Metagenome comparison (MC): A new framework for detecting unique/enriched OMUs (operational metagenomic units) derived from whole-genome sequencing reads.

BACKGROUND: Current methods for comparing metagenomes, derived from whole-genome sequencing reads, include top-down metrics or parametric models such as metagenome-diversity, and bottom-up, non-parametric, model-free machine learning approaches like Naïve Bayes for k-mer-profiling. However, both types are limited in their ability to effectively and comprehensively identify and catalogue unique or enriched metagenomic genes, a critical task in comparative metagenomics. This challenge is significant and complex due to its NP-hard nature, which means computational time grows exponentially, or even faster, with the problem size, rendering it impractical for even the fastest supercomputers without heuristic approximation algorithms. METHOD: In this study, we introduce a new framework, MC (Metagenome-Comparison), designed to exhaustively detect and catalogue unique or enriched metagenomic genes (MGs) and their derivatives, including metagenome functional gene clusters (MFGC), or more generally, the operational metagenomic unit (OMU) that can be considered the counterpart of the OTU (operational taxonomic unit) from amplicon sequencing reads. The MC is essentially a heuristic search algorithm guided by pairs of new metrics (termed MG-specificity or OMU-specificity, MG-specificity diversity or OMU-specificity diversity). It is further constrained by statistical significance (P-value) implemented as a pair of statistical tests. RESULTS: We evaluated the MC using large metagenomic datasets related to obesity, diabetes, and IBD, and found that the proportions of unique and enriched metagenomic genes ranged from 0.001% to 0.08 % and 0.08%-0.82 % respectively, and less than 10 % for the MFGC. CONCLUSION: The MC provides a robust method for comparing metagenomes at various scales, from baseline MGs to various function/pathway clusters of metagenomes, collectively termed OMUs.

Effects of O2 on accumulation of nitrous and elemental sulfur and microbial community structure in double short-cut sulfur autotrophic denitrification system.

Understanding the effect of O2 on the accumulation characteristics of NO2--N and S0 in the sulfur autotrophic denitrification (DSSADN) system is crucial for enhancing the denitrification efficiency of partial nitrification-anammox using DSSADN. The results revealed that in an environment without O2 entry, the NO2--N accumulation efficiency (NiAE) and S0 accumulation efficiency (S0AE) of the DSSADN system reached 89.40 % and 93.41 %, respectively. Once system entered O2, ORP value kept increasing. When ORP increased to -59.9 mV (DO = 0.1 mg/L), soxB and nirK gene expression rose and as well NiAE and S0AE continuously decreased to 48.13 % and 29.35 %. When ORP was above 30.9 mV (DO >0.2 mg/L) but below 81.0 mV (DO<0.4 mg/L), narG gene expression reduced and the relatively high sqr gene expression allowed NiAE and S0AE remained at 45.08 % and 33.31 %. O2 promoted the synergistic effect of Thiobacillus and Azoarcus without the proliferation of nitrite oxidizing bacteria.

Nitrogen metabolism network in the biotreatment combination of coking wastewater: Take the OHO process as a case.

As steel production increases, large volumes of highly toxic and nitrogen-rich coking wastewater (CWW) are produced, prompting the development of a novel oxic-hydrolytic-oxic (OHO) biological treatment combination designed for highly efficient removal of nitrogen-contained contaminants. However, previous studies have not comprehensively explored the CWW biotreatment from the perspective of nitrogen metabolism functional genes and pathways. Based on the investigation of taking the full-scale OHO biotreatment combination as a case, it was found that the O1 and O2 bioreactors remove nitrogen through the ammonia assimilation accounting for 33.87% of the total nitrogen (TN) removal rate, while the H bioreactor removes nitrogen through the simultaneous nitrification-denitrification accounting for 61.11% of the TN removal rate. The major ammonia assimilation taxa include Thauera, Immundisolibacter and Thiobacillus; the major nitrifying taxa include Nitrospira and Nitrosomonas; and the major denitrifying taxa include Thiobacillus, Lautropia and Mesorhizobium. Additionally, the H bioreactor exhibits the potential to be optimized for simultaneous nitrification-denitrification coupled with anaerobic ammonium oxidation (Anammox). These understandings will guide the optimization of engineering design and operational practices, contributing to more effective and sustainable wastewater treatment strategies.

Identification of Heilongjiang crossbred beef cattle pedigrees and reveals functional genes related to economic traits based on whole-genome SNP data.

Introduction: To enhance the beef cattle industry, Heilongjiang Province has developed a new Crossbred beef cattle variety through crossbreeding with exotic commercial breeds. This new variety exhibits relatively excellent meat quality, and efficient reproductive performance, catering to market demands. Method: This study employed whole genome resequencing technology to analyze the genetic pedigree and diversity of 19 Heilongjiang Crossbred beef cattle, alongside 59 published genomes from East Asian, Eurasian, and European taurine cattle as controls. In addition, genes related to production traits were also searched by identifying Runs of Homozygosity (ROH) islands and important fragments from ancestors. Results: A total of 14,427,729 biallelic SNPs were discovered, with the majority located in intergenic and intron regions and a small percentage in exon regions, impacting protein function. Population genetic analyses including Principal Component Analysis (PCA), Neighbor-Joining (NJ) tree, and ADMIXTURE identified Angus, Holstein, and Mishima as the main ancestors of Crossbred beef cattle. In genetic diversity analysis, nucleotide diversity, linkage disequilibrium, and inbreeding coefficient analysis reveal that the genetic diversity of Crossbred beef cattle is at a moderate level, and a higher inbreeding coefficient indicates the need for careful breeding management. In addition, some genes related to economic traits are identified through the identification of Runs of Homozygosity (ROH) islands and important fragments from ancestors. Conclusion: This comprehensive genomic characterization supports the targeted improvement of economically important traits in Crossbred beef cattle, facilitating advanced breeding strategies.

Highly accurate classification and discovery of microbial protein-coding gene functions using FunGeneTyper: an extensible deep learning framework.

High-throughput DNA sequencing technologies decode tremendous amounts of microbial protein-coding gene sequences. However, accurately assigning protein functions to novel gene sequences remain a challenge. To this end, we developed FunGeneTyper, an extensible framework with two new deep learning models (i.e., FunTrans and FunRep), structured databases, and supporting resources for achieving highly accurate (Accuracy > 0.99, F1-score > 0.97) and fine-grained classification of antibiotic resistance genes (ARGs) and virulence factor genes. Using an experimentally confirmed dataset of ARGs comprising remote homologous sequences as the test set, our framework achieves by-far-the-best performance in the discovery of new ARGs from human gut (F1-score: 0.6948), wastewater (0.6072), and soil (0.5445) microbiomes, beating the state-of-the-art bioinformatics tools and sequence alignment-based (F1-score: 0.0556-0.5065) and domain-based (F1-score: 0.2630-0.5224) annotation approaches. Furthermore, our framework is implemented as a lightweight, privacy-preserving, and plug-and-play neural network module, facilitating its versatility and accessibility to developers and users worldwide. We anticipate widespread utilization of FunGeneTyper (https://github.com/emblab-westlake/FunGeneTyper) for precise classification of protein-coding gene functions and the discovery of numerous valuable enzymes. This advancement will have a significant impact on various fields, including microbiome research, biotechnology, metagenomics, and bioinformatics.

Mitigating nitrous oxide emissions from low carbon to nitrogen ratio wastewater treatment: Utilizing sugarcane bagasse fermentation liquid for constructed wetlands.

Sugarcane bagasse was recycled to produce fermentation liquid (FL) as a supplementary carbon source that was added to constructed wetlands (CWs) for regulating influent carbon to nitrogen ratio (C/N), and then being applied to investigate nitrogen transformations and greenhouse gas emissions. Results showed that this FL achieved faster NO3--N removal and lower N2O fluxes than sucrose did, and the lowest N2O flux (67.6 µg m-2h-1) was achieved when FL was added to CWs in a C/N of 3. In contrast, CH4 emissions were higher by the FL addition than by the sucrose addition, although the fluxes under both additions were in a lower range of 0.06-0.17 mg m-2h-1. The utilization of FL also induced significant variations in microbial communities and increased the abundance of denitrification genes. Results showed the application of FL from sugarcane bagasse can be an effective strategy for improving nitrogen removal and mitigating N2O emissions in CWs.

Geochip 5.0 insights into the association between bioleaching of heavy metals from contaminated sediment and functional genes expressed in consortiums.

The heavy metal contamination in river and lake sediments endangers aquatic ecosystems. Herein, the feasibility of applying different exogenous mesophile consortiums in bioleaching multiple heavy metal-contaminated sediments from Xiangjiang River was investigated, and a comprehensive functional gene array (GeoChip 5.0) was used to analyze the functional gene expression to reveal the intrinsic association between metal solubilization efficiency and consortium structure. Among four consortiums, the Acidithiobacillus thiooxidans and Leptospirillum ferrooxidans consortium had the highest solubilization efficiencies of Cu, Pb, Zn, and Cd after 15 days, reaching 50.33, 29.93, 47.49, and 79.65%, while Cu, Pb, and Hg had the highest solubilization efficiencies after 30 days, reaching 63.67, 45.33, and 52.07%. Geochip analysis revealed that 31,346 genes involved in different biogeochemical processes had been detected, and the systems of 15 days had lower proportions of unique genes than those of 30 days. Samples from the same stage had more genes overlapping with each other than those from different stages. Plentiful metal-resistant and organic remediation genes were also detected, which means the metal detoxification and organic pollutant degradation had happened with the bioleaching process. The Mantel test revealed that Pb, Zn, As, Cd, and Hg solubilized from sediment influenced the structure of expressed microbial functional genes during bioleaching. This work employed GeoChip to demonstrate the intrinsic association between functional gene expression of mesophile consortiums and the bioleaching efficiency of heavy metal-contaminated sediment, and it provides a good reference for future microbial consortium design and remediation of river and lake sediments.

Resistance mechanisms of cereal plants and rhizosphere soil microbial communities to chromium stress.

Agricultural soils contaminated with heavy metals poison crops and disturb the normal functioning of rhizosphere microbial communities. Different crops and rhizosphere microbial communities exhibit different heavy metal resistance mechanisms. Here, indoor pot studies were used to assess the mechanisms of grain and soil rhizosphere microbial communities on chromium (Cr) stress. Millet grain variety 'Jingu 21' (Setaria italica) and soil samples were collected prior to control (CK), 6 hours after (Cr_6h), and 6 days following (Cr_6d) Cr stress. Transcriptomic analysis, high-throughput sequencing and quantitative polymerase chain reaction (qPCR) were used for sample determination and data analysis. Cr stress inhibited the expression of genes related to cell division, and photosynthesis in grain plants while stimulating the expression of genes related to DNA replication and repair, in addition to plant defense systems resist Cr stress. In response to chromium stress, rhizosphere soil bacterial and fungal community compositions and diversity changed significantly (p < 0.05). Both bacterial and fungal co-occurrence networks primarily comprised positively correlated edges that would serve to increase community stability. However, bacterial community networks were larger than fungal community networks and were more tightly connected and less modular than fungal networks. The abundances of C/N functional genes exhibited increasing trends with increased Cr exposure. Overall, these results suggest that Cr stress primarily prevented cereal seedlings from completing photosynthesis, cell division, and proliferation while simultaneously triggering plant defense mechanisms to resist the toxic effects of Cr. Soil bacterial and fungal populations exhibited diverse response traits, community-assembly mechanisms, and increased expression of functional genes related to carbon and nitrogen cycling, all of which are likely related to microbial survival during Cr stress. This study provides new insights into resistance mechanisms, microbial community structures, and mechanisms of C/N functional genes responses in cereal plants to heavy metal contaminated agricultural soils. Portions of this text were previously published as part of a preprint (https://www.researchsquare.com/article/rs-2891904/v1).

Enhanced nitrogen removal of the anaerobic ammonia oxidation process by coupling with an efficient nitrate reducing bacterium (Bacillus velezensis M3-1).

Bacillus velezensis M3-1 strain isolated from the sediment of Myriophyllum aquatium constructed wetlands was found to efficiently convert NO3--N to NO2--N, and the requirements for carbon source addition were not very rigorous. This work demonstrates, for the first time, the feasibility of using the synergy of anammox and Bacillus velezensis M3-1 microorganisms for nitrogen removal. In this study, the possibility of M3-1 that converted NO3--N produced by anammox to NO2--N was verified in an anaerobic reactor. The NO3--N reduction ability of M3-1 and denitrifying bacteria in coupling system was investigated under different C/N conditions, and it was found that M3-1 used carbon sources preferentially over denitrifying bacteria. By adjusting the ratio of NH4+-N to NO2--N, it was found that the NO2--N converted from NO3--N by M3-1 participated in the original anammox.The nitrogen removal efficacy (NRE) of the coupled system was increased by 12.1%, compared to the control group anammox system at C/N = 2:1. Functional gene indicated that it might be a nitrate reducing bacterium.This study shows that the nitrate reduction rate achieved by the Bacillus velezensis M3-1 can be high enough for removing nitrate produced by anammox process, which would enable improve nitrogen removal from wastewater.

Strawberry Yield Improvement by Hydrogen-Based Irrigation Is Functionally Linked to Altered Rhizosphere Microbial Communities.

Molecular hydrogen (H2) is crucial for agricultural microbial systems. However, the mechanisms underlying its influence on crop yields is yet to be fully elucidated. This study observed that H2-based irrigation significantly increased strawberry (Fragaria × ananassa Duch.) yield with/without nutrient fertilization. The reduction in soil available nitrogen (N), phosphorus (P), potassium (K), and organic matter was consistent with the increased expression levels of N/P/K-absorption-related genes in root tissues at the fruiting stage. Metagenomics profiling showed the alterations in rhizosphere microbial community composition achieved by H2, particularly under the conditions without fertilizers. These included the enrichment of plant-growth-promoting rhizobacteria, such as Burkholderia, Pseudomonas, and Cupriavidus genera. Rhizobacteria with the capability to oxidize H2 (group 2a [NiFe] hydrogenase) were also enriched. Consistently, genes related to soil carbon (C) fixation (i.e., rbcL, porD, frdAB, etc.), dissimilar nitrate reduction (i.e., napAB and nrfAH), and P solublization, mineralization, and transportation (i.e., ppx-gppA, appA, and ugpABCE) exhibited higher abundance. Contrary tendencies were observed in the soil C degradation and N denitrification genes. Together, these results clearly indicate that microbe-mediated soil C, N, and P cycles might be functionally altered by H2, thus increasing plant nutrient uptake capacity and horticultural crop yield.

Stable isotope labeling and functional gene prediction elucidate the carbon metabolism in fermentative bacteria and microalgae coupling system.

The application of the fermentative bacteria and microalgae coupling system in the wastewater treatment has been studied, but there remains few knowledge regarding the organic and inorganic carbon metabolism within this system. In this study, the carbon metabolism of microalgae and fermentative bacteria was elucidated by 13C stable isotope labeling and functional gene prediction, respectively. The 13C glucose and 13C NaHCO3 were used as stable isotope tracers to clarify the organic and inorganic carbon metabolism of microalgae, indicating that approximately 71.5 % of the Acetyl-CoA in microalgae was synthesized from organic carbon sources, while 26.8 % was synthesized through the utilization of inorganic carbon sources. Inorganic carbon sources can enhance the activity of photosynthetic system and facilitate the Calvin cycle. Considering the adequate organic carbon sources and insufficient inorganic carbon sources in the fermentative bacteria and microalgae coupling system, NaHCO3 was added to improve carbon utilization of microalgae. The maximum microalgal lipid yield reached 1130.37 mg/L with 1000 mg/L NaHCO3 supplementation. Functional gene prediction was used to analysis the effect of various carbon composition on the bacterial carbon metabolism. Notably, the additional inorganic carbon sources increased the abundance of bacterial functional genes associated with the fermentation and acetic acids synthesis, which was advantageous for VFAs production and further promoted microalgae growth. This study can gain a deeper understanding of microbial metabolic mechanisms during the operation of fermentative bacteria and microalgae system, and improve its sustained operational stability.

Integrated analysis of miRNAome and transcriptome reveals that microgravity induces the alterations of critical functional gene modules via the regulation of miRNAs in short-term space-flown C. elegans.

Microgravity, as a unique hazardous factor encountered in space, can induce a series of harmful effects on living organisms. The impact of microgravity on the pivotal functional gene modules stemming from gene enrichment analysis via the regulation of miRNAs is not fully illustrated. To explore the microgravity-induced alterations in critical functional gene modules via the regulation of miRNAs, in the present study, we proposed a novel bioinformatics algorithm for the integrated analysis of miRNAome and transcriptome from short-term space-flown C. elegans. The samples of C. elegans were exposed to two space conditions, namely spaceflight (SF) and spaceflight control (SC) onboard the International Space Station for 4 days. Additionally, the samples of ground control (GC) were included for comparative analysis. Using the present algorithm, we constructed regulatory networks of functional gene modules annotated from differentially expressed genes (DEGs) and their associated regulatory differentially expressed miRNAs (DEmiRNAs). The results showed that functional gene modules of molting cycle, defense response, fatty acid metabolism, lysosome, and longevity regulating pathway were facilitated by 25 down-regulated DEmiRNAs (e.g., cel-miR-792, cel-miR-65, cel-miR-70, cel-lsy-6, cel-miR-796, etc.) in the SC vs. GC groups, whereas these modules were inhibited by 13 up-regulated DEmiRNAs (e.g., cel-miR-74, cel-miR-229, cel-miR-70, cel-miR-249, cel-miR-85, etc.) in the SF vs. GC groups. These findings indicated that microgravity could significantly alter gene expression patterns and their associated functional gene modules in short-term space-flown C. elegans. Additionally, we identified 34 miRNAs as post-transcriptional regulators that modulated these functional gene modules under microgravity conditions. Through the experimental verification, our results demonstrated that microgravity could induce the down-regulation of five critical functional gene modules (i.e., molting cycle, defense response, fatty acid metabolism, lysosome, and longevity regulating pathways) via the regulation of miRNAs in short-term space-flown C. elegans.

Improving key gene expression and di-n-butyl phthalate (DBP) degrading ability in a novel Pseudochrobactrum sp. XF203 by ribosome engineering.

Di-n-butyl phthalate (DBP) is one of the important phthalates detected commonly in soils and crops, posing serious threat to human health. Pseudochrobactrum sp. XF203 (XF203), a new strain related with DBP biodegradation, was first identified from a natural habitat lacking human disturbance. Genomic analysis coupled with gene expression comparison assay revealed this strain harbors the key aromatic ring-cleaving gene catE203 (encoding catechol 2,3-dioxygenase/C23O) involved DBP biodegradation. Following intermediates identification and enzymatic analysis also indicated a C23O dependent DBP lysis pathway in XF203. The gene directed ribosome engineering was operated and to generate a desirable mutant strain XF203R with highest catE203 gene expression level and strong DBP degrading ability. The X203R removed DBP in soil jointly by reassembling bacterial community. These results demonstrate a great value of XF203R for the practical DBP bioremediation application, highlighting the important role of the key gene-directed ribosome engineering in mining multi-pollutants degrading bacteria from natural habitats where various functional genes are well conserved.

Effects of sulfamethazine on microbially-mediated denitrifying anaerobic methane oxidation in estuarine wetlands.

Nitrite/nitrate-dependent anaerobic methane oxidation (n-DAMO) is an important methane (CH4) consumption and nitrogen (N) removal pathway in estuarine and coastal wetlands. Antibiotic contamination is known to affect microbially mediated processes; however, its influences on n-DAMO and the underlying molecular mechanisms remain poorly understood. In the present study, using 13CH4 tracer method combined with molecular techniques, we investigated the responses of n-DAMO microbial abundance, activity, and the associated microbial community composition to sulfamethazine (SMT, a sulfonamide antibiotic, with exposure concentrations of 0.05, 0.5, 5, 20, 50, and 100 µg L-1). Results showed that the effect of SMT exposure on n-DAMO activity was dose-dependent. Exposure to SMT at concentrations of up to 5 µg L-1 inhibited the potential n-DAMO rates (the average rates of nitrite- and nitrate-DAMO decreased by 92.9 % and 79.2 % relative to the control, respectively). In contrast, n-DAMO rates tended to be promoted by SMT when its concentration increased to 20-100 µg L-1 (the average rates of nitrite- and nitrate-DAMO increased by 724.1 % and 630.1 % relative to the low-doses, respectively). Notably, low-doses of SMT suppressed nitrite-DAMO to a greater extent than nitrate-DAMO, indicating that nitrite-DAMO was more sensitive to SMT than nitrate-DAMO. Molecular analyses suggest that the increased n-DAMO activity under high-doses SMT exposure may be driven by changes in microbial communities, especially because of the promotion of methanogens that provide more CH4 to n-DAMO microbes. Moreover, the abundances of n-DAMO microbes at high SMT exposure (20 and 50 µg L-1) were significantly higher than that at low SMT exposure (0.05-5 µg L-1). These results advance our understanding of the ecological effects of SMT on carbon (C) and N interactions in estuarine and coastal wetlands.

Discovery and Characterization of the ddx41 Gene in Atlantic Salmon: Evolutionary Implications, Structural Functions, and Innate Immune Responses to Piscirickettsia salmonis and Renibacterium salmoninarum Infections.

The innate immune response in Salmo salar, mediated by pattern recognition receptors (PRRs), is crucial for defending against pathogens. This study examined DDX41 protein functions as a cytosolic/nuclear sensor for cyclic dinucleotides, RNA, and DNA from invasive intracellular bacteria. The investigation determined the existence, conservation, and functional expression of the ddx41 gene in S. salar. In silico predictions and experimental validations identified a single ddx41 gene on chromosome 5 in S. salar, showing 83.92% homology with its human counterpart. Transcriptomic analysis in salmon head kidney confirmed gene transcriptional integrity. Proteomic identification through mass spectrometry characterized three unique peptides with 99.99% statistical confidence. Phylogenetic analysis demonstrated significant evolutionary conservation across species. Functional gene expression analysis in SHK-1 cells infected by Piscirickettsia salmonis and Renibacterium salmoninarum indicated significant upregulation of DDX41, correlated with increased proinflammatory cytokine levels and activation of irf3 and interferon signaling pathways. In vivo studies corroborated DDX41 activation in immune responses, particularly when S. salar was challenged with P. salmonis, underscoring its potential in enhancing disease resistance. This is the first study to identify the DDX41 pathway as a key component in S. salar innate immune response to invading pathogens, establishing a basis for future research in salmonid disease resistance.

Effects of nitrogen application on ammonium assimilation and microenvironment in the rhizosphere of drip-irrigated sunflower under plastic mulch.

This study investigated the effect of nitrogen application on the rhizosphere soil microenvironment of sunflower and clarified the relationship between ammonium assimilation and the microenvironment. In a field experiment high (HN, 190 kg/hm2), medium (MN, 120 kg/hm2) and low nitrogen (CK, 50 kg/hm2) treatments were made to replicate plots of sunflowers using drip irrigation. Metagenomic sequencing was used to analyze the community structure and functional genes involved in the ammonium assimilation pathway in rhizosphere soil. The findings indicated that glnA and gltB played a crucial role in the ammonium assimilation pathway in sunflower rhizosphere soil, with Actinobacteria and Proteobacteria being the primary contributors. Compared with CK treatment, the relative abundance of Actinobacteria increased by 15.57% under MN treatment, while the relative abundance decreased at flowering and maturation stages. Conversely, the relative abundance of Proteobacteria was 28.57 and 61.26% higher in the MN treatment during anthesis and maturation period, respectively, compared with the CK. Furthermore, during the bud stage and anthesis, the abundance of Actinobacteria, Proteobacteria, and their dominant species were influenced mainly by rhizosphere soil EC, ammonium nitrogen (NH4+-N), and nitrate nitrogen (NO3--N), whereas, at maturity, soil pH and NO3--N played a more significant role in shaping the community of ammonium-assimilating microorganisms. The MN treatment increased the root length density, surface area density, and root volume density of sunflower at the bud, flowering, and maturity stages compared to the CK. Moreover, root exudates such as oxalate and malate were positively correlated with the dominant species of Actinobacteria and Proteobacteria during anthesis and the maturation period. Under drip irrigation, applying 120 kg/hm2 of nitrogen to sunflowers effectively promoted the community structure of ammonium-assimilating microorganisms in rhizosphere soil and had a positive influence on the rhizosphere soil microenvironment and sunflower root growth.

Treatment of high ammonia anaerobically digested molasses wastewater using aerobic granular sludge reactor.

This study addressed the treatment of high ammonia, low biodegradable chemical oxygen demand (bCOD) anaerobically digested molasses wastewater, utilizing an aerobic granular sludge (AGS) reactor. The AGS achieved 99 % ammonia removal regardless of the bCOD supplementation. By adding low ammonia (<60 mg/L), high bCOD raw molasses wastewater (before anaerobic digestion) as a carbon source, enhanced nitrogen removal, increasing from 10 % to 97 %, and improved sludge settleability via bio-induced calcite precipitation were observed. Functional genes prediction suggested two potential denitrification pathways, including heterotrophic denitrification by Paracoccus and Thauera, and autotrophic denitrification, specifically sulfide-oxidizing autotrophic denitrification by Thiobacillus. An increase in the relative abundance of microorganisms involved in heterotrophic denitrification was observed with the addition of high bCOD raw molasses wastewater. Consequently, incorporating raw molasses wastewater into the AGS presents a sustainable approach to achieve mixotrophic denitrification, maintain stable granular sludge and ensure stable treatment performance when treating anaerobically digested molasses wastewater.

Intermittent electrostimulation-modified direct interspecies electron transfer for enhanced methanogenesis in anaerobic digestion of sulfate-rich wastewater.

Methane recovery and organics removal in sulfate (SO42-)-rich wastewater anaerobic digestion are hindered by electron competition between methanogenesis and sulfidogenesis. Here, intermittently electrostimulated bioelectrodes were developed to facilitate direct interspecies electron transfer (DIET)-driven syntrophic methanogenesis, increasing substrate competition among methanogenic archaea (MA). By optimising the electrochemical environment, MA was able to employ electron transfer more efficiently than sulfate-reducing bacteria (SRB), resulting in significant methane accumulation (58.1 ± 1.0 mL-CH4/m3reactor) and COD removal (90.5 ± 0.5 %) at lower COD/SO42- ratio. Intermittent electrostimulation improved the metabolic pathway for electroactive bacteria to utilize acetate and direct electrons to electrotrophic MA, decreasing SRB abundance and affecting the sulfate reduction pathway. Intermittently electrostimulated biofilms significantly increased gene levels of key enzymes in electron transport for cytochrome and e-pili biosynthesis, crucial for DIET, demonstrating enhanced DIET-driven syntrophic methanogenesis. This study provides a strategic approach to optimize methanogenesis in sulfate-rich wastewater anaerobic digestion.

Elucidating sleep disorders: a comprehensive bioinformatics analysis of functional gene sets and hub genes.

Background: Sleep disorders (SD) are known to have a profound impact on human health and quality of life although their exact pathogenic mechanisms remain poorly understood. Methods: The study first accessed SD datasets from the GEO and identified DEGs. These DEGs were then subjected to gene set enrichment analysis. Several advanced techniques, including the RF, SVM-RFE, PPI networks, and LASSO methodologies, were utilized to identify hub genes closely associated with SD. Additionally, the ssGSEA approach was employed to analyze immune cell infiltration and functional gene set scores in SD. DEGs were also scrutinized in relation to miRNA, and the DGIdb database was used to explore potential pharmacological treatments for SD. Furthermore, in an SD murine model, the expression levels of these hub genes were confirmed through RT-qPCR and Western Blot analyses. Results: The findings of the study indicate that DEGs are significantly enriched in functions and pathways related to immune cell activity, stress response, and neural system regulation. The analysis of immunoinfiltration demonstrated a marked elevation in the levels of Activated CD4+ T cells and CD8+ T cells in the SD cohort, accompanied by a notable rise in Central memory CD4 T cells, Central memory CD8 T cells, and Natural killer T cells. Using machine learning algorithms, the study also identified hub genes closely associated with SD, including IPO9, RAP2A, DDX17, MBNL2, PIK3AP1, and ZNF385A. Based on these genes, an SD diagnostic model was constructed and its efficacy validated across multiple datasets. In the SD murine model, the mRNA and protein expressions of these 6 hub genes were found to be consistent with the results of the bioinformatics analysis. Conclusion: In conclusion, this study identified 6 genes closely linked to SD, which may play pivotal roles in neural system development, the immune microenvironment, and inflammatory responses. Additionally, the key gene-based SD diagnostic model constructed in this study, validated on multiple datasets showed a high degree of reliability and accuracy, predicting its wide potential for clinical applications. However, limited by the range of data sources and sample size, this may affect the generalizability of the results.

Carbon slow-release and enhanced nitrogen removal performance of plant residue-based composite filler and ecological mechanisms in constructed wetland application.

Stable carbon release and coupled microbial efficacy of external carbon source solid fillers are the keys to enhanced nitrogen removal in constructed wetlands. The constructed wetland plant residue Acorus calamus was cross-linked with poly (3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) to create composite solid carbon source fillers (Ac-BDPs). The study demonstrated the slow release of carbon sources from Ac-BDPs with 35.27 mg/g under an average release rate of 0.88 mg/(g·d). Excellent denitrification was also observed in constructed wetlands with Ac-BDPs. Moreover, the average removal rate of nitrate nitrogen (NO3--N) was increased by 1.94 and 3.85 times of the blank groups under initial NO3--N inputs of 5 and 15 mg/L, respectively. Furthermore, the relatively high abundances of nap, narG, nirKS, norB, qnorZ and nosZ guaranteed efficient denitrification performance in constructed wetlands with Ac-BDPs. The study introduced a reliable technique for biological nitrogen removal by using composite carbon source fillers in constructed wetlands.