological impact of pesticides to a large extent. Moreover, this study identified that eco-friendly pesticides should possess a value of pKa > 5 and a molecular weight in the range of 200-300 g/mol, which were found to be conducive to bacteria related to plant immunity promotion and exerted the lowest fluctuation of human opportunistic pathogen and keystone species. This guides the design of pesticides for which the impacts on soil biota are minimized.

Advanced glycation end products in food and their effects on intestinal tract.

With the development of living standards, harmful substances in diet and food safety have seriously endangered people health and life. Advanced glycation end products (AGEs), which formed by Maillard reactions in processed food, have been shown a significantly associated with many chronic diseases, such as nephropathy, atherosclerosis, Alzheimer's disease, and tumors. In recent years, the research about diet advanced glycation end products (dAGEs) have widespread controversy in academia. The main arguments include the production mechanism of dAGEs, metabolic pathways, and relationships with chronic diseases, especially related to the intestines, gut microbiota, and intestinal disorders. So this review attempts to briefly summarize the dAGE in following aspects, including the influencing factors, metabolism, absorption, and so forth. In addition, the effects of dAGEs on intestinal health and gut microbes were discussed, which can offer a goal for boff in to design low dAGEs products and provided some perspectives for further study with AGEs in the future.

Wheat bran, as the resource of dietary fiber: a review.

Wheat bran is a major by-product of white flour milling and had been produced in large quantities around the world; it is rich in dietary fiber and had already been used in many products such as whole grain baking or high dietary fiber addition. It has been confirmed that a sufficient intake of dietary fiber in wheat bran with appropriate physiological functions is beneficial to human health. Wheat bran had been considered as the addition with a large potential for improving the nutritional condition of the human body based on the dietary fiber supplement. The present review summarized the available information on wheat bran related to its dietary fiber functions, which may be helpful for further development of wheat bran as dietary fiber resource.

Does biological rhythm transmit from plants to rhizosphere microbes?

Plant physiological and metabolic processes are modulated by rhythmic gene expression in a large part. Meanwhile, plants are also regulated by rhizosphere microorganisms, which are fed by root exudates and provide beneficial functions to their plant host. Whether the biorhythms in plants would transfer to the rhizosphere microbial community is still uncertain and their intricate connection remains poorly understood. Here, we investigated the role of the Arabidopsis circadian clock in shaping the rhizosphere microbial community using wild-type plants and clock mutants (cca1-1 and toc1-101) with transcriptomic, metabolomic and 16S rRNA gene sequencing analysis throughout a 24-h period. Deficiencies of the central circadian clock led to abnormal diurnal rhythms for thousands of expressed genes and dozens of root exudates. The bacterial community failed to follow obvious patterns in the 24-h period, and there was lack of coordination with plant growth in the clock mutants. Our results suggest that the robust rhythmicity of genes and root exudation due to circadian clock in plants is an important driving force for the positive succession of rhizosphere communities, which will feedback on plant development.

microRNA-378 promotes autophagy and inhibits apoptosis in skeletal muscle.

The metabolic regulation of cell death is sophisticated. A growing body of evidence suggests the existence of multiple metabolic checkpoints that dictate cell fate in response to metabolic fluctuations. However, whether microRNAs (miRNAs) are able to respond to metabolic stress, reset the threshold of cell death, and attempt to reestablish homeostasis is largely unknown. Here, we show that miR-378/378* KO mice cannot maintain normal muscle weight and have poor running performance, which is accompanied by impaired autophagy, accumulation of abnormal mitochondria, and excessive apoptosis in skeletal muscle, whereas miR-378 overexpression is able to enhance autophagy and repress apoptosis in skeletal muscle of mice. Our in vitro data show that metabolic stress-responsive miR-378 promotes autophagy and inhibits apoptosis in a cell-autonomous manner. Mechanistically, miR-378 promotes autophagy initiation through the mammalian target of rapamycin (mTOR)/unc-51-like autophagy activating kinase 1 (ULK1) pathway and sustains autophagy via Forkhead box class O (FoxO)-mediated transcriptional reinforcement by targeting phosphoinositide-dependent protein kinase 1 (PDK1). Meanwhile, miR-378 suppresses intrinsic apoptosis initiation directly through targeting an initiator caspase-Caspase 9. Thus, we propose that miR-378 is a critical component of metabolic checkpoints, which integrates metabolic information into an adaptive response to reduce the propensity of myocytes to undergo apoptosis by enhancing the autophagic process and blocking apoptotic initiation. Lastly, our data suggest that inflammation-induced down-regulation of miR-378 might contribute to the pathogenesis of muscle dystrophy.

Nano-Sized Polystyrene at 1 mg/L Concentrations Does Not Show Strong Disturbance on the Freshwater Microbial Community.

In recent years, microplastics and nanoplastics have gained public attention, but their impacts on the freshwater microbial communities is rarely evaluated. In this study, the effects of 1 mg/L nano-sized polystyrene (nPS) and its modified forms (carboxyl-modified and amino-modified nPS) on the structures and functions of freshwater microbial community were determined. The nPS were found to slightly reduce the chlorophyll-a and increase the phycocyanin contents of freshwater microbial communities. Moreover, the richness of the microbial communities temporarily decreased during this process, while their diversity remained uninfluenced by treatment with nPS. Although the three tested nPS types were found to disturb the compositions of both the prokaryotic and eukaryotic communities to some degree, they did not affect the functions of freshwater bacterial communities significantly due to functional redundancy. Our study demonstrated that the ecotoxicities of the nPS itself were found to be lower than what is generally expected.

Pollutant toxicology with respect to microalgae and cyanobacteria.

Microalgae and cyanobacteria are fundamental components of aquatic ecosystems. Pollution in aquatic environment is a worldwide problem. Toxicological research on microalgae and cyanobacteria can help to establish a solid foundation for aquatic ecotoxicological assessments. Algae and cyanobacteria occupy a large proportion of the biomass in aquatic environments; thus, their toxicological responses have been investigated extensively. However, the depth of toxic mechanisms and breadth of toxicological investigations need to be improved. While existing pollutants are being discharged into the environment daily, new ones are also being produced continuously. As a result, the phenomenon of water pollution has become unprecedentedly complex. In this review, we summarize the latest findings on five kinds of aquatic pollutants, namely, metals, nanomaterials, pesticides, pharmaceutical and personal care products (PPCPs), and persistent organic pollutants (POPs). Further, we present information on emerging pollutants such as graphene, microplastics, and ionic liquids. Efforts in studying the toxicological effects of pollutants on microalgae and cyanobacteria must be increased in order to better predict the potential risks posed by these materials to aquatic ecosystems as well as human health.

Leaf metabolic influence of glyphosate and nanotubes on the Arabidopsis thaliana phyllosphere.

Chemical exposure can indirectly affect leaf microbiota communities, but the mechanism driving this phenomenon remains largely unknown. Results revealed that the co-exposure of glyphosate and multi-carbon nanotubes (CNTs) caused a synergistic inhibitory effect on the growth and metabolism of Arabidopsis thaliana shoots. However, only a slight inhibitory effect was induced by nanotubes or glyphosate alone at the tested concentrations. Several intermediate metabolites of nitrogen metabolism and fatty acid synthesis pathways were upregulated under the combined treatment, which increased the amount of energy required to alleviate the disruption caused by the combined treatment. Additionally, compared with the two individual treatments, the glyphosate/nanotube combination treatment induced greater fluctuations in the phyllosphere bacterial community members with low abundance (relative abundance (RA) <1%) at both the family and genus levels, and among these bacteria some plant growth promotion and nutrient supplement related bacteria were markable increased. Strikingly, strong correlations between phyllosphere bacterial diversity and metabolites suggested a potential role of leaf metabolism, particularly nitrogen and carbohydrate metabolism, in restricting the range of leaf microbial taxa. These correlations between phyllosphere bacterial diversity and leaf metabolism will improve our understanding of plant-microbe interactions and the extent of their drivers of variation and the underlying causes of variability in bacterial community composition.

Alteration of dominant cyanobacteria in different bloom periods caused by abiotic factors and species interactions.

Freshwater cyanobacterial blooms have drawn public attention because they threaten the safety of water resources and human health worldwide. Heavy cyanobacterial blooms outbreak in Lake Taihu in summer annually and vanish in other months. To find out the factors impacting the cyanobacterial blooms, the present study measured the physicochemical parameters of water and investigated the composition of microbial community using the 16S rRNA gene and internal transcribed spacer amplicon sequencing in the months with or without bloom. The most interesting finding is that two major cyanobacteria, Planktothrix and Microcystis, dramatically alternated during a cyanobacterial bloom in 2016, which is less mentioned in previous studies. When the temperature of the water began increasing in July, Planktothrix appeared first and showed as a superior competitor for M. aeruginosa in NO3--rich conditions. Microcystis became the dominant genus when the water temperature increased further in August. Laboratory experiments confirmed the influence of temperature and the total dissolved nitrogen (TDN) form on the growth of Planktothrix and Microcystis in a co-culture system. Besides, species interactions between cyanobacteria and non-cyanobacterial microorganisms, especially the prokaryotes, also played a key role in the alteration of Planktothrix and Microcystis. The present study exhibited the alteration of two dominant cyanobacteria in the different bloom periods caused by the temperature, TDN forms as well as the species interactions. These results helped the better understanding of cyanobacterial blooms and the factors which contribute to them.

Geniposide reduces cholesterol accumulation and increases its excretion by regulating the FXR-mediated liver-gut crosstalk of bile acids.

Hypercholesterolemia is the main risk factor to threaten human health and geniposide has been found to have hypolipidemic functions. However, its underlying mechanism is not clear. In this study, we firstly confirmed the hypolipidemic functions of geniposide in C57BL/6 and ApoE-/- mice (i.p, 50 mg/kg/d). Then hepatic or arterial lipid accumulation was analyzed through histomorphology. Moreover, the effects of geniposide on the bile acid metabolism were analyzed by the hepatic RNA-seq and biological molecular analysis. Mechanistically, GW4064, an FXR agonist, was carried out to verify the mechanisms of geniposide in human HepG2 and Caco2 cells. As expected, geniposide decreased the lipid accumulations both in plasma and liver. Morever, the atherosclerotic plaque shrank in HCD-fed ApoE-/- mice with geniposide treatment. The molecular analysis revealed that geniposide accelerated the hepatic synthesis of bile acids through inactivating the negative feedback regulation of bile acids mediated by FXR, led to the enhancive reverse cholesterol transport and cholesterol catabolism. What's more, geniposide reduced ileal FXR-mediated reabsorption of bile acids, resulting in the increasing excretion of bile acids. Our study pointed out the regulatory functions of geniposide on FXR-mediated liver-gut crosstalk of bile acids and geniposide might be a novel strategy for maintaining cholesterol homeostasis.