Unveiling the correlation between the catalytic efficiency and acidity of a metal-free catalyst in a hydrogenation reaction. A theoretical case study of the hydrogenation of ethene catalyzed by a superacid arising from a superhalogen.

A systematic quantum-chemical study of the hydrogenation of ethene, catalyzed by strong acids HX (X = F, Cl, Br) and superacids HA (A = MgX3, Mg2X5; X = F, Cl, Br) arising from octet superhalogens is explored. Two possible paths are proposed, concerted and stepwise, and the calculated results show that the concerted path is more favorable than the stepwise path. Compared to the hydrogenation reaction without any catalyst, the improvement of the catalytic efficiency of the superacid HA (A = MgX3, Mg2X5) is high, up to 38.8 to 59.4%. Compared to the strong acid HX (X = F, Cl, Br), the barrier energy is significantly reduced and the improvement of the catalytic efficiency of the superacid HA reaches 23.1 to 31.7%. In particular, for HMg2Br5, the barrier energy of the hydrogenation of ethene is only 36 kcal mol-1, which shows that the reaction could proceed under experimental conditions. In addition, the results show that the catalytic efficiency of the superacid HA is related to the acidity of the superacid. In general, the greater the acidity, the lower the barrier energy and the easier the hydrogenation reaction. From the analysis of the bond order, the newly formed C-H bond of the transition state (TS3) in the concerted path, in which the H atom comes from the superacid catalyst, directly affects the barrier energy of the entire reaction. For the more acidic catalyst, this H atom is provided more easily, and then the formed C-H bond in the transition state is stronger. Consequently, this stronger bond leads to a more stable transition state, and hence to a lower energy barrier as well as a higher efficiency of the superacid catalyst. Therefore, a positive correlation between the acidity of the metal-free catalyst and its catalytic efficiency is expected in the hydrogenation reaction.

Lactiplantibacillus plantarum BW2013 protects mucosal integrity and modulates gut microbiota of mice with colitis.

This study explored the effects of Lactiplantibacillus plantarum (previously Lactobacillus plantarum) BW2013 on mucosal integrity and gut microbiota of mice with dextran sulfate sodium (DSS)-induced colitis. The results show that the clinical symptoms in DSS-modelled ulcerative colitis (UC) were improved by L. plantarum BW2013 via decreasing disease activity index scores and suppressing inflammatory cell infiltration. Furthermore, L. plantarum BW2013 decreased the levels of diamine oxidase activity, myeloperoxidase, and D-lactic acid. The mRNA expression of ZO-1, occludin, and claudin-1 was upregulated by L. plantarum BW2013, which also increased IL-10 and reduced TNF-α, IL-1ß, and IL-6 in the colon. 16S rDNA sequencing showed that L. plantarum BW2013 enhanced α-diversity. L. plantarum BW2013 upregulated significantly the abundance of unidentfied Lachnospiraceae, Lactococcus, Rikenella, Lactobacillus, and Odoribacter, which had an inhibitory effect on inflammation and a protective effect on the integrity of the mucosa. These results demonstrate that L. plantarum BW2013 alleviates DSS-modelled UC by protecting mucosal integrity and ameliorating the composition of gut microbiota.

Fast start-up of anammox process: Effects of extracellular polymeric substances addition on performance, granule properties, and bacterial community structure.

The slow startup is the major obstacle to the application of anaerobic ammonium oxidation (anammox) process in mainstream wastewater treatment. Extracellular polymeric substances (EPS) are one potential resource for stable anammox reactor operation. Response surface analysis was used to optimize the specific anammox activity (SAA) with the addition of EPS; SAA was maximum at a temperature of 35 °C and the EPS concentration of 4 mg/L. By comparing the nitrogen removal of anammox reactors with no EPS (R0), immobilized EPS (EPS-alginate beads) (R1), and liquid EPS (R2), we found that EPS-alginate beads significantly speed up the startup of anammox process and enable the start time to be shortened from 31 to 19 days. As a result of the higher MLVSS content, higher zeta potential, and lower SVI30, anammox granules of R1 exhibited a stronger capacity to aggregate. Moreover, EPS extracted from R1 had higher flocculation efficiencies than EPS derived from R0 and R2. Phylogenetic analysis of 16S rRNA genes revealed that the main anammox species in R1 is Kuenenia taxon. To clarify the relative significance of stochastic vs deterministic processes in the anammox community, neutral model and network analysis are employed. In R1, community assembly became more deterministic and stable than in other cultures. Our results show that EPS might inhibit heterotrophic denitrification and thereby promote anammox activity. This study suggested a quick start-up strategy for the anammox process based on resource recovery, which is helpful for environmentally sustainable and energy-efficient wastewater treatment.

Toxicity evaluation of polycyclic aromatic hydrocarbons (PAHs) in soils of coal chemical industry areas, North China.

Objectives of this study were to investigate the concentrations, distributions, toxicities, and risk assessment of 16 polycyclic aromatic hydrocarbons in surface soils surrounding a coal chemical industrial zone in the southeast of Shanxi province, China. A total of 52 topsoil samples were collected from different land-use areas: cereal agriculture, roadsides, and parkland. Results show that the total PAHs (∑16PAHs) ranged from 3.87 × 103 to 116 × 103 µg kg-1 and that the total carcinogenicity PAHs (∑BPAHs) ranged from 3.11 × 103 to 94.2 × 103 µg kg-1, with the highest concentration of ∑16PAHs noted in the RS samples, followed by PS and AS. The entire risk quotient of all PAH maximum permissible concentrations (RQ∑PAHMPCi) was greater than 1.0, and the minimum concentration entire risk quotient (RQ∑PAHNCi) of 84.3% of all samples was higher than 800. The value of the total toxicity equivalent concentration of PAH (PAHBapeq) for areas surrounding the coal chemical industrial zone was higher than the value of the standard level, and the incremental lifetime cancer risk (ILCR) far exceeds the U.S. EPA's risk standard. The toxic properties of PAHs indicated that the soils in the survey areas have a high risk to human health and the environment.

Effects of lignocellulosic biomass type on nutrient recovery and heavy metal removal from digested sludge by hydrothermal treatment.

Sludge is a nutrient-rich organic waste generated from wastewater treatment plants. However, the application of sludge as a nutrient source is limited by its high contents of water and pollutants. In this study, the effects of biomass type on nutrient recovery and heavy metal removal from digested sludge by hydrothermal treatment (HTT) were investigated. Blending biomass with digested sludge for HTT at 180-240 °C increased the recovery of nitrogen in the treated solids. At the HTT temperature of 240 °C, HTT with hardwood sawdust led to the highest nitrogen recovery of 70.6%, compared to the lowest nitrogen recovery of 36.5% without biomass. Blending biomass slightly decreased the recovery of phosphorus compared to those without biomass. Nevertheless, the lowest phosphorus recovery of 91.3% with the use of hardwood sawdust at the HTT temperature of 240 °C was only ∼7.0% less than that without biomass. Blending biomass reduced the contents of macro-metals such as Ca, Fe, Mg and Al in treated solids but the metal contents varied with different biomasses. Regarding the heavy metals, the use of rice husk did not decrease the contents of Ni and Co while blending bagasse did not decrease the content of Cr at HTT temperatures of 210 °C and 240 °C compared to the use of other biomasses. The different effects of biomass type on nutrient recovery and heavy metals were likely related to the types and abundances of organic acids such as acetic acid, oxygen-containing functional groups such as C-OH and COOH, oxide minerals such as silica from biomasses and the overall effects of these factors. This study provides very useful information in selection of lignocellulosic biomass for HTT of sludge for nutrient recovery and heavy metal removal.

Ecological selection of bacterial taxa with larger genome sizes in response to polycyclic aromatic hydrocarbons stress.

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous priority pollutants that cause great damage to the natural environment and health. Average genome size in a community is critical for shedding light on microbiome's functional response to pollution stress within an environment. Here, microcosms under different concentrations were performed to evaluate the selection of PAHs stress on the average genome size in a community. We found the distinct communities of significantly larger genome size with the increase of PAHs concentration gradients in soils, and consistent trends were discovered in soils at different latitudes. The abundance of Proteobacteria and Deinococcus-Thermus with relatively larger genomes increased along with PAHs stress and well adapted to polluted environments. In contrast, the abundance of Patescibacteria with a highly streamlined and smaller genome decreased, implying complex interactions between environmental selection and functional fitness resulted in bacteria with larger genomes becoming more abundant. Moreover, we confirmed the increased capacity for horizontal transfer of degrading genes between communities by showing an increased connection number per node positively related to the nidA gene along the concentration gradients in the co-occurrence network. Our findings suggest PAHs tend to select bacterial taxa with larger genome sizes, with significant consequences for community stability and potential biodegradation strategies.

Efficiency and mechanism of reducing ammonia volatilization in alkaline farmland soil using Bacillus amyloliquefaciens biofertilizer.

Ammonia volatilization from the farmland caused by the application of synthetic nitrogen fertilizer is the most important source of anthropogenic ammonia emissions. Biofertilizer application has been considered as an alternative option for agriculture sustainability and soil improvement. In this study, field trials were carried out to investigate the efficiency of Bacillus amyloliquefaciens (BA) biofertilizer on alleviating ammonia volatilization in alkaline farmland soil and increasing crop yield and nitrogen utilization. Potential response mechanisms were investigated from soil enzyme, nitrogen cycle function genes and microbial community levels. Compared with conventional fertilization, BA biofertilizer application reduced the ammonia volatilization by 68%, increased the crop yield and nitrogen recovery by 19% and 19%, respectively. Soil enzyme activity analysis showed that BA biofertilizer inhibited the urease activity and enhanced the potential ammonia oxidation (PAO). In addition, BA biofertilizer application also increased the bacterial amoA gene abundance, while decreased the ureC gene abundance. BA biofertilizer also significantly altered the community structure and composition, and especially raised the abundance of ammonia oxidation bacteria (AOB), while no changes were observed in abundance of nitrite oxidation bacteria (NOB). Briefly, BA biofertilizer was approved to reduce the transformation of fertilizer nitrogen to NH4+-N, simultaneously accelerating NH4+-N into the nitrification process, thus decreasing the NH4+-N content remained in alkaline soil and consequently alleviating the ammonia volatilization. Thus, these results suggested that the application of BA biofertilizer is a feasible strategy to improve crop yields and reduce agricultural ammonia emissions.

Variety features differentiate microbiota in the grape leaves.

The dependence of plant health and crop quality on the epiphytic microbial community has been extensively addressed, but little is known about plant-associated microbial communities under natural conditions. In this study, the bacterial and fungal communities on grape leaves were analyzed by 16S rRNA gene and internal transcribed spacer high-throughput sequencing, respectively. The results showed differences in the composition of the microbial communities on leaf samples of nine wine grape varieties. The most abundant bacterial genus was Pseudomonas, and the top three varieties with Pseudomonas were Zinfandel (22.6%), Syrah (21.6%), and Merlot (13.5%). The most abundant fungal genus was Alternaria, and the cultivar with the lowest abundance of Alternaria was Zinfandel (33.6%), indicating that these communities had different habitat preferences. The linear discriminant analysis effect size of all species showed that the bacteria Enterococcus, Massilia, and Kocuria were significantly enriched on the leaves of Merlot, Syrah, Cabernet Sauvignon, respectively; Pseudomonadales and Pantoea on Zinfandel; and Bacillus, Turicibacter, and Romboutsia on Pinot Noir. Similarly, the fungi Cladosporium, Phoma, and Sporormiella were significantly enriched on Zinfandel, Lon, and Gem, respectively. Both Bray-Curtis and unweighted UniFrac revealed that bacteria and fungi have a significant impact (P < 0.01), and the results further proved that variety is the most important factor affecting the microbial community. The findings indicate that some beneficial or harmful microorganisms existing on the wine grape leaves might affect the health of the grape plants and the wine-making process.

Paenibacillus polymyxa biofertilizer application in a tea plantation reduces soil N2O by changing denitrifier communities.

Increasing the use of nitrogen fertilizers in tea orchards has led to intense nitrous oxide (N2O) emissions. Foliar application of Paenibacillus polymyxa biofertilizer has been proven to be beneficial for organic tea production. In this study, tea yield and quality were significantly improved after application of P. polymyxa biofertilizer compared with the control but were not significantly different from chemical fertilizer treatments. However, the average N2O fluxes in tea fields treated with chemical fertilizers and biofertilizers (225 kg N·ha-1·year-1 for both) were 50.6-973.7 and 0.6-29.1 times higher than those in the control treatment, respectively. Pot experiments conducted to explore the mechanism of N2O reduction induced by P. polymyxa biofertilizer showed that applying P. polymyxa in addition to urea could reduce N2O fluxes by 36.5%-73.1%. Quantitative PCR analysis suggested that a significant increase in the quantity of nirK and nosZ genes was linked to the reduction of N2O, and high-throughput sequencing of nosZ revealed active and potentially efficient denitrifiers in different treatments. Our findings suggest that P. polymyxa biofertilizer is in line with the requirements of modern agriculture, which aims to increase product yield and quality while reducing negative environmental impacts.

Effective removal of antibiotic resistance genes and potential links with archaeal communities during vacuum-type composting and positive-pressure composting.

As a major reservoir of antibiotics, animal manure contributes a lot to the augmented environmental pressure of antibiotic resistance genes (ARGs). This might be the first study to explore the effects of different ventilation types on the control of ARGs and to identify the relationships between archaeal communities and ARGs during the composting of dairy manure. Several ARGs were quantified via Real-time qPCR and microbial communities including bacteria and archaea were analyzed by High-throughput sequencing during vacuum-type composting (VTC) and positive-pressure composting (PPC). The total detected ARGs and class I integrase gene (intI1) under VTC were significantly lower than that under PPC during each stage of the composting (p<0.001). The relative abundance of potential human pathogenic bacteria (HPB) which were identified based on sequencing information and correlation analysis decreased by 74.6% and 91.4% at the end of PPC and VTC, respectively. The composition of archaeal communities indicated that methane-producing archaea including Methanobrevibacter, Methanocorpusculum and Methanosphaera were dominant throughout the composting. Redundancy analysis suggested that Methanobrevibacter and Methanocorpusculum were positively correlated with all of the detected ARGs. Network analysis determined that the possible hosts of ARGs were different under VTC and PPC, and provided new sights about potential links between archaea and ARGs. Our results showed better performance of VTC in reducing ARGs and potential HPB and demonstrated that some archaea could also be influential hosts of ARGs, and caution the risks of archaea carrying ARGs.

In vitro antioxidant activities of Rhodobacter sphaeroides and protective effect on Caco-2 cell line model.

The present study aimed to evaluate the in vitro antioxidant activities and the protective effect of Rhodobacter sphaeroides on H2O2-induced oxidative stress in Caco-2 cells. The results showed that the antioxidant action of R. sphaeroides varied with different cell concentrations and treatments. Also, the intact cells and intracellular cell-free extracts showed better antioxidant activities. Caco-2 cell-based oxidative stress model was developed by optimizing H2O2 concentration and culture time with the half lethal dose and methyl thiazolyl tetrazolium. By increasing the activity of endogenous antioxidant enzymes superoxide dismutase, catalase, and glutathione peroxidase, upregulating the antioxidant ability of the anti-superoxide anion and anti-hydroxyl radical, R. sphaeroides, especially the mutant strain R. sphaeroides (CGMCC No. 8513), exhibited significant protective activity against H2O2-induced oxidative stress in Caco-2 cells. Taken together, R. sphaeroides (CGMCC No. 8513) exhibits strong antioxidant activities and is a candidate to be investigated as a potential probiotic in the future.

Developmental stage has a greater effect than Cry1Ac expression in transgenic cotton on the phyllosphere mycobiome.

Transgenic Bt cotton is widely cultivated, yet its impact on the phyllosphere mycobiome is poorly understood. Hence, the objective of this study was to investigate the effects resulting from the planting of Bt cotton on fungal diversity composition. The α diversity for the Bt cotton line SGK321 was lower than that of control plants at the budding stage and the blossoming and boll-forming stage, while an obvious increase in diversity for Bt cotton XP188 was observed at the same stage. The Cry1Ac levels were higher at the seedling stage than at the budding stage and the blossoming and boll-forming stage. There was no direct relationship between the expression of the Bt protein and variation in the fungal community for Bt cotton. However, PCoA and PCA results indicated that community structure differed among developmental stages. These results indicated that developmental stage rather than Cry1Ac expression was the key factor shaping the phyllosphere mycobiome in transgenic cotton.

Genetic diversity of diazotrophs and total bacteria in the phyllosphere of Pyrus serotina, Prunus armeniaca, Prunus avium, and Vitis vinifera.

The phyllosphere, which supports a large number of microorganisms, represents the interface between the aboveground parts of plants and air. In this study, four nifH clone libraries were constructed from the phyllosphere of Pyrus serotina (L), Vitis vinifera (P), Prunus armeniaca (X), and Prunus avium (Y). Clones related to Skermanella (L, 12.1%; X, 15.6%; Y, 62.5%; P 70.8%), Bradyrhizobium (X, 2.1%; P, 15.1%; L, 63.7%), Erwinia (X, 68.8%), Pseudomonas (L, 3.3%; P, 7.6%), and Chroococcidiopsis (P, 0.9%; L, 4.4%, X; 5.2%, Y; 19.6%) were present at high percentages, highlighting their critical role in contributing nitrogen to the phyllosphere ecosystem. The 16S rDNA sequence analysis suggested that phyllosphere-associated bacteria were affiliated with a wide range of taxa, encompassing members from Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Cyanobacteria, Tenericutes, and Deinococcus-Thermus. Additionally, the abundance of the nifH gene and 16S rDNA was assessed with quantitative PCR. The number of copies of nifH and 16S rDNA ranged from 1.14 × 103 to 1.49 × 104 and from 3.72 × 106 to 7.02 × 107 copies/g fresh leaf sample, respectively. In conclusion, our work sheds light on the microbial communities of the phyllosphere that are important for plant growth. Moreover, we observed a unique composition of nitrogen-fixing bacteria in each phyllosphere sample, suggesting the existence of specific interactions between these functional microorganism and plants, which may provide information or be a reference for the development of bacterial fertilizers.

Transcriptomic Sequencing and Co-Expression Network Analysis on Key Genes and Pathways Regulating Nitrogen Use Efficiency in Myriophyllum aquaticum.

Massively input and accumulated ammonium is one of the main causes of eutrophication in aquatic ecosystems, which severely deteriorates water quality. Previous studies showed that one of the commonly used macrophytes, Myriophyllum aquaticum, was capable of not only withstanding ammonium of high concentration, but also efficiently assimilating extracellular ammonium to constitutive amino acids and proteins. However, the genetic mechanism regulating such efficient nitrogen metabolism in M. aquaticum is still poorly understood. Therefore, RNA-based analysis was performed in this study to understand the ammonium regulatory mechanism in M. aquaticum in response to various concentrations of ammonium. A total of 7721 genes were differentially expressed, of which those related to nitrogen-transport, assimilation, and remobilization were highly-regulated in response to various concentrations of ammonium. We have also identified transcription factors and protein kinases that were rapidly induced in response to ammonium, which suggests their involvement in ammonium-mediated signalling. Meanwhile, secondary metabolism including phenolics and anthocyanins biosynthesis was also activated in response to various concentrations of ammonium, especially at high ammonium concentrations. These results proposed a complex physiological and genetic regulation network related to nitrogen, carbohydrate, transcription factors, and secondary metabolism for nitrogen use efficiency in M. aquaticum.

Enhancement of facultative anaerobic denitrifying communities by oxygen release from roots of the macrophyte in constructed wetlands.

The radial oxygen loss (ROL) of wetland plants is a crucial factor that can influence the efficiency required for nitrogen (N) removal and microbial activities responsible for N removal in constructed wetlands (CWs). However, the shift of microbial community in different niches in response to ROL has been rarely studied. This study aims to unravel the link between the ROL and microbial response in sediment, water and rhizoplane by a surface flow CW planted with Myriophyllum aquaticum for treating high-strength swine wastewater. Ti3+-citrate colorimetric method demonstrated that M. aquaticum was a wetland species with a ROL of 0.019 mg/h/plant. Using quantitative polymerase chain reactions (qPCR) and high-throughput sequencing of microbial 16S rRNA gene, we demonstrated that the abundance of facultative anaerobic denitrifiers in the rhizoplane was the most of the three niches, that in the water (5-10 cm) was the less and that in the sediment was the least. Acinetobacter was enriched and dominated amongst denitrifiers in the water. Denitrifiers in the rhizoplane were mainly dominated by enriched Pseudomonas, Aeromonas, and Acinetobacter. The theoretical calculation of oxygen sources and consumptions indicated that water reaeration should support the oxygen demands for nitrification in the aerobic layer (0-5 cm), and the ROL could stimulate the growth of facultative anaerobic denitrifiers in the rhizoplane and water (5-10 cm) to achieve denitrification within CW systems.

The phyllosphere indigenous microbiota of Brassica campestris L. change its diversity in responding to di-n-butyl phthalate pollution.

In this study, the effects of di-n-butyl phthalate (DBP) on the phyllosphere bacterial community of field mustard (Brassica campestris L.) at the five-leaf stage were investigated. The indigenous alpha-diversity of the phyllosphere bacteria was altered after spraying with different concentrations of DBP. Shannon diversity indices were significantly changed on day 5 after treatment at DBP concentrations > 400 mg L-1 (P > 0.05). Nevertheless, the difference between treatment and control was not significant on day 9 after DBP treatment (P > 0.05). Exposure to DBP resulted in a decrease in Proteobacteria and Firmicutes, and an increase in Actinobacteria at all sampling intervals. These changes included significant increases in the relative abundance of Paracoccus and Rhodococcus, and significant decreases in that of Pseudomonas, Exiguobacterium, an unclassified genus of Pseudomonadaceae, and an unclassified genus of Enterobacteriaceae. This study provides new evidence for the possibility of using phyllosphere microbiota to remediate DBP contamination.

Long- and short-chain AHLs affect AOA and AOB microbial community composition and ammonia oxidation rate in activated sludge.

Quorum sensing (QS) regulation of the composition of ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB) communities and functions in wastewater treatment was investigated. Specifically, we explored the role of N-acyl-l-homoserine lactones (AHLs) in microbial community dynamics in activated sludge. On average, the specific ammonia-oxidising-rate increased from 1.6 to 2.8 mg NH4+-N/g MLSS/hr after treatment with long-chain AHLs for 16 days, and the addition of AHLs to sludge resulted in an increased number of AOA/AOB amoA genes. Significant differences were observed in the AOA communities of control and AHL-treated cultures, but not the AOB community. Furthermore, the dominant functional AOA strains of the Crenarchaeota altered their ecological niche in response to AHL addition. These results provide evidence that AHLs play an important role in mediating AOA/AOB microbial community parameters and demonstrate the potential for application of QS to the regulation of nitrogen compound metabolism in wastewater treatment.

The Occurrence of Putative Nitric Oxide Dismutase (Nod) in an Alpine Wetland with a New Dominant Subcluster and the Potential Ability for a Methane Sink.

Recently, a new oxygenic pathway has been proposed based on the disproportionation of NO with putative NO dismutase (Nod). In addition to a new process in nitrogen cycling, this process provides ecological advantages for the degradation of substrates in anaerobic conditions, which is of great significance for wastewater treatment. However, the Nod distribution in aquatic environments is rarely investigated. In this study, we obtained the nod genes with an abundance of 2.38 ± 0.96 × 105 copies per gram of dry soil from the Zoige wetland and aligned the molecular characteristics in the corresponding Nod sequences. These Nod sequences were not only found existing in NC10 bacteria, but were also found forming some other clusters with Nod sequences from a WWTP reactor or contaminated aquifers. Moreover, a new subcluster in the aquifer-similar cluster was even dominant in the Zoige wetland and was named the Z-aquifer subcluster. Additionally, soils from the Zoige wetland showed a high potential rate (10.97 ± 1.42 nmol of CO2 per gram of dry soil per day) for nitrite-dependent anaerobic methane oxidation (N-DAMO) with low abundance of NC10 bacteria, which may suggest a potential activity of Nod in other clusters when considering the dominance of the Z-aquifer subcluster Nod. In conclusion, we verified the occurrence of Nod in an alpine wetland for the first time and found a new subcluster to be dominant in the Zoige wetland. Moreover, this new subcluster of Nod may even be active in the N-DAMO process in this alpine wetland, which needs further study to confirm.

Environmental Adaptability and Quorum Sensing: Iron Uptake Regulation during Biofilm Formation by Paracoccus denitrificans.

Paracoccus denitrificans is a valuable model organism due to its versatile respiration capability and bioenergetic flexibility, both of which are critical to its survival in different environments. Quorum sensing (QS) plays a crucial role in the regulation of many cell functions; however, whether QS systems play a role in P. denitrificans is unknown. In this study, we demonstrated that iron uptake systems in P. denitrificans were directly regulated by a newly identified QS system. Genes coding for TonB-dependent systems, which transport chelated iron, were transcribed at higher levels in the QS-defective mutants. In contrast, genes coding for the Fbp system, which is TonB independent and transports unchelated ferric iron, were downregulated in the mutants. In brief, QS in P. denitrificans triggers a switch in iron uptake from TonB-dependent to TonB-independent transport during biofilm formation as higher concentrations of iron accumulate in the exopolysaccharide (EPS). Switching from TonB-dependent iron uptake systems to TonB-independent systems not only prevents cells from absorbing excess iron but also conserves energy. Our data suggest that iron uptake strategies are directly regulated by QS in Paracoccus denitrificans to support their survival in available ecological niches.IMPORTANCE As iron is an important trace metal for most organisms, its absorption is highly regulated. Fur has been reported as a prevalent regulator of iron acquisition. In addition, there is a relationship between QS and iron acquisition in pathogenic microbes. However, there have been few studies on the iron uptake strategies of nonpathogenic bacteria. In this study, we demonstrated that iron uptake systems in Paracoccus denitrificans PD1222 were regulated by a newly identified PdeR/PdeI QS system during biofilm formation, and we put forward a hypothesis that QS-dependent iron uptake systems benefit the stability of biofilms. This report elaborates the correlation among QS, iron uptake, and biofilm formation and thus contributes to an understanding of the ecological behavior of environmental bacteria.

Mitigation of nitrous oxide emissions from acidic soils by Bacillus amyloliquefaciens, a plant growth-promoting bacterium.

Nitrous oxide (N2 O) is a long-lived greenhouse gas that can result in the alteration of atmospheric chemistry and cause accompanying changes in global climate. To date, many techniques have been used to mitigate the emissions of N2 O from agricultural fields, which represent one of the most important sources of N2 O. In this study, we designed a greenhouse pot experiment and a microcosmic serum bottle incubation experiment using acidic soil from a vegetable farm to study the effects of Bacillus amyloliquefaciens (BA) on plant growth and N2 O emission rates. The addition of BA to the soil promoted plant growth enhanced the soil pH and increased the total nitrogen (TN) contents in the plants. At the same time, it decreased the concentrations of ammonium (NH4+ ), nitrate (NO3- ) and TN in the soil. Overall, the addition of BA resulted in a 50% net reduction of N2 O emissions compared with the control. Based on quantitative PCR and the network analysis of DNA sequencing, it was demonstrated that BA partially inhibited the nitrification process through the significant reduction of ammonia oxidizing bacteria. Meanwhile, it enhanced the denitrification process, mainly by increasing the abundance of N2 O-reducing bacteria in the treatment with BA. The results of our microcosm experiment provided evidence that strongly supported the above findings under more strictly controlled laboratory conditions. Taken together, the results of our study evidently demonstrated that BA has dual effects on the promotion of plant growth and the dramatic reduction of greenhouse emissions, thus suggesting the possibility of screening beneficial microbial organisms from the environment that can promote plant growth and mitigate greenhouse trace gases.