Abundance Of Functional Genes Research Articles

Artificial Cultivation of Aquatic Plants Promotes Nitrogen Transformation and the Abundance of Key Functional Genes in Agricultural Drainage Ditch Sediments in the Yellow River Irrigation Area in China

Excess nitrogen in agricultural drainage poses a serious threat to the water quality safety of the Yellow River basin. Utilizing aquatic plants to modify the rhizosphere microbial community structure and facilitate nitrogen transformation is a crucial strategy for mitigating regional water eutrophication. We here compare key processes of nitrogen transformation occurring in the rhizosphere of sediments of a ditch artificially planted with a mix of species (Phragmites australis, Typha orientalis, Nymphaea tetragon) with the rhizosphere of a ditch occupied by naturally occurring aquatic vegetation, dominated either by P. australis or T. orientalis. Our results revealed a species effect, with an increased denitrification rate (DR) and dissimilatory nitrate reduction to ammonium rate (DNRAR) in the cultivated ditch for P. australis, compared to the naturally occurring T. orientalis vegetation. The nitrogen fixation rate (NFR) increased in the artificial setting with T. orientalis in comparison to natural P. australis vegetation. The richness of the bacterial community and the relative abundances of Bacteroidota, Firmicutes, and Geobacter were significantly greater in the rhizosphere of the artificially cultivated ditch due a greater availability in nitrogen and organic carbon. In the artificially cultivated ditch, the dominant functional genes affecting DRNARs in the rhizosphere sediments of P. australis were nrfC and nrfA, whereas DRs were driven mainly by norB and napA, which were influenced by the nitrogen and carbon levels. The dominant functional genes affecting NFRs in the rhizosphere sediments of T. orientalis were nifD, nifK, and nifH. Our results provide a scientific basis for the use of aquatic plants for mitigating excess nitrogen levels in agricultural drainage.

How Does Triclocarban Affect Sulfur Transformation in Anaerobic Systems?

Triclocarban (TCC), as a typical antimicrobial agent, accumulates at substantial levels in natural environments and engineered systems. This work investigated the impact of TCC on anaerobic sulfur transformation, especially toxic H2S production. Experimental findings revealed that TCC facilitated sulfur flow from the sludge solid phase to liquid phase, promoted sulfate reduction and sulfur-containing amino acid degradation, and largely improved anaerobic H2S production, i.e., 50-600 mg/kg total suspended solids (TSS) TCC increased the cumulative H2S yields by 24.76-478.12%. Although TCC can be partially biodegraded in anaerobic systems, the increase in H2S production can be mainly attributed to the effect of TCC rather than its degradation products. TCC was spontaneously adsorbed by protein-like substances contained in microbe extracellular polymers (EPSs), and the adsorbed TCC increased the direct electron transfer ability of EPSs, possibly due to the increase in the content of electroactive polymer protein in EPSs, the polarization of the amide group C═O bond, and the increase of the α-helical peptide dipole moment, which might be one important reason for promoting sulfur bioconversion processes. Microbial analysis showed that the presence of TCC enriched the organic substrate-degrading bacteria and sulfate-reducing bacteria and increased the abundances of functional genes encoding sulfate transport and dissimilatory sulfate reduction.

Nutrient removal performance and the nitrogen-sulfur conversion pathways in sulfur-iron based biofilter under acidic/alkaline conditions

The nitrate and phosphate removal in sulfur based (Vp) and sulfur-iron based autotrophic denitrification systems (Sp) with sponge iron as the iron source was investigated under different pH (6–9). In this study, Sp (>98 %) and Vp (>97 %) had higher nitrate removal efficiency at pH 7–8 and the highest phosphate removal efficiency (94.9 % ± 3.57 %) at pH 6. The flow cytometry detection revealed that the cell integrity was damaged due to the formation of iron crusts at pH 6, which resulted in irreversible inhibition in Sp. Electron transfer and nitrogen transformation showed that compared with the sustained inhibition of denitrification at pH 6, the inhibition at pH 9 occurred mainly in the initial 0–2 h due to the enhanced flow of electrons toward the formation of biological element sulfur (Sbio0). Coupled sponge iron promoted the adsorption and reduction of NO2−/N2O and reduced N2O emissions. Metatranscriptomics analysis showed that significant upregulation of key gene expression for nitrogen and sulfur metabolism in Sp, with complex regulatory mechanisms enhancing system stability and performance. Acidic conditions reduced the abundance of denitrification and sulfur oxidation functional genes. However, alkaline conditions (pH of 9) mainly caused the decreased abundance of denitrification functional genes, which was favorable for accumulation of Sbio0. This study provides a theoretical basis for the stable operation and regulation of the sulfur-iron based autotrophic denitrification process.

Mechanism of biochar in alleviating the inhibition of anaerobic digestion under ciprofloxacin press

The antibiotic ciprofloxacin (CIP), detected in various aqueous environments, has broad-spectrum antimicrobial properties that can severely affect methanogenic performance in anaerobic systems. In this study, a novel strategy to alleviate the inhibition of AD performance under CIP press with the direct addition of biochar (BC) prepared from corn stover was proposed and the corresponding alleviation mechanism was investigated. When the dosage of BC was 5 and 20 g/L, the cumulative methane production in AD could reach 317.9 and 303.0 mL/g COD, and the CIP degradation efficiencies reached 94.1 % and 96.6 %, significantly higher than those of 123.0 mL/g COD and 81.2 % in the Control system. BC avoided excessive reactive oxygen species in anaerobic systems and induced severe oxidative stress response, while protecting the cell membrane and cell wall of microorganisms. Microorganisms could consume and utilize more organic extracellular polymeric substances for their growth and metabolism. When BC was involved in AD, fewer toxic intermediates were generated during CIP biodegradation, reducing acute and chronic toxicity in anaerobic systems. Microbial diversity suggested that BC could enrich functional microorganisms involved in direct interspecies electron transfer like Methanosaeta, norank_f_Bacteroidetes_vadinHA17, JGI-0000079-D21 and Syntrophomonas, thus facilitating the methanogenic process and CIP degradation. Genetic analyses showed that BC could effectively upregulate functional genes related to the conversion of butyrate-to-acetate and acetyl-to-methane under CIP stress, while functional gene abundance associated with CIP degradation enhanced partially, about encoding translocases, oxidoreductases, lyases, and ligases. Therefore, BC can be added to AD under CIP press to address its inhibited methanogenic performance.

Biological Decline of Alfalfa Is Accompanied by Negative Succession of Rhizosphere Soil Microbial Communities.

The growth and biological decline of alfalfa may be linked to the rhizosphere microbiome. However, plant-microbe interactions in the rhizosphere of alfalfa and associated microbial community variations with stand age remain elusive. This study explored the successional pattern of rhizosphere microbial communities across different aged alfalfa stands and its relationship with alfalfa decline. Rhizosphere soils were collected from 2- and 6-year-old alfalfa stands. Control soils were collected from interspaces between alfalfa plants in the same stands. Soil bacterial and fungal communities were characterized by 16S and ITS rRNA gene sequencing, respectively. Specific microbial taxa colonized the rhizosphere soils, but not the control soils. The rhizosphere-specific taxa mainly included potentially beneficial genera (e.g., Dechloromonas, Verrucomicrobium) in the young stand and harmful genera (e.g., Peziza, Campylocarpon) in the old stand. Alfalfa roots regulated soil microbial communities by selective promotion or inhibition of distinct taxa. The majority of time-enriched taxa were reported as harmful fungi, whose relative abundances were negatively correlated with plant traits. Time-depleted taxa were mostly known as beneficial bacteria, which had relative abundances positively correlated with plant traits. The relative abundances of functional bacterial genes associated with vancomycin biosynthesis, zeatin biosynthesis, and amino acid metabolism trended lower in rhizosphere soils from the old stand. An upward trend was observed for fungal pathogens and wood saprotrophs with increasing stand age. The results suggest that root activity drives the negative succession of rhizosphere microbial communities during alfalfa decline in old stands.

The piranha gut microbiome provides a selective lens into river water biodiversity

Advances in omics technologies have enabled the in-depth study of microbial communities and their metabolic profiles from all environments. Here metagenomes were sampled from piranha (Serrasalmus rhombeus) and from river water from the Rio São Benedito (Amazon Basin). Shotgun metagenome sequencing was used to explore diversity and to test whether fish microbiomes are a good proxy for river microbiome studies. The results showed that the fish microbiomes were not significantly different from the river water microbiomes at higher taxonomic ranks. However, at the genus level, fish microbiome alpha diversity decreased, and beta diversity increased. This result repeated for functional gene abundances associated with specific metabolic categories (SEED level 3). A clear delineation between water and fish was seen for beta diversity. The piranha microbiome provides a good and representative subset of its river water microbiome. Variations seen in beta biodiversity were expected and can be explained by temporal variations in the fish microbiome in response to stronger selective forces on its biodiversity. Metagenome assembled genomes construction was better from the fish samples. This study has revealed that the microbiome of a piranha tells us a lot about its river water microbiome and function.

Effects of exogenously added humic acid on the fate of aminoglycoside antibiotics and humification process during aerobic compost

Efficient elimination of antibiotics, particularly aminoglycosides, and Antibiotic resistance genes (ARGs) from agricultural and livestock waste, as well as enhancing the level of humification, remains a major challenge in the pursuit of high-value utilization of agricultural waste. Here, the roles of bacteria and fungus in the dissipation of aminoglycoside antibiotics, ARGs and the enhancement of humification with the addition of humic acid (HA) to compost systems were investigated. Compared to the control, the contents of humus (HS) and HA were increased by 41.3 and 143.3 %, respectively, and the content of fulvic acid (FA) was decreased by 74.1 % with HA addition. Interestingly, the abundance of aminoglycoside ARGs was decreased significantly (p < 0.05) as well as the abundance of functional genes involved in oxidative stress response and type IV secretion system (T4SS). The bacterium Nocardiopsis related to carbon cycle, and the fungi Ascomycota and Basidiomycota associated with ligocellulose degradation were significantly enriched (p < 0.05). Structural equation models revealed that the decrease in aminoglycoside ARGs abundance was attributed to bacteria promoting HA synthesis, thereby inhibiting the multiplication of aminoglycoside ARGs and ultimately mitigating oxidative damage to microbial cells. These findings shed light on the mechanism by which HA removes aminoglycoside ARGs, and provide valuable insights into enhancing the biosafety of compost products.

Management of Spartina alterniflora: Assessing the Efficacy of Plant Growth Regulators on Ecological and Microbial Dynamics

Spartina alterniflora is recognized as one of the most detrimental invasive species along China’s coastlines, highlighting the need for effective and environmentally safe management strategies to preserve intertidal zones. This study assessed the effectiveness of combining plant growth regulators (PRGs) with physical cutting to manage S. alterniflora, using 16S rRNA and 18S rRNA gene sequencing to evaluate the impacts on the plant and associated soil micro-organisms. The results showed that compared to the control (CK), the regeneration numbers for treatments with abscisic acid (ABA), gibberellin (GA), paclobutrazol (PP333), garcinol (GC), and glyphosate (GP) decreased by 29.75%, 23.25%, 15.75%, 94.50%, and 40.50%, respectively. Comparative analysis revealed no statistically significant variation in the inhibitory effects of ABA and GP on the germination of S. alterniflora (p &gt; 0.05). Additionally, applying PRGs and herbicides increased the diversity indices of soil bacteria and fungi. Principal Coordinates Analysis (PCoA) showed that the impact of PRGs on the fungal community was less pronounced than that of herbicides. Significant differences were also noted in the abundance of microbial functional genes related to methanotrophy, hydrocarbon degradation, and denitrification compared to the control (p &lt; 0.05). This study aimed to assess the potential of PRGs in controlling the invasion of S. alterniflora and to elucidate their impacts on soil microbial communities and functional gene expression.

Effects of Continuous Cropping on the Physiochemical Properties, Pesticide Residues, and Microbial Community in the Root Zone Soil of Lycium barbarum

Continuous cropping is a common obstacle limiting the high quality and yield of Lycium barbarum （wolfberry）. To clarify the response of soil characteristics of the wolfberry root zone to continuous cropping years, we systematically determined the physicochemical properties and pesticide residues of soils in the wolfberry root zone with different continuous cropping years. In addition, soil bacterial and fungal communities were characterized using high-throughput sequencing technology. The results were as follows： The content of total salt and imidacloprid in the root zone of wolfberry increased with increasing years of continuous cropping. Compared to that with 2 and 9 years, the total salt content in the root zone of wolfberry with 15 years of continuous cropping increased by 51.97% and 54.33%, respectively, and the imidacloprid content increased by 39.58% and 36.61%, respectively. Alkaline nitrogen and available potassium showed an increasing and then decreasing trend. Compared to that with 2 and 15 years, alkaline nitrogen and available potassium in the root-soil of wolfberry with 9 years of continuous cropping increased by 16.94%-28.09% and 18.31%-18.34%, respectively. The diversity and abundance of bacterial communities and the abundance of fungal communities were higher in the root-soil of wolfberry with 9 years of continuous cropping compared to that with 15 years of continuous cropping. In addition, the increase in continuous cropping years also increased the accumulation of harmful plant pathogens such as Pseudomonas, Arthrobacter, Actinomucor, and Trichoderma in the root zone of L. barbarum. Soil total salinity, organic matter, alkaline hydrolyzable nitrogen, and available potassium were the main factors influencing the distribution of bacterial communities. Soil alkaline hydrolyzable nitrogen, available potassium, and ammonium nitrogen were the main factors influencing the distribution of fungal communities. In addition, the soil bacteria in the root zone of L. barbarum were dominated by metabolic functions； in particular, amino acid metabolism, energy metabolism, and nucleotide metabolism were most abundant in the root soil of wolfberry with 9 years of continuous cropping, whereas the highest abundance of functional genes related to membrane translocation was found in the root-soil of wolfberry with 15 years of continuous cropping. The soil fungi were all dominated by saprophytic trophic types, followed by pathogenic cross-nutrients in the root zone of L. barbarum. In conclusion, long-term continuous cropping induced changes in the soil microenvironment in the root zone of L. barbarum, increased soil residues of harmful pesticides and the enrichment of plant pathogens, and reduced the diversity of soil bacterial and fungal communities. Therefore, it is necessary to control the rate of application of soil nutrients and pesticides in the management of L. barbarum and to carry out deep ploughing and deep tilling in good time, and the turnover of old plants in the cultivation of L. barbarum.

Selenium availability in tea: Unraveling the role of microbiota assembly and functions

Tea (Camellia sinensis (L.) O. Kuntze) plants have a strong ability to accumulate selenium (Se). However, the question of how tea plants affect Se availability has received little attention. In this study, five tea cultivars, including Soubei (SB), Aolǜ (AL), Longjing43 (LJ), Zhaori (ZR) and Fenglǜ (FL), were chosen for the study. Quantitative Microbial Ecology Chip and high-throughput sequencing were used to explore the effects of five tea cultivars on soil functions, microbial community structures and Se availability. The results showed that the total soil Se content in the FL garden was lower compared to LJ and SB gardens, whereas available Se was highest in the FL garden. Based on the Bray-Curtis distances, tea cultivar was the main factor affecting bacterial and fungal community structures. The abundance of functional genes concerning carbon, nitrogen, phosphorus and sulfur cycling processes varied among tea gardens. The higher soil NH4+ and NO3− contents, and higher abundance of functional genes like nifH, amoA1 and narG, whereas lower total nitrogen in the FL garden than in the AL and LJ tea gardens demonstrated that the FL tea plants induced microbes to accelerate soil nitrogen cycling processes. Dominant microbes that positively related with functional genes like nifH, narG, and amoA1 were also positively related with the available Se content. In conclusion, tea cultivars could regulate soil functions through affecting microbial community structures and then affecting the soil Se availability. The soil nitrogen cycle processes are suggested to be closely related with Se transformation in tea gardens.

Impact of nitrogen and phosphorus amendments on nitrogen‐cycling microbial abundances and potentials: A meta‐analysis

AbstractThe rapid increase in nitrogen (N) and phosphorus (P) availabilities in terrestrial ecosystems has led to sustained shifts in soil microbial communities and microbially‐mediated N‐cycling. However, the specific effects of N and P amendments on N‐cycling microbes are poorly understood. This meta‐analysis synthesizes the effects of N and/or P amendments on the abundances and functional potentials of N‐cycling genes involved in N₂ fixation, organic N mineralization, nitrification, and denitrification across natural ecosystems and diverse soil conditions in China. Our findings indicate that ammonia‐oxidizing bacteria (AOB) showed greater responsiveness to N amendment than ammonia‐oxidizing archaea (AOA), and AOB amoA abundance increased while AOA amoA abundance decreased with P amendments. Additionally, the abundance of nirS declined, while nirK abundance remained unresponsive to both N and P amendments. These findings highlight the distinct ecological niches occupied by microbial groups with equivalent functions in response to N and P amendments. Moreover, our findings indicate that soil N and P availabilities, along with soil acidification induced by N additions and microbial biomass carbon content, are key factors regulating N‐cycling gene abundances and potentials. The driving mechanisms for N‐cycling genes and their corresponding potentials appear to be distinct, with gene abundance showing only a limited influence on functional potentials. This suggests that factors such as soil properties and microbial community compositions may be more critical determinants of N‐cycling processes than functional gene abundances with regard to scenarios of increasing N and P deposition.

Soil and stone terraces offset the negative impacts of sloping cultivation on soil microbial diversity and functioning by protecting soil carbon

Cultivation of sloping land is a main cause for soil erosion. Conservation practices, such as soil and stone terraces, may reduce the impacts of erosion but their impacts on soil microbial diversity and functioning related to carbon (C) and nutrient metabolisms remain unclear. This study was conducted to evaluate the effects of slope gradients (5°, 8°, 15°, 25°) and conservation practices (cultivated, uncultivated, soil terrace, and stone terrace) on bacterial and fungal diversities, metagenomic and metabolomic functioning associated with basic soil properties. Our results showed that steep slopes at 25° significantly decreased soil pH, silt percentage, and bacterial and fungal abundances, but that soil and stone terraces increased soil organic C (SOC), silt and clay contents, and fungal abundance compared to sloping cultivated lands. In addition, soil and stone terraces increased both bacterial and fungal alpha diversities, and relative abundances of Crenarchaeota, Nitrospirota, and Latescibacterota, but reduced the proportions of Actinobacteriota and Patescibacteria, thus shifting microbial beta diversities, which were significantly associated with increased SOC and silt content. For metagenomics, soil and stone terraces greatly increased the relative abundance of functional genes related to Respiration, Virulence, disease and defense, Stress response, and nitrogen and potassium metabolisms, such as Denitrification and Potassium homeostasis. For soil metabolomics, a total of 22 soil metabolites was enriched by soil and stone terraces, such as Lipids and lipid-like molecules (Arachidonic acid, Gamma-Linolenic acid, and Pentadecanoic acid), and Organoheterocyclic compounds (Adenine, Laudanosine, Methylpyrazine, and Nicotinic acid). To sum up, soil and stone terraces could reduce some of the negative impacts of steep slope cultivation on soil microbial diversity as well as their metagenomic and metabolomic functioning related to C and nutrient metabolism useful for soil health improvement, potentially bolstering the impact of sustainable practices in erosion hotspots around the world.

Metagenomic analysis reveals enhanced sludge dewaterability through acidified sludge inoculation: Regulation of Fe (II) oxidation electron transport pathway

The bioleaching utilizing indigenous microbial inoculation can continuously improve the dewaterability of sludge. In this study, metagenomic analysis was innovative employed to identify the key microorganisms and functional genes that affect the dewatering performance of sludge in the bioleaching conditioning process. The results demonstrated that long-term repeated inoculation of acidified sludge resulted in increased abundance of many functional genes associated with the transport of carbohydrate and amino acid. Additionally, genes encoding key iron transport proteins (such as afuA, fhuC, and fhuD) and genes related to electron transfer carriers in ferrous iron oxidation process (such as rus and cyc2) were significantly enriched, thereby promoting the improvement of sludge dewatering performance through enhanced iron oxidation. Notably, Acidithiobacillus, Betaproteobacteria, and Hyphomicrobium were the major sources of functional genes. This study reveals the microscopic mechanisms underlying the improvement of sludge dewaterability through bioleaching based on mixed culture from a novel perspective of gene metabolism.

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.

Nitrogen deposition in the middle-aged and mature coniferous forest: Impacts on soil microbial community structure and function

The impact of nitrogen (N) deposition on soil microbial community structure and function has been a focal point of research; however, the influence of forest age and N form on the microbial response to N deposition has yet not to be fully understood. To address this gap, metagenomic sequencing was utilized to explore the responses of soil microbial community structure and functional genes to five years of N addition in middle-aged and mature coniferous forests in southwest China. Adopting a randomized block design, the experiment included two N forms ((NH4)2SO4 and KNO3) across four levels of addition (0, 10, 20 and 40 kg N ha−1 yr−1). Our findings reveal that the composition of the microbial community structure and functional genes involved in the carbon (C), N, phosphorus (P), and sulphur (S) cycling varied significantly between middle-aged and mature forest (P < 0.001). At the phylum level, the soil microbial community in the mature forest were dominated by Proteobacteria (30.4–38.8 %), Acidobacteriota (8.5–24.1 %), and Chloroflexota (8.1–21.5 %), and the soil microbial community in the middle-aged forest showed a greater presence of Acidobacteriota (28.9–34.0 %) and Actinobacteriota (13.3–19.2 %) with a lower proportion of Chloroflexota (0.4–1.2 %). In both middle-aged and mature forests, functional gene abundance, and the composition of microbial community and functional genes were unaffected by N addition rate (P = 0.793) and N form (P = 0.725). The taxonomic composition of soil microbial community in the mature forest showed a significant positive correlation with soil pH, soil organic carbon (SOC) and total nitrogen (TN) (P < 0.01), while the microbial community composition in the middle-aged forests was not significant correlated with soil pH, SOC and TN (P > 0.05). These findings underscore that N addition in the middle-aged and mature coniferous forest does not significantly impact the soil microbial community structure and function across different N forms and N addition rate, suggesting that soil microorganisms of the forest ecosystem exhibit strong resilience to increased N supply.

The Effects of Mixed Robinia pseudoacacia and Quercus variabilis Plantation on Soil Bacterial Community Structure and Nitrogen-Cycling Gene Abundance in the Southern Taihang Mountain Foothills.

Mixed forests often increase their stability and species richness in comparison to pure stands. However, a comprehensive understanding of the effects of mixed forests on soil properties, bacterial community diversity, and soil nitrogen cycling remains elusive. This study investigated soil samples from pure Robinia pseudoacacia stands, pure Quercus variabilis stands, and mixed stands of both species in the southern foothills of the Taihang Mountains. Utilizing high-throughput sequencing and real-time fluorescence quantitative PCR, this study analyzed the bacterial community structure and the abundance of nitrogen-cycling functional genes within soils from different stands. The results demonstrated that Proteobacteria, Acidobacteria, and Actinobacteria were the dominant bacterial groups across all three forest soil types. The mixed-forest soil exhibited a higher relative abundance of Firmicutes and Bacteroidetes, while Nitrospirae and Crenarchaeota were most abundant in the pure R. pseudoacacia stand soils. Employing FAPROTAX for predictive bacterial function analysis in various soil layers, this study found that nitrogen-cycling processes such as nitrification and denitrification were most prominent in pure R. pseudoacacia soils. Whether in surface or deeper soil layers, the abundance of AOB amoA, nirS, and nirK genes was typically highest in pure R. pseudoacacia stand soils. In conclusion, the mixed forest of R. pseudoacacia and Q. variabilis can moderate the intensity of nitrification and denitrification processes, consequently reducing soil nitrogen loss.

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 (39.61 mg/g), Mn (2.84 mg/g) and Ba (0.36 mg/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.

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.