Relative Abundance Of Genes Research Articles

Fermented soybean meal modified the rumen microbiota and increased the serum prolactin level in lactating Holstein cows

This study aimed to investigate the effects of fermented soybean meal (FSM) on milk production, blood parameters, and rumen fermentation and microbial community in dairy cows. In this study, 48 healthy Holstein cows (parity, 3.0 ± 0.6; days in milk, 86.0 ± 6.7) were used. Cows were randomly assigned into four groups (CON, T-200, T-400, and T-600) with 12 cows per group. Cows in CON were not supplemented with FSM. Cows in T-200, T-400, and T-600 were supplemented with 200, 400, and 600 g/head/day FSM, respectively. This study lasted 5 weeks (1-week adaptation and 4-week treatment). The results showed that FSM did not affect milk yield and milk components (p > 0.05). In the serum, FSM greatly increased prolactin (p < 0.01), and a dosage effect was observed. Aspartate aminotransferase and total protein were the highest in the T-400 (p < 0.05), and triglycerides was the lowest in T-200 (p < 0.05), and there was no difference for the 3 measurements between the other 3 groups (p > 0.05). In the rumen, FSM did not affect pH, microbial crude protein, acetate, propionate, butyrate, valerate, total volatile fatty acids and the ratio of acetate:propionate (p > 0.05), only changed NH3-N, isobutyrate and isovalerate (p < 0.05). The results of the rumen bacterial 16S rRNA genes sequencing showed that FSM decreased the richness (p < 0.05) and evenness (p < 0.05) of the bacterial communities. PCoA analysis showed that FSH altered the rumen bacterial community (ANOSIM, R = 0.108, p = 0.002). In the relative abundance of phyla, FSM increased Firmicutes (p = 0.015) and Actinobacteriota (p < 0.01) and Patescibacteria (p = 0.012), decreased Bacteroidota (p = 0.024). In the relative abundance of genera, FSM increased Christensenellaceae R-7 group (p = 0.011), Lactococcus (p < 0.01), Candidatus Saccharimonas (p < 0.01), Olsenella (p < 0.01), decreased Muribaculaceae_norank (p < 0.01). Conclusively, supplemented FSM altered the rumen fermentation parameters and bacterial community, and increased serum prolactin level in lactating Holstein cows. These findings may provide an approach to keep the peak of lactation in dairy cows.

Extracellular Enzymes of Soils Under Organic and Conventional Cropping Systems: Predicted Functional Potential and Actual Activity

Conventional cropping systems (CCSs) rely heavily on large-scale and intensive crop production, using mechanical tillage and synthetic inputs such as chemical fertilizers and pesticides. While these methods can be economically beneficial, they can also be environmentally destructive. Organic cropping systems (OCSs), on the other hand, offer a more sustainable approach with less harmful effects on the environment. CCSs exhibit higher prevalence rates compared to OCSs. This means that there is less research on soil processes in organic fields and the impact of these processes on soil quality. In this study, we aim to assess the functional potential of soils by analyzing their ability to transform carbon, nitrogen, phosphorus, and sulfur. We use shotgun sequencing data to predict the activities of enzymes involved in these cycles. These predictions are then compared to the actual enzyme activity measured in the soil. The objects of study are samples of Chernozem soil from fields cultivated for 11 years using the OCS method and 20 years using the CCS method. It was found that the chemical properties of the studied soils differed significantly in terms of total carbon and total and available nitrogen and phosphorus. Except for phosphorus, the concentration of these elements was significantly higher in the CCS than in the OCS. We assessed the quality of the soils by measuring their enzymatic activities. A comparison of the two cropping systems showed that the activities of the enzymes involved in the C, N, P, and S cycles were, on average, 2.91, 1.89, 1.74, and 1.86 times higher in the CCS than in the OCS, respectively. A two-way PERMANOVA showed that the cropping system was the main variable (F = 14.978, p < 0.01) determining the enzymatic activity of soils, followed by soil depth (F = 9.6079, p < 0.01). We used shotgun sequencing to identify functional genes involved in C, N, P, and S metabolism, as well as genes encoding the measured soil enzymes. Compared to the OCS, the CCS soils had a higher relative abundance of genes involved in N-conversion (log2(FC) +0.22), C-conversion (log2(FC) +0.14), P-conversion (log2(FC) +0.47), and S-conversion (log2(FC) +0.24). At the same time, we found no significant differences between the systems in the relative abundance of genes encoding the measured soil enzymes. Thus, the comparison of the two cropping systems studied showed that the soil microbiome in the CCS has a greater functional potential to support biogeochemical cycles of the key biogenic elements than in the OCS. In addition, this study links the data on the representation of functional genes with the actual activity of enzymes. Based on the results, it would be helpful to focus more specifically on actual enzyme activity or to combine several indicators to obtain a more accurate understanding of soil quality.

Identify the key factors driving the lignocellulose degradation of litter along a forest succession chronosequence from the perspective of functional genes

The purpose of this paper was to discover the key factors driving the lignocellulose degradation in litter along a forest succession chronosequence from the perspective of functional genes. We investigated four natural successive stages of forests (white birch forest, broad-leaved mixed forest, coniferous-broad-leaved mixed forest, and mixed broadleaved-Korean pine forest). We determined the lignocellulose degradation of litter and the absolute abundance of related functional genes by using high-throughput-qPCR. There was strong degradation of cellulose content, hemicellulose, and lignin contents in the litter decomposition layer in the early and late stages of forest succession, respectively. Furthermore, forest succession changed microbial communities' succession and fungal Shannon diversity, and then enhanced the absolute abundance of lignocellulose-degrading genes and nitrogen-cycling genes. By network analysis, bacterial and fungal module 1 were key modules for producing lignocellulose-degrading genes and nitrogen cycling genes, while fungal module 2 was a key module for lignin-degrading genes. Fungi were strongly correlated with functional genes based on Procrustes analysis. Additionally, cellulose-degrading genes were the key factor driving the cellulose degradation in the early period of forest succession, while fungal diversity and composition were key drivers in promoting the degradation of lignin in the late period of forest succession. Our study provided insight into the mechanisms underlying the soil microbe-driven functional changes in nutrient cycling and an understanding of the decomposition kinetics of litter at a more microscopic level in the process of forest succession.

Nitrogen enrichment stimulates nutrient cycling genes of rhizosphere soil bacteria in the Phoebe bournei young plantations

Anthropogenic nitrogen (N) deposition is expected to increase substantially and continuously in terrestrial ecosystems, endangering the balance of N and phosphorus (P) in P-deficient subtropical forest soil. Despite the widely reported responses of the microbial community to simulated N deposition, there is limited understanding of how N deposition affects the rhizosphere soil processes by mediating functional genes and community compositions of soil bacteria. Here, five levels of simulated N deposition treatments (N0, 0 g m−2·yr−1; N1, 100 g m−2·yr−1; N2, 200 g m−2·yr−1; N3, 300 g m−2·yr−1; and N4, 400 g m−2·yr−1) were performed in a 10-year-old Phoebe bournei plantation. Quantitative microbial element cycling smart chip technology and 16S rRNA gene sequencing were employed to analyze functional gene compositions involved in carbon (C), N, and P cycling, as well as rhizosphere bacterial community composition. N deposition significantly influenced C cycling relative abundance of genes in the rhizosphere soil, especially those involved in C degradation. Low and moderate levels (100–300 g m−2·yr−1) of N deposition promoted the relative abundance of the C decomposition-related genes (e.g., amyA, abfA, pgu, chiA, cex, cdh, and glx), whereas high N deposition (400 g m−2·yr−1) suppressed enzyme (e.g., soil invertase, soil urease, and soil acid phosphatase) activities, affecting the C cycling processes in the rhizosphere. Simulated N deposition affected the functional genes associated with C, N, and P cycling by mediating soil pH and macronutrients. These findings provide new insights into the management of soil C sequestration in P. bournei young plantations as well as the regulation of C, N, and P cycling and microbial functions within ecosystems.

Metagenomic Analysis Reveals the Effects of Different Land Use Types on Functional Soil Phosphorus Cycling: A Case Study of the Yellow River Alluvial Plain

Phosphorus (P) is a crucial limiting nutrient in soil ecosystems, significantly influencing soil fertility and plant productivity. Soil microorganisms adapt to phosphorus deficiency and enhance soil phosphorus effectiveness through various mechanisms, which are notably influenced by land use practices. This study examined the impact of different land use types (long-term continuous maize farmland, abandoned evolving grassland, artificial tamarisk forests, artificial ash forests, and wetlands) on soil phosphorus-cycling functional genes within the Tanyang Forest Farm in a typical region of the Yellow River alluvial plain using macro genome sequencing technology. The gene cluster related to inorganic phosphorus solubilization and organic phosphorus mineralization exhibited the highest relative abundance across different land use types (2.24 × 10−3), followed by the gene cluster associated with phosphorus transport and uptake (1.42 × 10−3), with the lowest relative abundance observed for the P-starvation response regulation gene cluster (5.52 × 10−4). Significant differences were found in the physical and chemical properties of the soils and the relative abundance of phosphorus-cycling functional genes among various land use types. The lowest relative abundance of soil phosphorus-cycling functional genes was observed in forestland, with both forestland types showing significantly lower gene abundance compared to wetland, farmland, and grassland. Correlation analysis and redundancy analysis (RDA) revealed a significant relationship between soil physicochemical properties and soil phosphorus-cycling functional genes, with ammonium nitrogen, organic carbon, total nitrogen, and pH being the main environmental factors influencing the abundance of these genes, explaining 70% of the variation in their relative abundance. Our study reveals land use’s impact on soil phosphorus-cycling genes, offering genetic insights into microbial responses to land use changes.

The effect of polyvinyl chloride microplastics on soil properties, greenhouse gas emission, and element cycling-related genes: Roles of soil bacterial communities and correlation analysis

Different shapes (membranes and particles) and concentrations (1 % (w/w) and 2 % (w/w)) of polyvinyl chloride (PVC) microplastics (MPs) were investigated to determine their impact on the soil environment. The incorporation of MPs can disrupt soil macroaggregates. Compared with 1 % (w/w) MPs, 2 % MPs resulted in a significant increase in soil organic carbon content. MP particles significantly increased soil CO2 emissions, and CH4 emissions were enhanced by both membrane and particle MPs at high concentrations. Microplastics can alter the abundance of Actinobacteria, Proteobacteria, Chloroflexi, Acidobacteriota, and Firmicutes at the phylum level, and Nocardioides, Rhodococcus and Bacillus at the genus level. MP particles had a more significant impact on soil bacterial communities than MP membranes. The relative abundances of genes involved in the C, N, and P cycles were detected by qPCR, and more remarkable changes were observed in MP membrane treatments. The relative abundance of Vicinamibacteraceae and Vicinamibacterales exhibited a positive correlation with most C/N/P cycle-related genes, whereas Pseudarthrobacter and Nocardioides demonstrated a negative correlation. This study highlights that the influence of MPs on soil parameters is mediated by soil microorganisms, providing insight into the effects of MPs on the soil microenvironment.

Impact of Harvest Method on Development of European Sea Bass Skin Microbiome during Chilled Storage

European sea bass (Dicentrarchus labrax) is one of the most significant species farmed in the Mediterranean, yet a very perishable product. Its quality deteriorates rapidly as a result of three mechanisms: microbial activity, chemical oxidation, and enzymatic degradation. Microbial spoilage is the mechanism that contributes most to the quality deterioration of fresh and non-processed fish. To this end, our study aims to identify for the first time the combined effect of aquatic environment and harvest method on the composition and trajectory at storage at 0 °C of the European sea bass skin microbiome. Sampling was performed in two commercial fish farms in Western (WG) and Central Greece (CG) where fish were harvested using different methods: direct immersion in ice water or a mixture of slurry ice; application of electro-stunning prior to immersion in ice water. Samples were collected on harvest day and one week post-harvest. To profile the bacterial communities in the fish skin, 16S ribosomal RNA gene sequencing was used. The results and the following analyses indicated that the aquatic environment shaped the original composition of the skin microbiome, with 815 ASVs identified in the WG farm as opposed to 362 ASVs in the CG farm. Moreover, Pseudomonas and Pseudoalteromonas dominated the skin microbiome in the WG farm, unlike the CG farm where Shewanella and Psychrobacter were the dominant genera. All these genera contain species such as Shewanella putrefaciens, Pseudomonas aeruginosa, Pseudoalteromonas spp., and Psychrobacter sp., all of which have been implicated in the deterioration and spoilage of the final product. The different harvest methods drove variations in the microbiome already shaped by the aquatic environment, with electro-stunning favoring more diversity in the skin microbiome. The aquatic environment in combination with the harvest method appeared to determine the skin microbiome trajectory at storage at 0 °C. Although Shewanella had dominated the skin microbiome in all samples one week post-harvest, the diversity and the relative abundance of genera were strongly influenced by the aquatic environment and the harvest method. This study sheds light on the hierarchy of the factors shaping the fish skin microbiome and their importance for controlling post-harvest quality of fresh fish.

Cow Dung Liquid Mulch Improves Maize Yields: Beneficial Microorganisms Are Enriched and Environmental Risks Are Reduced and Nutrient Cycling Is Promoted

Cow dung liquid mulch (CDLM), which uses cow dung as a raw material, has a good degradability and is a potential alternative to traditional plastic agricultural mulch, but there is a lack of research on the effects of CDLM on rhizosphere soil physicochemical properties, rhizosphere soil microbial functions, and crop yields. In this study, the link between maize yield, environmental factors, and functional genes as well as the responses of microbial community functions to CDLM and polyethylene mulch (PE) were studied using metagenomic sequencing. Functional annotation was also performed on clusters of orthologous groups of proteins, the Kyoto Encyclopedia of Genes and Genomes, and carbohydrate-active enzyme sequencing data. The results showed that CDLM significantly increased maize yield by 30.9% compared to CK while maintaining lower soil microplastic levels. CDLM promotes the enrichment of beneficial microorganisms such as Mycolicibacterium and Pseudomonas. The relative abundance of functional genes related to microbial metabolism, soil element cycling pathways, and organic matter degradation was significantly higher in CDLM than in CK. Microbial functional genes were positively correlated with maize yield and environmental factors such as soil nutrients. These results suggested that CDLM can improve maize yield by enriching beneficial microorganisms, reducing rhizosphere soil environmental risks, and enhancing rhizosphere soil microbial function. Rhizosphere soil nutrients and microbial functional genes together mediated the positive response of maize yield to CDLM. This study can provide a scientific basis and data support for the safe use of mulch in the future.

How biochar curbs the negative impacts of plastic mulching on soil enzymes and microorganisms while elevating crop yields in ridge-furrow systems

Ridge-furrow tillage is an important tillage and yield enhancement method used in dry farming areas; however, the spatial characteristics of the soil microenvironment under ridge-furrow tillage and the response of crop yields to mulching and biochar addition are not known. In this study, we conducted a three-year field experiment in which mulch and biochar, alone or combined, were introduced into ridge-furrow tillage system to explore their interactive effects on soil enzyme activities, bacterial communities, functional genes, and crop yields. The findings reveal significant spatial differences in soil physicochemical composition, enzyme activity, microbial communities, and functional genes under ridge-furrow tillage, which are further exacerbated by the addition of mulching and biochar. Under the premise of ridge-furrow tillage, both mulching and biochar addition reduce the α diversity of bacterial communities. Mulching simplifies the bacterial network, while biochar addition has the opposite effect. Mulching and biochar addition increase the relative abundance of carbon, nitrogen, and phosphorus functional genes and accelerate nutrient cycling, especially on the ridges. Mulching significantly improves crop yield but is detrimental to alkaline phosphatase activity and the abundance of the gene function. The addition of biochar mitigates the harm of mulching and further increases alfalfa yield. These findings not only provide scientific support for optimizing ridge-furrow tillage but also deepen our comprehensive understanding of the soil biochemical environment after the addition of mulching and biochar, further revealing their positive effects on yield formation.

Field Assessment of Biochar Interactions With Chemical and Biological N Fertilization in Pointed White Cabbage

ABSTRACTThe interaction of biochar with mineral fertilization has attracted attention as a strategy to reduce N losses and enhance nitrogen use efficiency. In this study, we investigated the coapplication of biochar with two optimized fertilization strategies based on split urea and a microbial inoculant (Azospirillum brasilense) in a commercial pointed white cabbage crop. Additionally, we evaluated a third optimized N fertilization alternative, a biochar‐based fertilizer (BBF) enriched in plant‐available N, which was developed from the same biochar. We assessed environmental impacts such as greenhouse gasses (GHG) and NH3 emissions, yield‐scaled N2O emissions, and global warming potential (GWP). Additionally, we evaluated agronomical outcomes such as crop yield, plant N, and chlorophyll concentration. Moreover, we examined the N‐fixing gene's total and relative abundance (nifH and nifH/16S). Biochar and BBF exhibited similar crop yield, GHG, and NH3 emissions compared to split applications of the synthetic fertilizer. The main difference was associated with the higher soil C sequestration in biochar and BBF treatments that reduced the associated GWP of these fertilization strategies. Finally, biochar favored the activity of the N‐fixing bacteria spread, compared to the sole application of bacteria and BBF demonstrated a promoting effect in the soil's total abundance of natural N‐fixing bacteria.

Depth-dependent Effects of Leguminous Crops on Soil Nitrogen-Fixing Microbial Communities Correlated with Carbon Degradation

Abstract Legumes play critical roles in agroecosystems by modulating nitrogen-fixing microorganisms to enhance soil fertility and promote crop productivity. Current research on the effects of legumes predominantly focuses on surface soil, lacking a comprehensive analysis of their overall impact across multiple soil layers and an in-depth understanding of associated microbial mechanisms. Here, the community structure of soil nitrogen-fixing microorganisms in three soil layers (0-20, 20-50, and 50-100 cm) under legume and non-legume cultivation was investigated through metagenomic sequencing. We found that only in topsoil (0-20 cm) legume treatment exhibited a significantly higher relative abundance of nitrogen-fixing genes than non-legume treatment. Under legume cultivation, the relative abundance of nitrogen-fixing genes was significantly higher in the topsoil layer than in deeper layers, whereas non-legume treatment displayed an inverse depth-dependent pattern. Combining soil physicochemical properties, the relative abundance of nitrogen-fixing genes correlated significantly with soil moisture, total carbon (TC), and dissolved organic carbon (DOC) content. Both TC and DOC were identified as key drivers of these genes. Subsequently, a similar depth-dependent pattern within the relative abundance of soil carbon degradation genes was found in response to the cultivation of both crops. The relative abundances of soil carbon degradation genes were negatively correlated with nitrogen-fixing genes under legume treatment individually, distinct from non-legume treatment. Our findings highlight the depth-dependent impact of legumes on nitrogen fixation and the critical interaction between soil carbon degradation and nitrogen fixation, providing insights into carbon management in legume cultivation practices to enhance nitrogen fixation in future agriculture.

Unveiling the Hidden Responses: Metagenomic Insights into Dwarf Bamboo (Fargesia denudata) Rhizosphere under Drought and Nitrogen Challenges.

Dwarf bamboo (Fargesia denudata) is a crucial food source for the giant pandas. With its shallow root system and rapid growth, dwarf bamboo is highly sensitive to drought stress and nitrogen deposition, both major concerns of global climate change affecting plant growth and rhizosphere environments. However, few reports address the response mechanisms of the dwarf bamboo rhizosphere environment to these two factors. Therefore, this study investigated the effects of drought stress and nitrogen deposition on the physicochemical properties and microbial community composition of the arrow bamboo rhizosphere soil, using metagenomic sequencing to analyze functional genes involved in carbon and nitrogen cycles. Both drought stress and nitrogen deposition significantly altered the soil nutrient content, but their combination had no significant impact on these indicators. Nitrogen deposition increased the relative abundance of the microbial functional gene nrfA, while decreasing the abundances of nirK, nosZ, norB, and nifH. Drought stress inhibited the functional genes of key microbial enzymes involved in starch and sucrose metabolism, but promoted those involved in galactose metabolism, inositol phosphate metabolism, and hemicellulose degradation. NO3--N showed the highest correlation with N-cycling functional genes (p < 0.01). Total C and total N had the greatest impact on the relative abundance of key enzyme functional genes involved in carbon degradation. This research provides theoretical and technical references for the sustainable management and conservation of dwarf bamboo forests in giant panda habitats under global climate change.

Temporal enrichment of comammox Nitrospira and Ca. Nitrosocosmicus in a coastal plastisphere.

Plastic marine debris is known to harbor a unique microbiome (termed the "plastisphere") that can be important in marine biogeochemical cycles. However, the temporal dynamics in the plastisphere and their implications for marine biogeochemistry remain poorly understood. Here, we characterized the temporal dynamics of nitrifying communities in the plastisphere of plastic ropes exposed to a mangrove intertidal zone. The 39-month colonization experiment revealed that the relative abundances of Nitrospira and Candidatus Nitrosocosmicus representatives increased over time according to 16S rRNA gene amplicon sequencing analysis. The relative abundances of amoA genes in metagenomes implied that comammox Nitrospira were the dominant ammonia oxidizers in the plastisphere, and their dominance increased over time. The relative abundances of two metagenome-assembled genomes of comammox Nitrospira also increased with time and positively correlated with extracellular polymeric substances content of the plastisphere but negatively correlated with NH4+ concentration in seawater, indicating the long-term succession of these two parameters significantly influenced the ammonia-oxidizing community in the coastal plastisphere. At the end of the colonization experiment, the plastisphere exhibited high nitrification activity, leading to the release of N2O (2.52ng N2O N g-1) in a 3-day nitrification experiment. The predicted relative contribution of comammox Nitrospira to N2O production (17.9%) was higher than that of ammonia-oxidizing bacteria (4.8%) but lower than that of ammonia-oxidizing archaea (21.4%). These results provide evidence that from a long-term perspective, some coastal plastispheres will become dominated by comammox Nitrospira and thereby act as hotspots of ammonia oxidation and N2O production.

Fungal communities in three root herbs: Insights and implications

The roots of Astragali Radix (AM), Dioscoreae Rhizome (DR), and Codonopsis Radix (CR) are frequently used in classical tonic formulations and dietary supplements. Given the extended exposure of rhizomes to complex biological environments, it is necessary to investigate the fungal composition of their surface. In this study, the fungal communities in the three root herbs were analyzed by DNA metabarcoding, and an extensive comparison of the fungal diversity at each taxonomic level was carried out. Furthermore, we examined the effects of species, collection site, and processing method on the fungal community. In Astragali Radix and Codonopsis Radix samples, Cladosporium was the predominant genus, with relative abundances of 1.98 %-76.81 % and 1.69 %-85.59 %, respectively. Aspergillus (0.08 %–99.92 %) was the prevailing genus in Dioscoreae Rhizome samples. Meanwhile, a total of 12 potential toxigenic fungi were identified, including Aspergillus restrictus, Fusarium oxysporum, and Penicillium citrinum. Moreover, the variations in fungal diversity and community composition from different collection sites and processing approaches were observed. Linear discriminant analysis effect size indicated significant differences in the relative abundance of genera among the three root herbs. Gibberella and Mucor genera were significantly enriched in Astragali Radix samples, while Yarrowia and Cladosporium genera exhibited significant enrichment in Dioscoreae Rhizome and Codonopsis Radix samples, respectively (p≤0.001). This study presents novel insights into the fungal profiles of three root herbs, thereby providing references for their safe utilization and quality improvement.

Responses of SNEDPR-AGS system under long-term exposure of polyethylene terephthalate microplastics for treating low C/N wastewater: Granular effect and microbial structure

The removal of nutrients in sewage treatment plants can be significantly impacted by carbon limitations, especially for treating low carbon to nitrogen ratio (C/N) wastewater, which can markedly increase operational costs. Simultaneous nitrification, endogenous denitrification, and phosphorus removal combined with aerobic granular sludge (SNEDPR-AGS) has emerged as one of the optimal processes for treating low C/N wastewater owing to its high carbon utilization efficiency; however, the long-term effect of microplastics (MPs) on this system remains unclear. This study investigated the granular effect and microbial response of an SNEDPR-AGS system for treating low C/N wastewater under long-term exposure (180 d) to polyethylene terephthalate microplastics (PET-MPs). The results showed that the integrity of the AGS structure was disrupted significantly as the PET-MP concentration increased, with clear AGS cracks appearing on days 180, 124, and 74 after exposure to 1, 10, and 100 mg/L of PET-MPs, respectively. Additionally, the addition of PET-MPs also inhibited denitrification and phosphorus removal due to a decrease in the relative abundance of functional genes (napAB, nirK/nirS, ppk1, ppk2, and ppx). Notably, both chemometric and high-throughput sequencing results indicated that the metabolic form of the system would shift from a polyphosphate-accumulating metabolism to a glycogen-accumulating metabolism. The reason may be that PET-MP stress inhibited the relative abundance of functional genes related to carbon, glycogen, phosphorus, and energy metabolism pathways in Candidatus Accumulibacter and Dechloromonas, but promoted their relative abundance of Candidatus Competibacter. Flow cytometry and molecular docking simulations have also demonstrated the direct toxic effects of PET-MPs on the SNEDPR-AGS system. The biological enhancement and functional recovery of damaged SNEDPR-AGS systems must be further investigated in future studies.

Microbial production of methyl-uranium via the Wood-Ljungdahl pathway

The misuse of uranium is a major threat to human health and the environment. In microbial ecosystems, microbes deploy various strategies to cope with uranium-induced stress. However, the exact ecological strategies and mechanisms underlying uranium tolerance in microbes remain unclear. Therefore, this study aimed to investigate the survival strategies and tolerance mechanisms of microbial communities in uranium-contaminated soil and groundwater. Microbial co-occurrence networks and molecular biology techniques were used to analyze the properties of microbes in groundwater and soil samples from various depths of uranium-contaminated areas in Northwest China. Uranium pollution altered microbial ecological strategies. Uranium stress facilitated the formation of microbial community structures, leading to symbiosis. Furthermore, microbes primarily resisted uranium hazards by producing polysaccharides and phosphate groups that chelate uranium, releasing phosphate substances that precipitate uranium, and reducing U(VI) through sulfate- and iron-reducing processes. The relative abundance of metal-methylation genes in soil microorganisms positively correlated with uranium concentration, indicating that soil microorganisms can produce methyl uranium via the Wood-Ljungdahl pathway. Furthermore, soil and groundwater microorganisms demonstrated different responses to uranium stress. This study provides new insights into microbial responses to uranium stress and novel approaches for the bioremediation of uranium-contaminated sites.

Enhancing nitrogen removal in low C/N wastewater with recycled sludge-derived biochar: A sustainable solution

Denitrification is an important biological process in wastewater treatment plants (WWTPs). However, a low carbon-to-nitrogen (C/N) ratio limits the availability of organic carbon, potentially reducing denitrification efficiency. This study investigates the impact of sludge-derived biochar on the nitrogen removal of activated sludge for low C/N ratio municipal wastewater. Sludge-based biochar was characterized by its physicochemical properties, revealing that biochar prepared at 400 °C exhibited the highest specific surface area and the most favorable surface functional groups for electron transfer. The results from batch tests showed that adding 4 g/L of biochar dosage enhanced denitrification rates and total nitrogen (TN) removal efficiency the most. Sequencing batch reactors (SBRs) experiments further confirmed that biochar dosgae improved the removal efficiencies of COD, NH4+-N, and TN, achieving stable values of 97.2 ± 1.2 %, 99.2 ± 0.6 %, and 83.8 ± 2.4 %, respectively. Metabolic and electrochemical analyses revealed that biochar addition enhanced the activity of denitrification enzymes, increasing the ammonia oxidation rate by 12.9 ± 0.7 %, nitrite oxidation rate by 14.7 ± 1.2 %, nitrate reduction rate by 36.9 ± 1.5 %, and nitrite reduction rate by 16.4 ± 0.8 %. The relative abundance of denitrification functional genes (amoA, nirS, nirK, narG, nosZ) increased, and the activities of the corresponding enzymes (AMO, NXR, NAP, NIR) rose by 23±6 %, 53±5 %, 260±15 %, and 55±7 %, respectively. This increase in enzyme activity suggested enhanced denitrification processes, which was further supported by the 60.1 ± 3.7 % increase in electron transfer system activity (ETSA), indicating that biochar acted as an electron shuttle. This study proposes a potential sustainable approach for sludge recycling and enhanced wastewater nitrogen removal under low C/N conditions.

Metagenomic Analysis to Assess the Impact of Plant Growth-Promoting Rhizobacteria on Peanut (Arachis hypogaea L.) Crop Production and Soil Enzymes and Microbial Diversity.

Peanut production could be increased through plant growth-promoting rhizobacteria (PGPR). In this regard, the present field research aimed at elucidating the impact of PGPR on peanut yield, soil enzyme activity, microbial diversity, and structure. Three PGPR strains (Bacillus velezensis, RI3; Bacillus velezensis, SC6; Pseudomonas psychrophila, P10) were evaluated, along with Bradyrhizobium japonicum (BJ), taken as a control. PGPR increased seed yield by 8%, improving the radiation use efficiency (4-14%). PGPR modified soil enzymes (fluorescein diacetate activity by 17% and dehydrogenase activity by 28%) and microbial abundance (12%). However, PGPR did not significantly alter microbial diversity; nonetheless, it modified the relative abundance of key phyla (Actinobacteria > Proteobacteria > Firmicutes) and genera (Bacillus > Arthrobacter > Pseudomonas). PGPRs modified the relative abundance of genes associated with N-fixation and nitrification while increasing genes related to N-assimilation and N-availability. PGPR improved agronomic traits without altering rhizosphere diversity.

Rearing of Black Soldier Fly Larvae with Corn Straw and the Assistance of Gut Microorganisms in Digesting Corn Straw.

Corn straw is considered a renewable biomass energy source, and its unreasonable disposal leads to resource waste and environmental pollution. Black soldier fly (Hermetia illucens L.) larvae (BSFL) facilitate the bioconversion of various types of organic wastes. In this study, we found that 88% of BSFL survived, and 37.4% of corn straw was digested after 14 days of feeding with corn straw. Contrary to expectations, the pretreatment of corn straw with alkaline hydrogen peroxide did not promote its digestion but rather reduced the growth and survival rates of BSFL. Acinetobacter, Dysgonomonas, and unclassified Enterobacteriaceae were the abundant genera in the BSFL gut fed with corn straw. Compared with the standard diet, the relative abundances of carbohydrate metabolism genes, such as the gene abundances of β-glucosidase and α-glucosidase, were higher with corn straw as the substrate. These results suggested that the gut microbial community could regulate suitable and functional microorganisms in response to the substrates. Furthermore, four cellulase-producing strains, namely Klebsiella pneumoniae, Proteus mirabilis, Klebsiella oxytoca, and Providencia rettgeri, were isolated from the guts of corn straw BSFL. These four strains helped increase the conversion rates of corn straw, the weights of BSFL, and survival rates. In summary, we reared BSFL with corn straw and discovered the functions of gut microorganisms in adapting to the substrates. We also isolated four cellulase-producing strains from the BSFL guts and declared the benefits of BSFL digesting corn straw.

Enhancing medium-chain fatty acids production via alkyl polyglucose modulation of electron acceptor generation, microbial community and metabolic traits in anaerobic fermentation of waste activated sludge

Production of medium chain fatty acids (MCFAs) through anaerobic fermentation is an essential pathway for efficient resource recovery and utilization of waste activated sludge (WAS). In this study, a novel strategy utilizing polyglucose (APG) to enhance MCFAs production from WAS by anaerobic fermentation was proposed. The results showed that the maximum MCFAs production reached 14745.0 mg COD/L with 0.3 g APG/g TSS, which was 20.2 times of that without APG treatment. The transformation of intermediates demonstrated that APG promoted the generation of electron acceptors (i.e., short-chain fatty acids) and conversion of substrate to MCFAs. Microbial community analysis indicated that APG selectively enriched microbe involved in hydrolysis, acidogenesis and chain elongation (CE). Also, the presence of APG had a negative impact on methanogens and potential excessive ethanol oxidation (EEO) microbe, which were competitors of CE bacteria in mixed-culture system. Metagenomic analysis showed an increase in relative abundance of genes encoding metabolic functions responsible for hydrolysis, acidogenesis, CE and energy generation, thus maintained high microbial activity in MCFAs biosynthesis. These enhanced metabolic functions were accompanied by a reduction in relative abundance of genes encoding methanogenesis and EEO metabolism, which together result in boosting the efficiency of substrate and energy flow to MCFAs production. This study presents a promising approach to improve the biotransformation of polysaccharides and proteins from WAS into MCFAs.