Abundance Of Functional Genes Research Articles

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-β-D-Glucosidase (NAG) activity at harvest. Compared with the CK treatment, the S, SC, and SCPA treatment significantly increased soil β-glucosidase (β-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.

Seasonal dynamics and driving mechanisms of microbial biogenic elements cycling function, assembly process, and co-occurrence network in plateau lake sediments

Microbial community diversity significantly varies with seasonality. However, little is known about seasonal variation of microbial community functions in lake sediments and their associated environmental influences. In this study, metagenomic sequencing of sediments collected from winter, summer, and autumn from Caohai Lake, Guizhou Plateau, were used to evaluate the composition and function of sediment microbial communities, the potential interactions of functional genes, key genes associated with seasons, and community assembly mechanisms. The average concentrations of nitrogen (TN) and phosphorus (TP) in lake sediments were higher, which were 6.136 and 0.501 g/kg, respectively. TN and organic matter (OM) were the primary factors associated with sediment community composition and functional profiles. The diversity and structure of the microbial communities varied with seasons, and Proteobacteria relative abundances were significantly lower in summer than in other seasons (58.43–44.12 %). Seasons were also associated with the relative abundances of functional genes, and in particular korA, metF, narC, nrfA, pstC/S, and soxB genes. Network complexity was highest in the summer and key genes in the network also varied across seasons. Neutral community model analysis revealed that the assembly mechanisms related to carbon (C), nitrogen (N), phosphorus (P), and sulfur (S) cycle-related genes were primarily associated with random processes. In summary, diverse functional genes were identified in lake sediments and exhibited evidence for synergistic interactions (Positive proportion: 74.91–99.82 %), while seasonal factors influenced their distribution. The results of this study provide new insights into seasonal impacts on microbial-driven biogeochemical cycling in shallow lakes.

Soil pH amendment alters the abundance, diversity, and composition of microbial communities in two contrasting agricultural soils.

This study delves into the impact of soil pH on microbial communities, investigating whether pH directly or indirectly influences bacterial and fungal communities. The research involved two contrasting soils subjected to a 1-2 pH unit amendment. Results indicate bacterial community composition was shaped by soil pH through physiological constraints and nutrient limitations. We found that most taxa relative abundances at the phylum and family levels responded to pH with a quadratic fitting pattern, indicating that soil pH is a reliable predictor. Additionally, soil pH was found to significantly influence the predicted abundance of functional genes involved in the nitrogen cycle as well as in methane production and consumption processes. These insights can contribute to develop more effective soil management and conservation strategies.

Effects of Irrigation with Slightly Algae-Contaminated Water on Soil Moisture, Nutrient Redistribution, and Microbial Community

The presence of excessive algae in water is always considered as a negative factor in irrigation. However, the optimal balance between algal removal and retention in irrigation water when the algal biomass is controllable remains unknown. Therefore, this study explores the impact of low-level algal presence (Scytonema javanicum) on soil and microbial activity through controlled soil column experiments. Soil moisture was measured, and 16S rRNA gene amplicons sequencing was applied to characterize the microbial community. Slight community changes indicated no negative impact on the local microbial community of S. javanicum. Enzyme assays and quantitative polymerase chain reaction (qPCR) revealed that algae improved soil moisture retention, and enhanced the nutrient content of the topsoil. The decrease in moisture in the treatment group (from 27.53% to 26.42%) was significantly reduced (p < 0.05) compared to the control (from 27.55% to 25.17%), while the contents of ammonium (NH3-N) and total nitrogen (TN) in the treatment (0.70 mg/kg and 0.54 g/kg) were also higher (p < 0.05) than that of the control (0.43 mg/kg and 0.49 g/kg). The results of the abundance of functional gene suggested algae facilitated nitrogen fixation and nitrification. This research offers innovative insights for diversifying the sources of irrigation water.

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. Urban rivers are significant hotspots of greenhouse gases (GHGs, CO2, N2O, and CH4) emissions. This study examined the GHGs distributions in the Guanxun River, an effluents-receiving subtropical urban 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 GWP 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 urban 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 urban 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.

Long term impact of electrical resistance heating on soil bacterial community based on a field test

Thermal remediation is an effective technology for organic contaminant remediation. However, the application of thermal remediation may have negative effects on soil properties and ecological functions, which requires further investigation. Based on a pilot test of electrical resistance heating remediation (ERH), soil samples were collected at different locations after heating for 116 days. Most soil physicochemical properties were less affected by the heating temperature difference. Application of high temperature increased microbial abundance but inhibited alpha diversity of the bacterial community. More significant changes in microbial communities were observed at temperatures above 60 °C. The genera mainly affected by heating temperature included Flavobacteria, Brockia, and S085, while the increase in temperature also inhibited the abundance of nitrochlorobenzene functional genes. At 140 days after the end of the pilot test, the bacterial community affected by thermal remediation could recover effectively, and the recovery of the bacterial community was not affected by temperature difference during the heating period. This study provides valuable field evidence of the long term impact of soil ERH treatment on soil properties and microbial communities, and provide further references for optimization of remediation performance with coupled technologies.

Significant correlations between heavy metals and prokaryotes in the Okinawa Trough hydrothermal sediments

Prokaryotes play crucial roles in hydrothermal vent ecosystems, yet their interactions with heavy metals are not well understood. This study explored the diversity of prokaryotic communities and their correlations with heavy metals and nutrient elements in hydrothermal sediments from Okinawa Trough. A total of 117 bacterial genera in 26 bacterial phyla and 10 archaeal classes in 3 archaeal phyla were identified, including dominant prokaryotic phyla Planctomycetes, Acidobacteria, Verrucomicrobia, and Euryarchaeota. Furthermore, Fe (39.61mg/g), Mn (2.84mg/g) and Ba (0.36mg/g) were found to be the most abundant heavy metals in the Okinawa hydrothermal sediments. Notably, the concentrations of Zn, Ba, Mn, total organic carbon, and total nitrogen significantly increased, whereas the total sulfur concentration distinctively decreased at sampling sites farther from hydrothermal vents. These changes corresponded with reductions in prokaryotic abundance and diversity. Most heavy metals, including Mn, Fe, Co, Cu and As, presented significant positive correlations with a number of prokaryotic genera in the nearby sediment samples. In contrast, both positive and negative correlations with prokaryotes were observed in remote sediment. The keystone taxa include Magnetospirillum, GOUTA19, Lysobacter, Kaistobacter, Treponema, and Clostridium were detected through prokaryote interspecies interactions. The functional predictions revealed significant genes involved in carbon fixation, nitrogen/sulfur cycling, heat shock protein, and metal resistance pathways. Structural equation modeling confirmed that metal and nutrient elements directly influence the composition of prokaryotic communities, which in turn affects the relative abundance of functional genes.

Enhancing bioremediation of petroleum-contaminated soil by sophorolipids-modified biochar: Combined metagenomic and metabolomic analyses

In this study, sophorolipids (SLs)-modified biochar (BC-SLs) was used to enhance the bioremediation of petroleum hydrocarbons (PHs) contaminated soil. The biodegradation rate of petroleum hydrocarbons (PHs) by BC-SLs and BC treatments were 62.86 % and 52.64 % after 60 days of remediation experiments, respectively, higher than non-biochar treatment group (24.09 %). The metagenomic analysis showed that the abundance of petroleum-degrading bacteria Actinobacteria and Proteobacteria were increased by 3.8 % and 5.3 %, respectively in BC-SLs treatment, and the abundance of functional genes for PHs degradation, such as alkB, nidA and pcaG, were significantly increased by 12.85 %, 30.08 % and 21.01 %, respectively. The metabolomic analysis showed that BC-SLs facilitated the metabolic process of PHs, the microbial metabolism of petroleum hydrocarbons (PHs) became more active. Fatty acid degradation and polycyclic aromatic hydrocarbons (PAHs) degradation were up-regulated, indicating the promoting effect of the BC-SLs for PHs metabolism. The combined metagenomic and metabolomic analysis demonstrated the strong positive correlations between PHs metabolites and PHs-degrading bacteria, such as lauric acid vs. Actinobacteria, benzoic vs. Proteobacteria. The strong positive correlations between PHs metabolites and PHs-degrading genes were also observed, such as o-ehyltoluene vs. nahD, 4-isopropylbenzoic acid vs. etbAa. The modification of biochar with SLs increased the oxygen-containing functional groups on the surface of biochar. Meanwhile, the emulsification and solubilization of SLs promoted the bioavailability of PHs. The effects of BC-SLs on the nitrogen cycle during PHs remediation showed that it facilitated the accumulation of nitrogen-fixing genes, promoted nitrification but inhibited denitrification process. This study confirms that the application of BC-SLs is an effective remediation of PHs contamination and a sustainable method for controlling agricultural waste resources.

Molecular evidence of internal carbon-driven partial denitrification in a mainstream pilot A-B system coupled with side-stream EBPR treating municipal wastewater

Achieving mainstream short-cut nitrogen removal via nitrite has become a carbon and energy efficient way, but still remains challenging for low-strength municipal wastewaters. This study integrated sidestream enhanced biological phosphorus removal system in a pilot-scale adsorption/bio-oxidation (A-B) process (named A-B-S2EBPR system) and nitrite accumulation was successfully achieved for treating the municipal wastewater. Nitrite could accumulate to 5.5 ± 0.3 mg N/L in the intermittently aerated tanks of B-stage with the nitrite accumulation ratio (NAR) of 79.1 ± 6.5 %. The final effluent concentration and removal efficiency of total inorganic nitrogen (TIN) were 4.6 ± 1.8 mg N/L and 84.9 ± 5.6 %, respectively. In-situ process performance of nitrogen conversions, routine batch nitrification/denitrification activity tests and functional gene abundance of nitrifiers collectively suggested that the nitrite accumulation was mainly caused by partial denitrification rather than out-selection of nitrite oxidizing bacteria (NOB). Moreover, the single-cell Raman spectroscopy analysis first demonstrated that there was a specific microbial population that could utilize polyhydroxyalkanoates (PHA) as the potential internal carbon source during the partial denitrification process. The integration of S2EBPR brings unique features to the conventional A-B process, such as extended anaerobic retention time, lower oxidation–reduction potential (ORP), much higher and complex volatile fatty acids (VFAs) etc., which can largely reshape the microbial communities. The dominant genera were Acinetobacter and Comamonadaceae, which accounted for (17.8 ± 15.5)% and (6.7 ± 3.4)%, respectively, while the relative abundance of conventional nitrifiers was less than 0.2%. This study provides insights into phylogenetic and phenotypic shifts of microbial communities when incorporating S2EBPR into the sustainable A-B process to achieve mainstream short-cut nitrogen removal.

Quorum sensing improves start-up and stability of sulfate-reducing biocathode in autotrophic microbial electrolytic cell for low-organic-carbon sulfate wastewater treatment

The utilization of autotrophic microorganisms in microbial electrolysis cell (MEC) is promising for the treatment of industrial wastewater that lacks carbon source and electron donor. However, constructing an autotrophic biocathode is time-consuming, and the population induction technologies may alleviate this challenge. In this study, N-butyryl-L-Homoserine lactone (C4-HSL) was added to the MEC biocathode run for 60 cycles to investigate quorum sensing effects on sulfate reduction efficiency, electrochemical properties, microbial community structure and functional genes. The results showed that the addition of C4-HSL significantly expedited the startup of the MEC cathode with a 47.1 % reduction. Its electrochemical performance was also improved, with the cyclic voltammetry area averaging 1.19 times higher than that without the addition of the signaling molecule. Under the regulation of C4-HSL, the biodiversity in the initiation phase became richer. The relative abundance of Desulfobacterota and sulfate reduction-related functional genes increased to 4 times and 1.43 times of the control, respectively. This discovery reveals the potential of signaling molecules in enhancing the construction of sulfate wastewater treatment reactors and improving the performance of autotrophic microorganisms, aiming to improve wastewater treatment efficiency and broaden the practical possibilities of MEC.

Enhanced methane production from anaerobic digestion of waste activated sludge with weak magnetic field: Insights into performances and mechanisms

The impact of weak magnetic field (WMF) on anaerobic digestion (AD) performance of waste activated sludge (WAS) and underlying mechanism were investigated. Results showed that WMF significantly stimulated the methane yield by 12.9∼25.1% with 15 and 30 mT WMF addition, but high WMF (60 mT) attenuated the positive effect. The WMF enriched the anaerobic microbes, especially the acetoclastic and hydrogenotrophic methanogen. Additionally, the WMF dramatically facilitated the metabolic pathways of key enzymes for methanogenesis, which was validated by the significant increase of absolute abundance of anaerobic functional genes (mcrA). The enzyme activities of ATP and F420 were also significantly promoted by 30 mT WMF, but high WMF (60 mT) resulted in increased activity of lactate dehydrogenase. This study reveals that low WMF can promote AD performance of WAS through enhancing microbial activities especially methanogen, but high WMF leads to the loss of cell membrane integrity and attenuates its positive effect.

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.

Conversion of monocropping to intercropping promotes rhizosphere microbiome functionality and soil nitrogen cycling

Intercropping can increase soil nutrient availability and provide greater crop yields for intensive agroecosystems. Despite its multiple benefits, how intercropping influences rhizosphere microbiome assemblages, functionality, and complex soil nitrogen cycling is not fully understood. Here, a three-year field experiment was carried out on different cropping system with five fertilization treatments at the main soybean production regions. We found that soybean yields in intercropped systems were on average 17 % greater than in monocropping system, regardless of fertilization treatments. We also found that intercropping systems significant increased network modularity (by 46 %) and functional diversity (by 11 %) than monocropping systems. Metagenomics analyses further indicated intercropping promotes microbiome functional adaptation, particularly enriching core functions related to nitrogen metabolism. Cropping patterns had a stronger influence on the functional genes associated with soil nitrogen cycling (R2 = 0.499). Monocropping systems increased the abundance of functional genes related to organic nitrogen ammonification, nitrogen fixation, and denitrification, while functional guilds of nitrate assimilation (by 28 %), nitrification (by 31 %), and dissimilatory nitrate reduction (by 10.1 %) genes were enriched in intercropping systems. Furthermore, we found that abiotic factors (i.e. AP, pH, and Moisture) are important drivers in shaping soil microbial community assemblage and nitrogen cycling. The functional genes include hzsB, and nrfA, and nxrA that affected by these biotic and abiotic variables were strongly related to crop yield (R2 = 0.076 ~ R2 = 0.249), suggesting a key role for maintaining crop production. We demonstrated that land use conversion from maize monocropping to maize-soybean intercropping diversify rhizosphere microbiome and functionality signatures, and intercropping increased key gene abundance related to soil nitrogen cycling to maintain the advantage of crop yield. The results of this study significantly facilitate our understanding of the complex soil nitrogen cycling processes and lay the foundation for manipulating desired specific functional taxa for improved crop productivity under sustainable intensification.

Enhancement of Biological Nitrogen Removal System Resilience to Chronic Exposure of Zinc Oxide Nanoparticles by Quorum Sensing Modulation: Physiochemical, Microbial, and Metabolic Insights

The effects of three typical N-acyl-homoserine lactones (AHLs) on the tolerance of biological nitrogen removal (BNR) system to chronic exposure of zinc oxide nanoparticles (NPs) were investigated. C4-HSL successfully delayed the crash time of nitrogen removal performances in the NP-stressed system, while C6-HSL and C10-HSL maintained total nitrogen removal efficiencies throughout the 90-day NP exposure. All three AHLs increased NPs’ contents captured in extracellular polymeric substances, alleviating membrane damage and preserving floc structure. The activities of tricarboxylic acid cycle-related enzymes and the relative abundances of BNR-related functional genes and genera were significantly enhanced. Besides, C6-HSL and C10-HSL augmented antioxidant enzyme activities and the abundances of functional genes and metabolites related to antioxidation, flagellar assembly, and chemotaxis, which synergistically reduced the reactive oxygen species’ excessive accumulation. The tested AHLs effectively enhanced BNR systems’ tolerance to chronic NP exposure, providing inspiration for quorum sensing applications in emerging contaminant removal.

Geographical factor dominates spatial patterns of potential nitrate reduction rates in coastal wetland sediments in Fujian Province, China

Nitrate (NO3−) reduction is a key process governing the nitrogen (N) dynamics of coastal wetland sediments. Although the effects of environmental factors on the NO3− reduction mechanism in coastal wetland sediments have been examined in various studies, the effects of spatial variation in potential NO3− reduction processes in coastal wetland sediments and the factors driving geographical variation in these processes have not been widely examined. Here, we conducted research on surface sediment samples from four different vegetation types at six coastal wetland sites across two regions. We characterized potential rates of NO3− reduction processes (including denitrification (DF), anammox (ANA), and dissimilatory nitrate reduction to ammonium (DNRA)) using a15N tracer method. Additionally, we assessed the abundances of functional genes, and microbial community structure using high-throughput sequencing, and metagenomic sequencing. In six wetland sites, the contribution ranges of DF, ANA, and DNRA to NO3− reduction were 38.43%–55.69%, 31.33%–45.65%, and 5.26%–17.11%, respectively, and potential NO3− reduction was mainly driven by N removal via gaseous N (DF+ANA). Significant spatial differences were observed in the structure of bacterial and fungal microbial communities, suggesting that geographical distance has a major effect on microbial community structure. Environmental factors and Functional gene abundances were significantly related to potential NO3− reduction processes, and physicochemical properties had a stronger effect on potential NO3− reduction processes than gene abundances. Factors showing significant differences across regions were the main drivers of variation in potential NO3− reduction processes. Overall, our study showed that sediment substrates and geographical environmental factors rather than the abundance of functional genes and vegetation types were the main indicators of potential NO3− reduction activities in coastal wetlands.

Microbial diversity and gene abundance in denitrifying bioreactors: A comparison of the woodchip surface biofilm versus the interior wood matrix.

Excessive amounts of nitrogen (N) and phosphorus (P) can lead to eutrophication in water sources. Woodchip bioreactors have shown success in removing N from agricultural runoff, but less is known regarding P removal. Woodchip bioreactors are subsurface basins filled with woodchips installed downgradient of agricultural land to collect and treat drainage runoff. Microorganisms use the woodchips as a carbon (C) source to transform N in the runoff, with unresolved biological impacts on P. This study aims to explore microbial communities present in the bioreactor and determine whether milling woodchips to probe the microbial communities within them reveals hidden microbial diversities or potential activities. Metagenomic sequencing and bioinformatic analyses were performed on six woodchip samples (i.e., three unmilled and three milled) collected from a 10-year-old woodchip bioreactor treating agricultural tile drainage. All samples had similar DNA purity, yield, quality, and microbial diversity regardless of milling. However, when sequences were aligned against various protein libraries, our results indicated greater relative abundance of denitrification and P transformation proteins on the outside of the woodchips (unmilled), while the interior of woodchips (milled) exhibited more functional gene abundance for carbohydrate breakdown. Thus, it may be important to characterize microbial communities both within woodchips, and on woodchip surfaces, to gain a more holistic understanding of coupled biogeochemical cycles on N, P, and C in woodchip bioreactors. Based on these findings, we advise that future microbial research on woodchips (and potentially other permeable organic materials) examine both the surface biofilm and the interior organic material during initial studies. Once researchers determine where specific proteins or enzymes of interest are most prevalent, subsequent studies may then focus on either one or both aspects, as needed.

Ex vivo metabolism kinetics of primary to secondary bile acids via a physiologically relevant human faecal microbiota model

Bile acids (BA) are synthesized in the human liver and undergo metabolism by host gut bacteria. In diseased states, gut microbial dysbiosis may lead to high primary unconjugated BA concentrations and significant perturbations to secondary BA. Hence, it is important to understand the microbial-mediated formation kinetics of secondary bile acids using physiologically relevant ex vivo human faecal microbiota models. Here, we optimized an ex vivo human faecal microbiota model to recapitulate the metabolic kinetics of primary unconjugated BA and applied it to investigate the formation kinetics of novel secondary BA metabolites and their sequential pathways. We demonstrated (1) first-order depletion of primary BA, cholic acid (CA) and chenodeoxycholic acid (CDCA), under non-saturable conditions and (2) saturable Michaelis-Menten kinetics for secondary BA metabolite formation with increasing substrate concentration. Notably, relatively lower Michaelis constants (Km) were associated with the formation of deoxycholic acid (DCA, 14.3 μM) and lithocholic acid (LCA, 140 μM) versus 3-oxo CA (>1000 μM), 7-keto DCA (443 μM) and 7-keto LCA (>1000 μM), thereby recapitulating clinically observed saturation of 7α-dehydroxylation relative to oxidation of primary BA. Congruently, metagenomics revealed higher relative abundance of functional genes related to the oxidation pathway as compared to the 7α-dehydroxylation pathway. In addition, we demonstrated gut microbial-mediated hyocholic acid (HCA) and hyodeoxycholic acid (HDCA) formation from CDCA. In conclusion, we optimized a physiologically relevant ex vivo human faecal microbiota model to investigate gut microbial-mediated metabolism of primary BA and present a novel gut microbial-catalysed two-step pathway from CDCA to HCA and, subsequently, HDCA.

Vertical Distribution Characteristics and Driving Factors of Bacterioplankton and Nitrogen Phosphorus Cycle Genes in Danjiangkou Reservoir

Danjiangkou Reservoir is a critical water source for the South-to-North Water Diversion Project, which harbors a diverse bacterioplankton community with varying depths, and the understanding of its nitrogen and phosphorus cycle and associated driving factors remains limited. In this study, we selected five ecological sites within Danjiangkou Reservoir and conducted metagenomics analysis to investigate the vertical distribution of bacterioplankton communities in the surface, middle, and bottom layers. Furthermore, we analyzed and predicted the function of nitrogen and phosphorus cycles, along with their driving factors. Our findings revealed the dominance of Proteobacteria, Actinobacteria, and Planctomycetes in the Danjiangkou Reservoir. Significant differences were observed in the structure of bacterioplankton communities across different depths, with temperature （T）, oxidation-reduction potential （ORP）, dissolved oxygen （DO）, and Chla identified as primary factors influencing the bacterioplankton composition. Analysis of nitrogen cycle functional genes identified 39 genes, including gltB, glnA, gltD, gdhA, NRT, etc., which were involved in seven main pathways, encompassing nitrogen fixation, nitrification, denitrification, and dissimilatory nitrate reduction. Phosphorus cycle function gene analysis identified 54 genes, including pstS, ppx-gppA, glpQ, ppk1, etc., primarily participating in six main pathways, including organic P mineralization, inorganic P solubilization, and regulatory. Cluster analysis indicated that different depths were significant factors influencing the composition and abundance of nitrogen and phosphorus cycle functional genes. The composition and abundance of nitrogen and phosphorus cycle functional genes in the surface and bottom layers differed and were generally higher than those in the middle layer. Deinococcus, Hydrogenophaga, Limnohabitans, Clavibacter, and others were identified as key species involved in the nitrogen and phosphorus cycle. Additionally, we found significant correlations between nitrogen and phosphorus cycle functional genes and environmental factors such as DO, pH, T, total dissolved solids （TDS）, electrical conductivity （EC）, and Chla. Furthermore, the content of these environmental factors exhibited depth-related changes in the Danjiangkou Reservoir, resulting in a distinct vertical distribution pattern of bacterioplankton nitrogen and phosphorus cycle functional genes. Overall, this study sheds light on the composition, function, and influencing factors of bacterioplankton communities across different layers of Danjiangkou Reservoir, offering valuable insights for the ecological function and diversity protection of bacterioplankton in this crucial reservoir ecosystem.

Insight into the effect of CaO2 addition on the prevalence and removal of antibiotic resistance genes during anaerobic sludge fermentation under ambient conditions

This study investigated the effect of CaO2 and its related hydrolysis products on the prevalence and removal of antibiotic resistance genes (ARGs) during anaerobic fermentation of waste activated sludge (WAS) under ambient conditions. Comprehensive analyses were conducted to elucidate the mechanisms underlying the effects of CaO2 addition, focusing on the microbial community structure, host bacteria, cell membrane permeability and the interaction between ARGs and environmental factors. Results showed the alkalinity, oxidation and calcium of CaO2 synergistically contributed to the elimination of ARGs. The top ARGs, such as sulI, sulII, tetC, tetX and ereA, were effectively reduced by 43.9–84.9 % with CaO2 addition during the ambient anaerobic fermentation. Ca(OH)2 treatment also shows good effectiveness in removing typical ARGs, followed by H2O2 treatment, while NaOH treatment increases ARGs abundance and raise the risk of their transmission. Among the influencing factors, the abundance and diversity of microbial community, organic matters, calcium and pH were the primary factors for ARGs migration. The effective reduction of Proteobacteria was an important reason for the removal of typical ARGs, particularly sulfonamide resistance genes. CaO2 also downregulated the relative abundance of autoinducer and functional genes related to outer membrane proteins (OMPs) and ARGs dissemination, thereby inhibiting ARGs transmission. This work provides a deep insight into the advantage of CaO2 in reducing ARGs, thus expanding its potential application in sludge treatment and ARGs elimination.

Deciphering taxonomic and functional patterns of microbial communities associated with the tiger tail seahorse (Hippocampus comes).

Gaining insight into the diversity, structure, and metabolic functions of microbial communities is essential for understanding their roles in host health and ecosystem dynamics. However, research on the seahorse-associated microbiome remains limited, despite these threatened fish facing increasing human pressures worldwide. Here, we explored the microbial diversity and metabolic functions of the skin and gut of the tiger tail seahorse (Hippocampus comes) and its surrounding environment using shotgun metagenomics and bioinformatics. Members of the Pseudomonadota phylum were dominant in the skin microbiome, whereas Bacteroidota was dominant in the gut. Bacillota, Actinomycetota, and Planctomycetota were also detected in the seahorse-associated microbiome. Statistical analysis revealed significant differences (P < 0.01) in species diversity between skin and gut microbiomes, with members belonging to the Moraxellaceae family being dominant on the skin and the Bacteroidaceae family in the gut. Moreover, the surrounding environment (water or sediment) did not have a direct effect on the seahorse microbiome composition. The skin microbiome exhibited a higher abundance of functional genes related to energy, lipid, and amino acid metabolism as well as terpenoids and polyketides metabolism, xenobiotics biodegradation, and metabolism compared with the gut. Despite differences among classes, the total abundance of bacteriocins was similar in both gut and skin microbiomes, which is significant in shaping microbial communities due to their antimicrobial properties. A better knowledge of seahorse microbiomes benefits conservation and sustainable aquaculture efforts, offering insights into habitat protection, disease management, and optimizing aquaculture environments, thereby promoting seahorse health and welfare while minimizing environmental impact and enhancing aquaculture sustainability.NEW & NOTEWORTHY To the best of our knowledge, this study represents the first comprehensive examination of the taxonomic and functional patterns of the skin and gut microbiome in the tiger tail seahorse. These findings have the potential to significantly enhance our understanding of the seahorse-associated microbiome, thereby contributing to the prediction and control of bacterial infections in seahorses, which are a leading cause of high mass mortality rates in seahorse aquaculture and other fish species.