CRISPR-Mediated Library Screening of Gene-Knockout Cell Lines for Investigating Antiviral Innate Immunity.

The application of CRISPR-mediated library screening has fundamentally transformed functional genomics by revealing the complexity of virus-host interactions. This protocol describes the use of CRISPR-mediated library screening to identify key functional genes regulating the innate immune response to PEDV infection. We detail a step-by-step process, starting from the design and construction of a customized CRISPR knockout library targeting genes involved in innate immunity to the effective delivery of these constructs into cells using lentiviral vectors. Subsequently, we outline the process of identifying functional genes postviral attack, including the use of next-generation sequencing (NGS), to analyze and identify knockout cells that exhibit altered responses to infection. This integrated approach provides researchers in immunology and virology with a resource and a robust framework for uncovering the genetic basis of host-pathogen interactions and the arsenal of the innate immune system against viral invasions.

Lake ecological restoration of vegetation removal mitigates algal blooms and alters landscape patterns of water and sediment bacteria.

Elucidating the influences of ecological restoration measure of lakeshore vegetation removal on water quality and biological community is an important but underestimated subject. We adopted molecular and statistical tools to estimate ecological restoration performance in a plateau lake receiving vegetation removal and simultaneously investigated variabilities of bacterial communities in water and sediment. Significant decreases in lake trophic level and algal bloom degree followed notable decreases in water total nitrogen and total phosphorus after vegetation removal. Non-significant changes in sediment nutrients accompanied remarkable variabilities of abundance and composition of nutrient-cycling functional genes (NCFGs) of sediment bacteria. Taxonomic and phylogenetic α-diversities, functional redundancies, and dispersal potentials of bacteria in water and sediment decreased after vegetation removal, and community successions of water and sediment bacteria were separately significant and non-significant. There were opposite changes in ecological attributes of bacteria in water and sediment in response to vegetation removal, including niche breadth, species replacement, richness difference, community complexity, and community stability. Species replacement rather than richness difference affected more on taxonomic ß-diversities of bacteria in water and sediment before and after vegetation removal, and determinism rather than stochasticity dominated bacterial community assemblage. Our results highlighted vegetation removal mitigated algal bloom and affected differently on landscapes of water and sediment bacteria. These findings point to dominant ecological mechanisms underlying landscape shifts in water and sediment bacteria in a disturbed lake receiving vegetation removal and have the potential to guide lake ecological restoration.

Harnessing microbial power: Enhancing phosphorus recovery through initial carbon and phosphorus ratio modulation in sewage sludge compost.

Phosphorus is an essential nutrient for organisms, but excessive amounts can cause environmental pollution. Phosphorus-rich sludge can solve the problem of the loss of phosphorus resources after resource treatment.This study aimed to explore the mechanism between phosphorus functional genes and phosphorus availability by regulating the initial carbon and phosphorus ratio in sludge compost, with the goal of improving sludge phosphorus recovery efficiency. The results showed that a higher initial carbon and phosphorus ratiocan promote the conversion of phosphorusfrom sludge to Olsen phosphorus and increase the contents of Water soluble phosphorusand Citric acid phosphorusin compost products. With the increase of the initial carbon and phosphorus ratio,phoDgene andpqqCgene abundance (P < 0.05) were significantly up-regulated, thus increasing the secretion of phosphodiesterase and organic acid, improving the phosphorus availability in compost products.The potential host of phosphorus solubilizing geneswas gradually transitionedfrom Proteobacteria to Firmicutes. Theppkgene and phosphorus accumulating bacteria abundance were significantly higher (CP20, CP25) at the later stage of composting (P < 0.05), indicating that the phosphorusaccumulating potential of the bacterial community was more prominent in the low initial carbon and phosphorus ratiocompost. This study elucidated the potential mechanism of action between functional genes and phosphorus availability, and demonstrated the feasibility of improving sludge phosphorus recovery efficiency by regulating the initial carbon and phosphorus ratio.

Influence of long-term ecological reclamation on carbon and nitrogen cycling in soil aggregates: The role of bacterial community structure and function.

Understanding the influence of microbial taxa and functions on soil carbon (C) and nitrogen (N) cycling, particularly concerning soil aggregate sizes, is crucial for ecosystem management. This study examines the taxonomic and functional dynamics of soil bacterial communities within different aggregate sizes over time. Soil samples from a reclamation forest on the Loess Plateau in North China were collected across reclamation ages of 0, 3, 18, and 28 years. Soil aggregates were categorized into large macro-aggregates (>2000 µm), small macro-aggregates (250-2000 µm), and micro-aggregates (<250 µm) using a modified dry-sieving method. Soil aggregate stability, C and N concentrations, newly derived plant C, enzyme activities, bacterial communities, and functional genes in each aggregate fraction were systematically analyzed. There was a notable increase in soil aggregate stability and a higher proportion of large aggregates was found with increasing forest age. There were significant differences in bacterial community structures, particularly between micro-aggregates and large macro-aggregates and across different forest ages. Reclamation led to an increased abundance of copiotrophic bacterial taxa. Decreases in N-acquiring enzyme activity in micro-aggregates were contrasted by an increase in C, N, and phosphorus (P) acquisition activities in larger aggregates over time. Larger aggregates showed a faster recovery of C and N cycling genes accompanied by a significant enhancement in acetyl-CoA and ammonia oxidation processes, underscoring their importance in soil nutrient cycling. These results highlight the critical role of aggregate size in shaping microbial community structures and functions that influence soil C and N cycling during reclamation and provide new perspectives highlighting the significance of incorporating aggregate size considerations into soil management and reclamation strategies.

Insight into using multi-omics analysis to elucidate nitrogen removal mechanisms in a novel improved constructed rapid infiltration system: Functional gene and metabolite signatures.

In this study, a laboratory-scale improved constructed rapid infiltration (imCRI) system with non-saturated and saturated layers was constructed, and corn cobs as solid carbon source were added to the saturated layer to enhance the removal of nitrogen. Combined analyses of metagenomics and metabolomics were conducted to elucidate the nitrogen removal mechanism in the imCRI system. The results showed that the hydraulic load significantly influenced the treatment performance of the imCRI system, and a hydraulic load of 1.25 m3/(m2⋅d) was recommended. Under optimal conditions, the imCRI system using simulated wastewater achieved average removal efficiencies of 97.8 % for chemical oxygen demand, 85.7 % for total nitrogen (TN), and 97.6 % for ammonia nitrogen. Metagenomic and metabolomic analyses revealed that besides nitrification and denitrification, dissimilatory nitrate reduction to ammonium (DNRA), anammox, etc., are also involved in nitrogen metabolism in the imCRI system. Although nitrification was the predominant pathway in the non-saturated layer, aerobic denitrification also occurred, accounting for 22.59 % of the TN removal. In the saturated layer, nitrogen removal was attributed to synergistic effects of denitrification, DNRA and anammox. Moreover, correlation analysis among nitrogen removal, functional genes and metabolites suggested that metabolites related to the tricarboxylic acid cycle generated from the glycolysis of corn cobs provided sufficient energy for denitrification. Our results can offer a promising technology for decentralized wastewater treatment with stringent nitrogen removal requirements, and provide a foundation for understanding the underlying nitrogen transformation and removal mechanism.

Functional gene signature offers a powerful tool for characterizing clinicopathological features and depicting tumor immune microenvironment of colorectal cancer.

BACKGROUND: Colorectal cancer, a prevalent malignancy worldwide, poses a significant challenge due to the lack of effective prognostic tools. In this study, we aimed to develop a functional gene signature to stratify colorectal cancer patients into different groups with distinct characteristics, which will greatly facilitate disease prediction. RESULTS: Patients were stratified into high- and low-risk groups using a prediction model built based on the functional gene signature. This innovative approach not only predicts clinicopathological features but also reveals tumor immune microenvironment types and responses to immunotherapy. The study reveals that patients in the high-risk group exhibit poorer pathological features, including invasion depth, lymph node metastasis, and distant metastasis, as well as unfavorable survival outcomes in terms of overall survival and disease-free survival. The underlying mechanisms for these observations are attributed to upregulated tumor-related signaling pathways, increased infiltration of pro-tumor immune cells, decreased infiltration of anti-tumor immune cells, and a lower tumor mutation burden. Consequently, patients in the high-risk group exhibit a diminished response to immunotherapy. Furthermore, the high-risk group demonstrates enrichment in extracellular matrix-related functions and significant infiltration of cancer-associated fibroblasts (CAFs). Single-cell transcriptional data analysis identifies CAFs as the primary cellular type expressing hub genes, namely ACTA2, TPM2, MYL9, and TAGLN. This finding is further validated through multiple approaches, including multiplex immunohistochemistry (mIHC), polymerase chain reaction (PCR), and western blot analysis. Notably, TPM2 emerges as a potential biomarker for identifying CAFs in colorectal cancer, distinguishing them from both colorectal cancer cell lines and normal colon epithelial cell lines. Co-culture of CAFs and colorectal cancer cells revealed that CAFs could enhance the tumorigenic biofunctions of cancer cells indirectly, which could be partially inhibited by knocking down CAF original TPM2 expression. CONCLUSIONS: This study introduces a functional gene signature that effectively and reliably predicts clinicopathological features and the tumor immune microenvironment in colorectal cancer. Moreover, the identification of TPM2 as a potential biomarker for CAFs holds promising implications for future research and clinical applications in the field of colorectal cancer.

Isotope analysis of nitrogen removal pathways and N2O production potential in the SDAD-anammox system under different N/S ratios.

This study explored the impact of varying nitrate to sulfide (N/S) ratios on nitrogen removal efficiency (NRE) in the sulfide-driven autotrophic denitrification and anammox (SDAD-anammox) system. Optimal nitrogen removal was observed at N/S ratios between 1.5 and 2.0. Isotope tracing results showed that the contribution of anammox to nitrogen removal was enhanced with increasing N/S ratios, reaching up to 37 % at the N/S ratio of 2.5. Additionally, complex nitrogen pathways were identified, including dissimilatory nitrate reduction to ammonium (DNRA). Furthermore, isotope tracing was innovatively applied to investigate N2O emissions, demonstrating that higher N/S ratios significantly reduced N2O emissions, with the lowest emissions at N/S ratio of 2.5. Gene expression analysis indicated that nitrogen and sulfide transformation genes decreased with increasing N/S ratios, while anammox-related genes first increased and then decreased, reflecting the system's microbial dynamics. These findings offer insights into nitrogen transformation pathways and N2O production mechanisms in the SDAD-anammox process.

Enhancing the performance of microalgal-bacterial systems with sodium bicarbonate: A step forward to carbon neutrality of municipal wastewater treatment.

The microalgal-bacterial granular sludge (MBGS) process, enhanced with sodium bicarbonate (NaHCO3), offers a sustainable alternative for wastewater treatment aiming for carbon neutrality. This study demonstrates that NaHCO3, which can be derived from the flue gases and alkaline textile wastewater, significantly enhances pollutant removal and biomass production. Optimal addition of NaHCO3 was found to achieve an inorganic-to-organic carbon ratio of 1.0 and a total carbon-to-nitrogen ratio of 5.0. Metagenomic analysis and structural equation modeling showed that NaHCO3 addition increased dissolved oxygen concentrations and pH levels, creating a more favorable environment for key microbial communities, including Proteobacteria, Chloroflexi, and Cyanobacteria. Confocal laser scanning microscopy further confirmed enhanced interactions between Cyanobacteria and Proteobacteria/Chloroflexi, facilitating the MBGS process. These microbes harbored functional genes (gap2, GLU, and ppk) critical for removing organics, nitrogen, and phosphorus. Carbon footprint analysis revealed significant reductions in CO2 emissions by the NaHCO3-added MBGS process in representative countries (China, Australia, Canada, Germany, and Morocco), compared to the conventional activated sludge process. These findings highlight the effectiveness of NaHCO3 in optimizing MBGS process, establishing it as a key strategy in achieving carbon-neutral wastewater treatment globally.

Dry season irrigation promotes nutrient cycling by reorganizing Eucalyptus rhizosphere microbiome.

In southern China, seasonal droughts and low soil phosphorus content constrain the productivity of Eucalyptus trees. To understand the rhizosphere microbiome response to the dry season, metagenomic sequencing analysis was used to investigate the 6-year-old Eucalyptus rhizosphere microbiome under four different irrigation and fertilization treatments. The results showed that irrigation and fertilization during the dry season significantly altered the composition of microbiome in the rhizosphere soil of Eucalyptus plantations. The soil physicochemical properties and enzyme activity explained 30.73 % and 29.75 % of the changes in bacterial and fungal community structure in Eucalyptus rhizosphere soil, respectively. Irrigation and fertilization during the dry season significantly altered the physicochemical properties of rhizosphere soil. Compared with the seasonal drought without fertilizer treatment (CK), the dry season irrigation with fertilizer treatment (WF) significantly increased the content of total nitrogen (46.34 %), available nitrogen (37.72 %), available phosphorus (440.9 %), and organic matter (35.34 %). Soil organic matter (OM), pH, and available phosphorus (AP) were key environmental factors influencing the microbial community composition. Moreover, irrigation and fertilization promoted carbon fixation and nitrogen and phosphorus mineralization, increasing soil OM content and the availability of inorganic nitrogen and phosphorus. Meanwhile, compared to the CK, the increase of acid phosphatase (16.81 %), invertase (146.89 %)and urease (59.45 %) in rhizosphere soil under irrigation (W) treatment further proves that dry season irrigation promote the soil carbon, nitrogen and phosphorus cycles. Irrigation and fertilization treatment alleviated the constraints of low phosphorus in southern China's soil, which promoted Eucalyptus productivity. In conclusion, we suggest implementing reasonable irrigation and fertilization strategies in the production practice of Eucalyptus and utilizing microbial resources to improve soil fertility and Eucalyptus productivity.

From reduction to rebalancing: Insights into the long-term effects of sediment dredging on nitrogen transformations in river ecosystems.

Although sediment dredging is a widely employed water management and restoration technique for the removal of internal nitrogen (N), the long-term effects of dredging on N transformation in dredged rivers remain largely undetermined. In this study, we investigated the effects of dredging on N transformation processes spanning three years at ten sites in the purple-soil watershed within the middle reaches of the Fu River Basin. We combined isotopic and molecular techniques to provide novel insights into the interactions associated with microbial utilization capacities between sediment and river water before, during, and after dredging. Initially, dredging was found to significantly reduce the total nitrogen content by approximately 75 %, although over time, there was a slight increase in concentrations. Secondly, significant reductions in microbial richness and diversity were detected in both river water and sediment, with 39 classes reduced, 12 new classes emerging, and an increase in archaea, reshaping the microbial community. Lastly, dredging was found to promote a significant shift in functional contributions, with increases in the abundance of key enzyme activities (1.7.5.1 and 1.7.2.5) and denitrification genes (nirK, norB, and nosZ). This enhancement notably promoted denitrification and dissimilatory nitrate reduction to ammonium (DNRA), accompanied by significant environmental changes in sediment and river water. These changes facilitated the removal of nitrates in the Xiangshuitan watershed. Our study overcomes the limitations associated with watershed and microenvironment scales, providing insights into the mechanisms where by dredging activities influence the interplay between external and internal N transformations.

Wastewater treatment plant effluents increase the global warming potential in a subtropical urbanized river.

Rivers play a pivotal role in global carbon (C) and nitrogen (N) biogeochemical cycles. Urbanized rivers are significant hotspots of greenhouse gases (GHGs, N2O, CO2 and CH4) emissions. This study examined the GHGs distributions in the Guanxun River, an effluents-receiving subtropical urbanized river, as well as the key environmental factors and processes affecting the pattern and emission characteristics of GHGs. Dissolved N2O, CO2, and CH4 concentrations reached 228.0 nmol L-1, 0.44 mmol L-1, and 5.2 µmol L-1 during the wet period, and 929.8 nmol L-1, 0.7 mmol L-1, and 4.6 µmol L-1 during the dry period, respectively. Effluents inputs increased C and N loadings, reduced C/N ratios, and promoted further methanogenesis and N2O production dominated by incomplete denitrification after the outfall. Increased urbanization in the far downstream, high hydraulic residence time, low DO and high organic C environment promoted methanogenesis. The strong CH4 oxidation and methanogenic reactions inhibited by the effluents combined to suppress CH4 emissions in downstream near the outfall, and the process also contributed to CO2 production. The carbon fixation downstream from the outfall were inhibited by effluents. Ultimately, it promoted CO2 emissions downstream from the outfall. The continuous C, N, and chlorine inputs maintained the high saturation and production potential of GHGs, and altered microbial community structure and functional genes abundance. Ultimately, the global warming potential downstream increased by 186 % and 84 % during wet and dry periods on the 20-year scale, and increased by 91 % and 49 % during wet and dry periods on the 100-year scale, respectively, compared with upstream from the outfall. In urbanized rivers with sufficient C and N source supply from WWTP effluents, the large effluent equivalently transformed the natural water within the channel into a subsequent "reactor". Furthermore, the IPCC recommended EF5r values appear to underestimate the N2O emission potential of urbanized rivers with high pollution loading that receiving WWTP effluents. The findings of this study might aid the development of effective strategies for mitigating global climate change.

PBAT biodegradable microplastics enhanced organic matter decomposition capacity and CO2 emission in soils with and without straw residue.

Recent studies show that biodegradable microplastics (BMPs) could increase soil CO2 emission, but whether altered carbon emission results from modified soil organic matter (SOM) decomposition remains underexplored. In this study, the effect and mechanisms of BMPs on CO2 emission from soil were investigated, using poly(butylene adipate-co-terephthalate) (PBAT, the main component of agricultural film) as an example. Considering that straw returning is a common agronomic measure which may interact with microplastics through affecting microbial activity, both soils with and without wheat straw were included. After 120 d, 1 % (w/w) PBAT BMPs ificantly increased cumulative CO2 emission by 1605.6 and 1827.7 mg C kg-1 in soils without and with straw, respectively. Cracks occurred on the surface of microplastics, indicating that CO2 was partly originated from plastic degradation. Soil dissolved organic matter (DOM) content, carbon degradation gene abundance (such as abfA, xylA and manB for hemicellulose, mnp, glx and lig for lignin, and chiA for chitin) and enzyme activities increased, which significantly positively correlated with CO2 emission rate (p < 0.05), suggesting that PBAT enhanced carbon emission by stimulating the decomposition of SOM (and possibly the newly added straw) via co-metabolism and nitrogen mining. This is supported by DOM molecular composition analysis which also demonstrated stimulated turnover of carbohydrates, amino sugars and lignin following PBAT addition. The findings highlight the potential of BMPs to affect SOM stability and carbon emission.

Effects of biochar on the transformation and utilization of nitrogen fertilizer in the black soil region of Northeast China.

Nitrogen (N) fertilizer is often used in production practice to effectively maintain crop productivity; however, low nitrogen use efficiency (Nue) has always been a problem. Specifically, the transformation and utilization of nitrogen fertilizer by biochar and the driving mechanisms remain unclear. We used four biochar application rates (0, 3750, 7500, and 11,250 kg·ha-1) and analyzed the effects of biochar on nitrogen fertilizer utilization, residue, and loss over three years using 15N isotope tracer technology. The results showed that (1) biochar improved the nitrogen use efficiency of maize plants, reduced total nitrogen loss, and increased the maize yield. Compared to the control treatment in the same year, the application of 7500 kg·ha-1 biochar increased the nitrogen use efficiency by 24.27 %, 27.77 %, and 35.82 %, and the yield increased by 21.1 %, 26.7 %, and 24.5 %, respectively. (2) Biochar increased the proportion of mineral nitrogen supplied by fertilizer in the mineral nitrogen pool. The application of 7500 kg·ha-1 biochar increased mineral nitrogen by 3.05 %, 3.22 %, and 3.8 %, respectively, compared to the control treatments in the same year. Biochar promoted the transformation of nitrogen in the 0-40 cm soil layer to three different soil nitrogen pools, especially the organic nitrogen pool. (3) Biochar significantly improved the soil bacterial community and increased the abundances of N transformation functional genes. The redundancy analysis (RDA) showed that the gdhA mineralization gene was the driving factor of nitrogen fertilizer transformation, contributing 43.6 % of the variance. In summary, the application of 7500 kg·ha-1 of biochar for two consecutive years was conducive to maintaining farmland soil fertility, while its use would not be recommended for more than three consecutive years.

Composted maize straw under fungi inoculation reduces soil N2O emissions and mitigates the microbial N limitation in a wheat upland.

Enhancement of microbial assimilation of inorganic nitrogen (N) by straw addition is believed to be an effective pathway to improve farmland N cycling. However, the effectiveness of differently pretreated straws on soil N2O emissions and soil N-acquiring enzyme activities remains unclear. In this study, a pot experiment with four treatments (I, no addition, CK; II, respective addition of maize straw, S; III, composted maize straw under no fungi inoculation, SC; and IV, composted maize straw under fungi inoculation, SCPA) at the same quantity of carbon (C) input was conducted under the same amount of inorganic N fertilization. Results showed that the seasonal cumulative N2O emissions following the SCPA treatment were the lowest at 4.03 kg N ha-1, representing a significant reduction of 19 % compared with the CK treatment. The S and SC treatments had no significant effects on N2O emissions. The decrease of soil N2O emissions following the SCPA treatment was mainly attributed to the increase of microbial N assimilation and the increased abundance of functional genes related to N2O reductase. The SCPA treatment significantly decreased soil alkaline phosphatase (ALP) activity and increased leucine aminopeptidase (LAP) activity at the basal fertilization, while increased soil ALP and LAP activity, decreased soil N-Acetyl-ß-D-Glucosidase (NAG) activity at harvest. Compared with the CK treatment, the S, SC, and SCPA treatment significantly increased soil ß-glucosidase (ß-GC) activity at harvest. The decrease in the (NAG+LAP)/ALP ratio following the SCPA treatment indicated that the composted maize straw under fungi inoculation alleviated microbial N limitation at harvest. Moreover, PICRUSt analysis also suggested that the SCPA treatment increased the abundance of bacterial genes associated with N assimilation and N2O reduction, whereas the S and SC treatment did not significantly affect the abundance of N2O reduction genes compared with the CK treatment. Our results suggest that the composted maize straw under fungi inoculation would reduce the risk of N2O emissions and effectively mitigate the microbial N limitation in dryland wheat system.

Performance and mechanism of antibiotic resistance removal by biochar-enhanced sediment microbial fuel cell.

This study is the first to explore the performance and mechanism of biochar-impacted sediment microbial fuel cell for removing antibiotic resistance genes (ARGs), and examines the effects of different biochar contents. The addition of 5% biochar produced the highest output voltage and power density, which increased by 100% and 219%, respectively, while simultaneously reducing the abundance and risk of ARGs. Comparatively, the addition of moderate amount of biochar (1-5%) promoted the removal of ARGs, while the opposite was true for excessive (10%) biochar. Biochar affected ARGs through prophages, insertion sequence, and transposons. Biological factors and voltage jointly influenced ARGs variation, with the former accounting for 56%. Further analysis of functional genes indicated that biochar controlled ARGs by regulating the synthesis of genetic material and amino acids to influence metabolism. Overall, findings of this study shed light on the potential removal of ARGs in microbial electrochemical systems.

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.

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.

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.

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.

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.