Predicting metabolic pathways and microbial interactions in dark fermentation systems treating real cheese whey effluents.

Dark fermentation of agro-industrial effluents is a promising way for waste valorization. However, understanding the complex microbial dynamics and metabolic interactions within the microbial communities remains challenging. This study investigates the microbial communities involved in continuous hydrogen production from cheese whey and fermented cheese whey using functional profiling with PICRUSt2. The analysis reveals the primary roles of key microbial genera. Lactobacillus dominates carbohydrate consumption and lactate production, while Clostridium sensu stricto 12 and Caproiciproducens are engaged in a competitive dynamic for lactate utilization. Clostridium sensu stricto 12 drives hydrogen production via electron bifurcation reactions, whereas Caproiciproducens may utilize alternative energy conservation mechanisms. The interaction between these genera is influenced by substrate availability and process conditions. This study highlights the utility of functional profiling in elucidating microbial interactions and metabolic pathways in dark fermentation. The findings emphasize the importance of understanding microbial interactions to optimize biohydrogen production processes.

Exploring the Rhizospheric Microbial Communities under Long-Term Precipitation Regime in Norway Spruce Seed Orchard.

The rhizosphere is the hotspot for microbial enzyme activities and contributes to carbon cycling. Precipitation is an important component of global climate change that can profoundly alter belowground microbial communities. However, the impact of precipitation on conifer rhizospheric microbial populations has not been investigated in detail. In the present study, using high-throughput amplicon sequencing, we investigated the impact of precipitation on the rhizospheric soil microbial communities in two Norway Spruce clonal seed orchards, Lipová Lhota (L-site) and Prenet (P-site). P-site has received nearly double the precipitation than L-site for the last three decades. P-site documented higher soil water content with a significantly higher abundance of Aluminium (Al), Iron (Fe), Phosphorous (P), and Sulphur (S) than L-site. Rhizospheric soil metabolite profiling revealed an increased abundance of acids, carbohydrates, fatty acids, and alcohols in P-site. There was variance in the relative abundance of distinct microbiomes between the sites. A higher abundance of Proteobacteria, Acidobacteriota, Ascomycota, and Mortiellomycota was observed in P-site receiving high precipitation, while Bacteroidota, Actinobacteria, Chloroflexi, Firmicutes, Gemmatimonadota, and Basidiomycota were prevalent in L-site. The higher clustering coefficient of the microbial network in P-site suggested that the microbial community structure is highly interconnected and tends to cluster closely. The current study unveils the impact of precipitation variations on the spruce rhizospheric microbial association and opens new avenues for understanding the impact of global change on conifer rizospheric microbial associations.

Enhancement of methane production from anaerobic co-digestion of food waste and dewatered sludge by thermal, ultrasonic and alkaline technologies integrated with protease pretreatment.

Pretreatments to improve the efficiency of anaerobic digestion (AD) have gained more attention. The efficiency and mechanism of neutral protease (NP) integrated with other methods remain unclear. This study investigated the efficacy of thermal, alkaline and ultrasonic technologies integrated with NP as the pre-treatments for AD of food waste and dewatered sludge. Results showed the thermal method integrated with NP (TH-NP) was the most effective, achieving a 104.2% improvement in methane production. In this case, TH-NP increased soluble chemical oxygen demand and protein concentrations by 8.6% and 39.8%, respectively. Microbial community analysis indicated that TH-NP promoted the symbiosis between Woesearchaeales and hydrogenotrophic methanogenesis. Furthermore, the PICRUSt2 analysis revealed that TH-NP increased the activities of most enzymes in the acetate and propionate metabolic pathways. In summary, TH-NP is more effective in increasing the AD efficiency compared to other combined pretreatments. This study provides theoretical support for protease-induced pretreatment technology.

Stratified Effects of Tillage and Crop Rotations on Soil Microbes in Carbon and Nitrogen Cycles at Different Soil Depths in Long-Term Corn, Soybean, and Wheat Cultivation.

Understanding the soil bacterial communities involved in carbon (C) and nitrogen (N) cycling can inform beneficial tillage and crop rotation practices for sustainability and crop production. This study evaluated soil bacterial diversity, compositional structure, and functions associated with C-N cycling at two soil depths (0-15 cm and 15-30 cm) under long-term tillage (conventional tillage [CT] and no-till [NT]) and crop rotation (monocultures of corn, soybean, and wheat and corn-soybean-wheat rotation) systems. The soil microbial communities were characterized by metabarcoding the 16S rRNA gene V4-V5 regions using Illumina MiSeq. The results showed that long-term NT reduced the soil bacterial diversity at 15-30 cm compared to CT, while no significant differences were found at 0-15 cm. The bacterial communities differed significantly at the two soil depths under NT but not under CT. Notably, over 70% of the tillage-responding KEGG orthologs (KOs) associated with C fixation (primarily in the reductive citric acid cycle) were more abundant under NT than under CT at both depths. The tillage practices significantly affected bacteria involved in biological nitrogen (N2) fixation at the 0-15 cm soil depth, as well as bacteria involved in denitrification at both soil depths. The crop type and rotation regimes had limited effects on bacterial diversity and structure but significantly affected specific C-N-cycling genes. For instance, three KOs associated with the Calvin-Benson cycle for C fixation and four KOs related to various N-cycling processes were more abundant in the soil of wheat than in that of corn or soybean. These findings indicate that the long-term tillage practices had a greater influence than crop rotation on the soil bacterial communities, particularly in the C- and N-cycling processes. Integrated management practices that consider the combined effects of tillage, crop rotation, and crop types on soil bacterial functional groups are essential for sustainable agriculture.

Analysis of the Diversity and Functional Potential of Bacterial Communities in Tuberculomas.

The dynamics of lung microbiota in tuberculosis remains poorly understood. Sequencing of variable regions of the 16S rRNA gene from surgically excised tuberculosis foci and biopsy specimens of normal lung tissue allowed characterization of the diversity and predictive potential of bacterial communities. Taxonomic diversity indices attested to differences in the structure of microbial communities between "healthy" lungs and tuberculomas. The microbial composition of "healthy" lungs varied in taxonomic diversity and was presented by both gram-positive and gram-negative bacteria with sufficiently similar metabolic potential. The microbiota of the examined tuberculomas consisted of Mycobacterium tuberculosis in 99.9% of cases. A significant part of the metabolic pathways predicted by PICRUSt2 included cholesterol catabolism, sulfate assimilation, and various pathways for the biosynthesis of cell wall components.

Impacts of organophosphate pesticide types and concentrations on aquatic bacterial communities and carbon cycling.

Organophosphorus pesticides (OPPs) are important chemical stressors in aquatic ecosystems, and they attract increasing more attentions recently. However, the impacts of different OPPs on carbon cycling remain unclear, particularly for those functional-yet-uncultivable microbes. This study investigated the change in lake aquatic microbial communities in the presence of dichlorvos, monocrotophos, omethoate and parathion. All OPPs significantly inhibited biomass (p < 0.05) and the expression of carbon cycle-related cbbLG gene (p < 0.01), and altered aquatic microbial community structure, interaction, and assembly. Variance partitioning analysis showed a stronger impact of pesticide type on microbial biomass and community structure, where pesticide concentration played more significant roles in carbon cycling. From analysis of cbbLG gene and PICRUSt2, Luteolibacter and Verrucomicrobiaceae assimilated inorganic carbon through Wood-Ljungdahl pathway, whereas it was Calvin-Benson-Bassham cycle for Cyanobium PCC-6307. This work provides a deeper insight into the behavior and mechanisms of microbial community change in aquatic system in response to OPPs, and explicitly unravels the impacts of OPPs on their carbon-cycling functions.

Inhibition effect of Cu(II) on nitrogen removal in anammox-denitrification couple system.

Due to the wide application in industries, copper can be detected in some nitrogen-rich wastewater. In this research, short-term and long-term experiments were conducted to explore the effects of Cu(II) on the anammox-denitrification couple system. It concluded that the half inhibition concentration (IC50) of Cu(II) was 35.54 mg/L. The system in reactor could tolerate low concentrations of Cu(II) (≤5 mg/L), while the total nitrogen removal efficiency decreased from 93 % to 33 % under 10 mg/L of Cu(II). After 45 days exposure to Cu(II) (1-10 mg/L), 14.54 mg/g SS copper accumulated in the sludge, which largely inhibited the microbial activity. More extracellular polymeric substances (EPS) were secreted to defend against copper toxicity. Proteobacteria (19.18 %-44.04 %) was the dominant phylum and showed excellent tolerance and adaptability to Cu(II). The dominant anammox bacteria, Candidatus_Brocadia, was slightly enhanced under low concentrations of Cu(II), but was highly inhibited under 10 mg/L of Cu(II). PICRUSt2 results showed that some metabolic activities were suppressed under the exposure of copper while defensive responses were also induced. Metabolic disorders eventually led to the death of some microbes, resulting in unrecoverable deterioration in microbial activity. Overall, this study explores the effect of Cu(II) on the anammox-denitrification process and provides a possible inhibition mechanism.

Changes in chemical properties and microbial communities' composition of a forest litter-based biofertilizer produced through aerated solid-state culture under different oxygen conditions.

Fermented forest litter (FFL) is a bioproduct used as biofertilizer for several decades in Eastern Asia and Latin America. It is locally handcrafted by farmers in anaerobic conditions by fermenting forest litter added with agricultural by-products such as whey, cereal bran, and molasses. The aim of this study was to characterize the FFL process and product through gas and liquid chromatography analyses. It also provides some highlights on the influence of O2 on this solid-state culture. Under anoxic condition, a maximum CO2 production rate (CDPR) of 0.41 mL/h∙g dry matter (dm) was reached after 8 days. The main volatile organic compounds (VOCs) were ethanol and ethyl acetate, with a production rate profile similar to CDPR. After 21 days of culture, no residual sucrose nor lactose was detected. Lactic and acetic acids reached 58.8 mg/g dm and 10.2 mg/g dm, respectively, ensuring the acidification of the matrix to a final pH of 4.72. A metabarcoding analysis revealed that heterolactic acid bacteria (Lentilactobacillus, Leuconostoc), homolactic acid bacteria (Lactococcus), and yeasts (Saccharomyces, Clavispora) were predominant. Predicted genes in the microbiome confirmed the potential link between detected bacteria and acids and VOCs produced. When O2 was fed to the cultures, final pH reached values up to 8.5. No significant amounts of lactic nor acetic acid were found. In addition, a strong shift in microbial communities was observed, with a predominance of Proteobacteria and molds, among which are potential pathogens like Fusarium species. This suggests that particular care must be brought to maintain anoxic conditions throughout the process.

Oral microbiota transplantation for intra-oral halitosis: a feasibility analysis based on an oral microbiota colonization trial in Wistar rats.

BACKGROUND: Intra-oral halitosis (IOH) is bad breath produced locally by the mouth in addition to systemic diseases and is one of the main causes of interpersonal communication and psychological disorders in modern society. However, current treatment modalities still only alleviate IOH and do not eradicate it. Therefore, based on the differential performance of oral microecology in IOH patients, we propose a microbiota transplantation treatment aimed at restoring oral microecological balance and analyze its feasibility by oral flora colonization test in Wistar rats. OBJECTIVE: Saliva flora samples were collected from IOH patients and healthy subjects to analyze the feasibility of oral microbiota transplantation (OMT) for the treatment of IOH by the Wistar rat oral flora colonization test. METHODS: Seven patients with IOH who visited the First Affiliated Hospital of Xinjiang Medical University from June 2017 to June 2022 with the main complaint of halitosis and three healthy subjects were randomly selected. A Halimeter portable breath detector was used to record breath values and collect saliva flora samples. Sixteen SPF-grade male Wistar rats were housed in the Animal Experiment Center of Xinjiang Medical University and randomly divided into an experimental group (Group E) and a control group (Group C) for the oral flora colonization test. Species composition and associated metabolic analysis of oral flora during the Wistar rat test using 16SrRNA sequencing technology and PICRUSt metabolic analysis. Also, the changes in the breath values of the rats were recorded during the test. RESULTS: The proportion of Porphyromonas, Fusobacterium, Leptotrichia, and Peptostreptococcus was significantly higher in group E compared to group C after colonization of salivary flora of IOH patients (all P < 0.05), and the abundance with Gemella was zero before colonization, while no colonization was seen in group C after colonization compared to baseline. PICRUSt metabolic analysis also showed significantly enhanced IOH-related metabolic pathways after colonization in group E (all P < 0.05), as well as significantly higher breath values compared to baseline and group C (all P < 0.0001). After colonization by salivary flora from healthy subjects, group E rats showed a decrease in the abundance of associated odor-causing bacteria colonization, a reduction in associated metabolism, and a significant decrease in breath values. In contrast, group C also showed differential changes in flora structure and breath values compared to baseline after salivary flora colonization of IOH patients. CONCLUSIONS: OMT for IOH is a promising green treatment option, but the influence of environmental factors and individual differences still cannot be ignored.

Bioaugmentation of anaerobic digesters with the enriched lignin-degrading microbial consortia through a metagenomic approach.

The recalcitrance of lignin impedes the efficient utilization of lignocellulosic biomass, hindering the efficient production of biogas and value-added materials. Despite the emergence of anaerobic digestion as a superior alternative to the aerobic method for lignin processing, achieving its feasibility requires thorough characterization of lignin-degrading anaerobic microorganisms, assessment of their biomethane production potential, and a comprehensive understanding of the degradation pathway. This study aimed to address the aforementioned necessities by bioaugmenting seed sludge with three distinct enriched lignin-degrading microbial consortia at both 25 °C and 37 °C. Enhanced biomethane yields was detected in the bioaugmented digesters, while the highest production was observed as 188 mLN CH4 gVS-1 in digesters operated at 37 °C. Moreover, methane yield showed a significant improvement in the samples at 37 °C ranging from 110% to 141% compared to the control, demonstrating the efficiency of the enriched lignin-degrading microbial community. Temperature and substrate were identified as key factors influencing microbial community dynamics. The observation that microbial communities tended to revert to the initial state after lignin depletion, indicating the stability of the overall microbiota composition in the digesters, is a promising finding for large-scale studies. Noteworthy candidates for lignin degradation, including Sporosarcina psychrophila, Comamonas aquatica, Shewanella baltica, Pseudomonas sp. C27, and Brevefilum fermentans were identified in the bioaugmented samples. PICRUSt2 predictions suggest that the pathway and specific proteins involved in anaerobic lignin degradation might share similarities with those engaged in the degradation of aromatic compounds.

Both the scion and rootstock of grafted grapevines influence the rhizosphere and root endophyte microbiomes, but rootstocks have a greater impact.

BACKGROUND: Soil microorganisms play an extensive role in the biogeochemical cycles providing the nutrients necessary for plant growth. Root-associated bacteria and fungi, originated from soil, are also known to influence host health. In response to environmental stresses, the plant roots exude specific molecules influencing the composition and functioning of the rhizospheric and root microbiomes. This response is host genotype-dependent and is affected by the soil microbiological and chemical properties. It is essential to unravel the influence of grapevine rootstock and scion genotypes on the composition of this microbiome, and to investigate this relationship with plant growth and adaptation to its environment. Here, the composition and the predicted functions of the microbiome of the root system were studied using metabarcoding on ten grapevine scion-rootstock combinations, in addition to plant growth and nutrition measurements. RESULTS: The rootstock genotype significantly influenced the diversity and the structure of the bacterial and fungal microbiome, as well as its predicted functioning in rhizosphere and root compartments when grafted with the same scion cultivar. Based on ß-diversity analyses, 1103P rootstock showed distinct bacterial and fungal communities compared to the five others (RGM, SO4, 41B, 3309 C and Nemadex). The influence of the scion genotype was more variable depending on the community and the investigated compartment. Its contribution was primarily observed on the ß-diversity measured for bacteria and fungi in both root system compartments, as well as for the arbuscular mycorrhizal fungi (AMF) in the rhizosphere. Significant correlations were established between microbial variables and the plant phenotype, as well as with the plant mineral status measured in the petioles and the roots. CONCLUSION: These results shed light on the capacity of grapevine rootstock and scion genotypes to recruit different functional communities of microorganisms, which affect host growth and adaptation to the environment. Selecting rootstocks capable of associating with positive symbiotic microorganisms is an adaptation tool that can facilitate the move towards sustainable viticulture and help cope with environmental constraints.

Enhancing the Startup Rate of Microbial Methanogenic Systems through the Synergy of ß-lactam Antibiotics and Electrolytic Cells.

The slow startup and suboptimal efficiency of microbial carbon sequestration and methane-production systems have not been fully resolved despite their contribution to sustainable energy production and the reduction of greenhouse gas emissions. These systems often grapple with persistent hurdles, including interference from miscellaneous bacteria and the slow enrichment of methanogens. To address these issues, this paper examines the synergistic effect of coupling ß-lactam antibiotics with an electrolytic cell on the methanogenic process. The results indicated that ß-lactam antibiotics exhibited inhibitory effects on Campylobacteria and Alphaproteobacteria (two types of miscellaneous bacteria), reducing their relative abundance by 53.03% and 87.78%, respectively. Nevertheless, it also resulted in a decrease in hydrogenogens and hindered the CO2 reduction pathway. When coupled with an electrolytic cell, sufficient electrons were supplied for CO2 reduction to compensate for the hydrogen deficiency, effectively mitigating the side effects of antibiotics. Consequently, a substantial improvement in methane production was observed, reaching 0.57 mL·L-1·d-1, exemplifying a remarkable 6.3-fold increase over the control group. This discovery reinforces the efficiency of methanogen enrichment and enhances methane-production levels.

Naturalization of treated wastewater by a constructed wetland in a water-scarce Mediterranean region.

The effluents from conventional wastewater treatment plants (WWTP), even if accomplishing quality regulations, substantially differ in their characteristics with those of waters in natural environments. Constructed wetlands (CWs) serve as transitional ecosystems within WWTPs, mitigating these differences and restoring natural features before water is poured into the natural environment. Our study focused on an experimental surface-flow CW naturalizing the WWTP effluent in a semiarid area in Eastern Spain. Despite relatively low pollutant concentrations entering the CW, it effectively further reduced settled organic matter and nitrogen. Dissolved organic matter (DOM) reaching the CW was mainly protein-like, yet optical property changes in the DOM indicated increased humification, aromaticity, and stabilization as it flowed through the CW. Flow cytometry analysis revealed that the CW released less abundant but more active bacterial populations than those received. MiSeq Illumina sequencing highlighted changes in the prokaryotic community composition, with phyla Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria dominating the CW outflow. Functional prediction tools (FaproTax and PICRUSt2) demonstrated a shift towards microbial guilds aligned with those of the natural aquatic environments, increased aerobic chemoheterotrophs, photoautotrophs, and metabolic reactions at higher redox potentials. Enhanced capabilities for degrading plant material correlated well with changes in the DOM pool. Our findings emphasize the role of CWs in releasing biochemically stable DOM and functionally suited microbial populations for natural receiving environments. Consequently, we propose CWs as a naturalization nature-based solution (NBS) in water-scarce regions like the Mediterranean, where reclaimed discharged water can significantly contribute to ecosystem's water resources compared to natural flows.

Microbial Communities and Functional Genes in Periodontitis and Healthy Controls.

BACKGROUND: Periodontitis is a chronic progressive disease and the leading cause of tooth loss in adults. Recent studies have shown the impact of oral microbial communities on systemic health and diseases such as cancer, atherosclerosis, rheumatoid arthritis, inflammatory bowel disease, diabetes, hypertension, and Alzheimer's disease. In previous case control studies investigatin the relationship between periodontal disease and the oral microbiota, little attention has been paid to the intersections of these domains. METHODS: Here, we used high-throughput 16S rRNA sequencing to analyse the differences in the microbial composition in saliva between a group of patients with chronic periodontitis (C; n = 51) and a healthy control group (H; n = 61) and predicted the functional gene composition by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States. RESULTS: We found significant alterations in oral microbial diversity between C and H (P = 0.002). Sixteen genera were significantly different between C and H, and 15 of them were enriched in C linear discriminant analysis (LDA > 2). Fifty functional genes were significantly different between C and H, and 34 of them were enriched in C (P < .025). CONCLUSIONS: Periodontitis is associated with significant changes in the oral microbial community.

Gut microbiota profiling in obese children from Southeastern China.

Childhood obesity not only has a negative impact on a child's health but is also a significant risk factor for adult obesity and related metabolic disorders, making it a major global public health concern. Recent studies have revealed the crucial role of gut microbiota in the occurrence and development of obesity, in addition to genetic and lifestyle factors. In this study, we recruited 19 normal-weight children and 47 children with varying degrees of obesity. A questionnaire survey was conducted to inquire about the family background, lifestyle habits and dietary composition of the 66 children. Findings indicate that fathers of obese children tend to be obese themselves, while children with highly educated mothers are more likely to maintain a normal weight. Furthermore, overweight children tend to spend more time on electronic devices and less time on physical activities compared to their normal-weight counterparts. Obese children exhibit significant differences in breakfast and dinner dietary composition when compared to children with normal weight. Additionally, the gut microbiota of these 66 children was analyzed using 16S rRNA sequencing. Analysis of gut microbiota composition showed similar compositions among children with varying degrees of obesity, but significant differences were observed in comparison to normal-weight children. Obese children exhibited a reduced proportion of Bacteroidota and an increased proportion of Firmicutes, resulting in an elevated Firmicutes/Bacteroidota ratio. Moreover, Actinobacteriota were found to be increased in the gut microbiota of children with varying degrees of obesity. PICRUSt analysis indicated significant metabolic differences in the microbiota functions between obese and normal-weight children, suggesting the composition of gut microbiota could be a crucial factor contributing to obesity. These findings provide valuable insights for the treatment of childhood obesity.

[Effects of Combined Stress of High Density Polyethylene Microplastics and Chlorimuron-ethyl on Soybean Growth and Rhizosphere Bacterial Community].

With the vigorous development of agriculture in China， plastic mulch film and pesticides are widely used in agricultural production. However， the accumulation of microplastics （formed by the degradation of plastic mulch film） and pesticides in soil has also caused many environmental problems. At present， the environmental biological effects of microplastics or pesticides have been reported， but there are few studies on the combined effects on crop growth and the rhizosphere soil bacterial community. Therefore， in this study， the high density polyethylene microplastics （HDPE， 500 mesh） were designed to be co-treated with sulfonylurea herbicide chlorimuron-ethyl to study their effects on soybean growth. In addition， the effects of the combined stress of HDPE and chlorimuron-ethyl on soybean rhizosphere soil bacterial community diversity， structure composition， microbial community network， and soil function were investigated using high-throughput sequencing technology， interaction network， and PICRUSt2 function analysis to clarify the combined toxicity of HDPE and chlorimuron-ethyl to soybean. The results showed that the half-life of chlorimuron-ethyl in soil was prolonged by the 1% HDPE treatment （from 11.5 d to 14.3 d）， and the combined stress of HDPE and chlorimuron-ethyl had more obvious inhibition effects on soybean growth than that of the single pollutant or control. The HiSeq 2 500 sequencing showed that the rhizosphere bacterial community of soybean was composed of 20 phyla and 312 genera under combined stress， the number of phyla and genera was significantly less than that of the control and single pollutant treatment， and the relative abundances of bacteria with potential biological control and plant growth-promoting characteristics （such as Nocardioides and Sphingomonas） were reduced. Alpha diversity analysis showed that the combined stress significantly reduced the richness and diversity of the soybean rhizosphere bacterial community， and Beta diversity analysis showed that the combined stress significantly changed the structure of the bacterial community. The dominant flora of the rhizosphere bacterial community were regulated， and the abundances of secondary functional layers such as amino acid metabolism， energy metabolism， and lipid metabolism were reduced under combined stress by the analysis of LEfSe and PICRUSt2. It was inferred from the network analysis that the combined stress of HDPE and chlorimuron-ethyl reduced the total number of connections and network density of soil bacteria， simplified the network structure， and changed the important flora species to maintain the stability of the network. The results above indicated that the combined stress of HDPE and chlorimuron-ethyl significantly affected the growth of soybean and changed the rhizosphere bacterial community structure， soil function， and network structure. Compared with that of the single pollutant treatment， the potential risk of combined stress was greater. The results of this study can provide guidance for evaluating the ecological risks of polyethylene microplastics and chlorimuron-ethyl and for the remediation of contaminated soil.

Involvement of functional metabolism promotes the enrichment of antibiotic resistome in drinking water: Based on the PICRUSt2 functional prediction.

Biofilters are the important source and sink of antibiotic resistance genes (ARGs) and antibiotic resistance bacteria (ARB) in the drinking water. Current studies generally ascribed the prevalence of BAR in biofilter from the perspective of gene behavior, i.e. horizontal gene transfer (HGT), little attentions have been paid on the ARGs carrier- ARB. In this study, we proposed the hypothesis that ARB participating in pollutant metabolism processes and becoming dominant is an important way for the enrichment of ARGs. To verify this, the antibiotic resistome and bacterial functional metabolic pathways of a sand filter was profiled using heterotrophic bacterial plate counting method (HPC), high-throughput qPCR, Illumina Hiseq sequencing and PICRUSt2 functional prediction. The results illustrated a significant leakage of ARB in the effluent of the sand filter with an average absolute abundance of approximately 102-103 CFU/mL. Further contribution analysis revealed that the dominant genera, such as Acinetobacter spp., Aeromonas spp., Elizabethkingia spp., and Bacillus spp., were primary ARGs hosts, conferring resistance to multiple antibiotics including sulfamethoxazole, tetracycline and ß-lactams. Notably, these ARGs hosts were involved in nitrogen metabolism, including extracellular nitrate/nitrite transport and nitrite reduction, which are crucial in nitrification and denitrification in biofilters. For example, Acinetobacter spp., the dominant bacteria in the filter (relative abundance 69.97 %), contributed the majority of ARGs and 53.79 % of nitrite reduction function. That is, ARB can predominate by participating in the nitrogen metabolism pathways, facilitating the enrichment of ARGs. These findings provide insights into the stable presence of ARGs in biofilters from a functional metabolism perspective, offering a significant supplementary to the mechanisms of the emergence, maintenance, and transmission of BARin drinking water.

On the limits of 16S rRNA gene-based metagenome prediction and functional profiling.

Molecular profiling techniques such as metagenomics, metatranscriptomics or metabolomics offer important insights into the functional diversity of the microbiome. In contrast, 16S rRNA gene sequencing, a widespread and cost-effective technique to measure microbial diversity, only allows for indirect estimation of microbial function. To mitigate this, tools such as PICRUSt2, Tax4Fun2, PanFP and MetGEM infer functional profiles from 16S rRNA gene sequencing data using different algorithms. Prior studies have cast doubts on the quality of these predictions, motivating us to systematically evaluate these tools using matched 16S rRNA gene sequencing, metagenomic datasets, and simulated data. Our contribution is threefold: (i) using simulated data, we investigate if technical biases could explain the discordance between inferred and expected results; (ii) considering human cohorts for type two diabetes, colorectal cancer and obesity, we test if health-related differential abundance measures of functional categories are concordant between 16S rRNA gene-inferred and metagenome-derived profiles and; (iii) since 16S rRNA gene copy number is an important confounder in functional profiles inference, we investigate if a customised copy number normalisation with the rrnDB database could improve the results. Our results show that 16S rRNA gene-based functional inference tools generally do not have the necessary sensitivity to delineate health-related functional changes in the microbiome and should thus be used with care. Furthermore, we outline important differences in the individual tools tested and offer recommendations for tool selection.

Comparison of microbial communities in unleached and leached ionic rare earth mines.

The leaching of ionic rare earth elements has caused serious environmental pollution and ecological damage. Microorganisms play a crucial role in soil ecosystems and are one of the most important components of these systems. However, there are fewer studies related to the changes that occur in microbial community structure and diversity before and after leaching in ionic rare earth mines. In this study, Illumina high-throughput sequencing was used to examine the diversity and composition of soil microorganisms on the summit, hillside, and foot valley surfaces of unleached and leached mines after in situ leaching. The results showed that microbial diversity and abundance in the surface soil of the unleached mine were higher than those in the leached mine, and leaching had a significant impact on the microbial community of mining soil. pH was the main factor affecting the microbial community. Proteobacteria, Actinobacteriota, and Chloroflexi were phyla that showed high abundance in the soil. Network analysis showed that microbial interactions can improve microbial adaptation and stability in harsh environments. PICRUSt2 predictions indicate functional changes and linkages in soil microbial communities.

[Prediction of Soil Bacterial Community Structure and Function in Minqin Desert-oasis Ecotone Artificial Haloxylon ammodendron Forest].

Exploring the effects of artificial Haloxylon ammodendron forest planting on the structure and function of a desert soil bacterial community provides data reference for soil micro-ecological restoration and land quality improvement in desert oasis transition zones. Illumina high-throughput sequencing technology and PICRUSt2 functional prediction analysis were used to identify and analyze the structure and function of soil bacterial communities, and the Mantel correlation test and RDA analysis were used to explain the physicochemical factors affecting the structure and function of soil bacterial communities. The results showed that:① the soil bacterial OTU number, Chao1 index, and Shannon index were significantly higher in the H. ammodendron forest than in the mobile dune soil, and the PCoA analysis and Adonis test showed significant differences in the soil bacterial community structure between H. ammodendron and mobile dune soil (P=0.001). ② A total of 34 phyla, 89 classes, 174 orders, 262 families, and 432 genera of bacteria were detected in all samples, and the phyla Proteobacteria, Actinobacteria, Cyanobacteria, and Chloroflexi accounted for 76.05% of the relative abundance of soil bacteria, which belonged to the dominant soil bacteria, among which the relative abundance of Actinobacteria in H. ammodendron forest soil was extremely significantly higher than that in mobile dune soil (P < 0.01). ③PICRUSt2 function prediction revealed that the soil bacterial community of H. ammodendron forest included six categories of primary functions and 28 categories of secondary functions, among which the metabolism of carbohydrates, metabolism of amino acids, and metabolism of cofactors and vitamins were all greater than 10% in relative abundance and were the main metabolic functions of H. ammodendron forest soil bacteria. ④ The planting of H. ammodendron forest significantly improved the nutrient content of soil organic matter and other nutrients. Soil pH, organic matter, total nitrogen, and fast-acting phosphorus were the main physicochemical factors affecting the bacterial community, with soil organic matter significantly affecting the soil bacterial community structure (P < 0.05) and metabolic function (P < 0.05). In conclusion, the artificial H. ammodendron forest helped to increase desert soil microbial diversity, increase the relative abundance of soil bacterial metabolic function genes, and improve the desert soil microenvironment.