Soil Type Driven Change in Microbial Community Affects Poly(butylene adipate-co-terephthalate) Degradation Potential.

Biodegradable mulch films have been developed as a suitable alternative to conventional nondegradable polyethylene films. However, the key factors controlling the degradation speed of biodegradable mulch films in soils remain unclear. Here, we linked changes in the soil microbiome with the degradation rate of a promising biodegradable material poly(butylene adipate-co-terephthalate) (PBAT) in four soil types, a lou soil (LS), a fluvo-aquic soil (CS), a black soil (BS), and a red soil (RS), equivalent to Inceptisols (the first two soils), Mollisols, and Ultisols, using soil microcosms. The PBAT degradation rate differed with the soil type, with PBAT mineralization levels of 16, 9, 0.3, and 0.9% in LS, CS, BS, and RS, respectively, after 120 days. Metagenomic analysis showed that the microbial community in LS was more responsive to PBAT than the other three soils. PBAT hydrolase genes were significantly enriched in LS but were not significantly stimulated by PBAT in CS, BS, or RS. Several members of Proteobacteria were identified as novel potential degraders, and their enrichment extent was significantly positively correlated with PBAT degradation capacity. Overall, our results suggest that soil environments harbored a range of PBAT-degrading bacteria and the enrichment of potential degraders drives the fate of PBAT in the soils.

Enhanced biomass and cadmium accumulation by three cadmium-tolerant plant species following cold plasma seed treatment.

Cold plasma seed treatment can promote plant growth and enhance the resistance of agricultural crops to adverse stress. However, the effects of plasma seed treatment on the growth and phytoextraction response of plants to cadmium (Cd) remain poorly documented. Here, we have investigated the feasibility of using plasma seed treatment to enhance the biomass and Cd accumulation of three Cd-tolerant species, namely Bidens pilosa L, Solanum nigrum L. and Trifolium repens L, under different plasma treatment conditions. Possible enhancement mechanisms are also proposed according to the levels of organic acids in the roots and the Cd fractions in rhizosphere soil following different plasma treatment conditions. The optimum plasma power was 100 W (B. pilosa) or 500 W (S. nigrum and T. repens). The optimum plasma exposure time for all three species was 60 s. Plasma seed treatment under the optimum treatment conditions enhanced plant dry biomass by ~17.3-45.0% and Cd accumulation by 8.8-54.4% across all three species compared to the controls. Furthermore, the phytoremediation efficiencies, bioaccumulation factors and transfer factors of the three species also increased significantly after seed plasma treatment. The promotion of plasma treatment on the biomass and Cd accumulation of three species might be due to increased exudation of organic acids from the roots into the rhizosphere soil, thus increasing the concentrations of acid-soluble Cd to form Cd-organic acid complexes that facilitated the uptake and translocation of Cd by the plants. Results of this study revealed that cold plasma seed treatment is an environmentally friendly, economical and efficient means to develop the application of phytoremediation for Cd-contaminated soils.

Low Concentrations of Silver Nanoparticles and Silver Ions Perturb the Antioxidant Defense System and Nitrogen Metabolism in N2-Fixing Cyanobacteria.

Although toxic effects of silver nanoparticles (AgNPs) on aquatic organisms have been extensively reported, responses of nitrogen-fixing cyanobacteria to AgNPs/Ag+ under environmentally relevant concentrations are largely unknown. Here, cyanobacteria were exposed to different concentrations of AgNPs (0.01, 0.1, and 1 mg/L) or Ag+ (0.1, 1, and 10 µg/L) for 96 h. The impacts of AgNPs and Ag+ on photosynthesis and N2 fixation in cyanobacteria (Nostoc sphaeroides) were evaluated. In addition, gas chromatography-mass spectrometry (GC-MS)-based metabolomics was employed to give an instantaneous snapshot of the physiological status of the cells under AgNP/Ag+ exposure. Exposure to high doses of AgNPs (1 mg/L) or Ag+ (10 µg/L) caused growth inhibition, reactive oxygen species overproduction, malondialdehyde accumulation, and decreased N2 fixation. In contrast, low doses of AgNPs (0.01 and 0.1 mg/L) and Ag+ (0.1 and 1 µg/L) did not induce observable responses. However, metabolomics revealed that metabolic reprogramming occurred even at low concentrations of AgNP and Ag+ exposure. Levels of a number of antioxidant defense-related metabolites, especially phenolic acid and polyphenols (gallic acid, resveratrol, isochlorogenic acid, chlorogenic acid, cinnamic acid, 3-hydroxybenzoic acid, epicatechin, catechin, and ferulic acid), significantly decreased in response to AgNPs or Ag+. This indicates that AgNPs and Ag+ can disrupt the antioxidant defense system and disturb nitrogen metabolism even at low-dose exposure. Metabolomics was shown to be a powerful tool to detect "invisible" changes, not observable by typical phenotypic-based endpoints.

Pesticide residues in soils planted with Panax notoginseng in south China, and their relationships in Panax notoginseng and soil.

In this study, 73 samples from soils planted with Panax notoginseng and six P. notoginseng samples were collected in Yunnan Province to investigate the residual levels of six pesticides and their relationships with P. notoginseng and soil. All six pesticides were detected in the soils planted with P. notoginseng located in three regions of Shilin, Kaiyuan, and Yanshan. The detection frequencies of the pesticides in the soils followed the order: quintozene (100%) > iprodione (96%) > procymidone (69%) > chlorothalonil (51%) > pyrimethanil (49%) > pyraclostrobin (29%). The median concentrations of iprodione, pyraclostrobin, pyrimethanil, quintozene, procymidone, and chlorothalonil were 46.40, 6.4, 3.1, 2.86, 2.69, and 0.24 µg/kg, respectively. The mean concentrations of pesticides in the three regions followed the order: Kaiyuan > Shilin > Yanshan, except for iprodione. Furthermore, the concentrations of pesticide residues in soils in each region followed the order: soils never planted with P. notoginseng < soils previously planted with P. notoginseng < soils currently planted with P. notoginseng. The concentration of chlorothalonil in P. notoginseng followed the order: root > stem > leaf, whereas those of the other five pesticides followed the opposite order: root < stem < leaf. There were significant positive correlations between the mean concentrations of pesticides in P. notoginseng and those in the corresponding soils. These results indicate that the rational application of pesticides in P. notoginseng cultivation would be effective for reducing the accumulation of pesticides in P. notoginseng to protect people from the harmful effects of residual pesticides.

Coupling between Nitrogen Fixation and Tetrachlorobiphenyl Dechlorination in a Rhizobium-Legume Symbiosis.

Legume-rhizobium symbioses have the potential to remediate soils contaminated with chlorinated organic compounds. Here, the model symbiosis between Medicago sativa and Sinorhizobium meliloti was used to explore the relationships between symbiotic nitrogen fixation and transformation of tetrachlorobiphenyl PCB 77 within this association. 45-day-old seedlings in vermiculite were pretreated with 5 mg L-1 PCB 77 for 5 days. In PCB-supplemented nodules, addition of the nitrogenase enhancer molybdate significantly stimulated dechlorination by 7.2-fold and reduced tissue accumulation of PCB 77 (roots by 96% and nodules by 93%). Conversely, dechlorination decreased in plants exposed to a nitrogenase inhibitor (nitrate) or harboring nitrogenase-deficient symbionts (nifA mutant) by 29% and 72%, respectively. A range of dechlorinated products (biphenyl, methylbiphenyls, hydroxylbiphenyls, and trichlorobiphenyl derivatives) were detected within nodules and roots under nitrogen-fixing conditions. Levels of nitrogenase-derived hydrogen and leghemoglobin expression correlated positively with nodular dechlorination rates, suggesting a more reducing environment promotes PCB dechlorination. Our findings demonstrate for the first time that symbiotic nitrogen fixation acts as a driving force for tetrachlorobiphenyl dechlorination. In turn, this opens new possibilities for using rhizobia to enhance phytoremediation of halogenated organic compounds.

Isolation of the PCB-degrading bacteria Mesorhizobium sp. ZY1 and its combined remediation with Astragalus sinicus L. for contaminated soil.

A bacterial strain ZY1 capable of utilizing PCBs as its carbon source was isolated from the root nodules of Chinese milk vetch (Astragalus sinicus L.). The strain was identified as Mesorhizobium sp. according to its physiological-biochemical properties and the analysis of its 16S rRNA gene sequence. When the initial OD600 was 0.15, 62.7% of 15 mg L(-1) 3,3',4,4'-TCB in a liquid culture was degraded by Mesorhizobium sp. ZY1 within 10 days. Mesorhizobium sp. ZY1 also greatly increased the biotransformation of soil PCBs. Pot experiments indicated that the soil PCB concentrations of a single incubation of strain ZY1 (R) and a single planting of A. sinicus (P) decreased by 20.5% and 23.0%, respectively, and the concentration of PCBs in soil treated with A. sinicus and strain ZY1 decreased by 53.1%. We also observed that A. sinicus-Mesorhizobium sp. ZY1 treatment (PR) improved plant biomass and the concentration of PCBs in plants compared with a single A. sinicus planting treatment (P). The results suggest that the synergistic association between A. sinicus and PCBs-degrading Mesorhizobium sp. ZY1 can stimulate the phytoextraction of PCBs and the rhizosphere microflora to degrade PCBs, and might be a promising bioremediation strategy for PCB-contaminated soil.

Involvement of abscisic acid and salicylic acid in signal cascade regulating bacterial endophyte-induced volatile oil biosynthesis in plantlets of Atractylodes lancea.

The enormous biological diversity of endophytes, coupled with their potential to enhance the production of bioactive metabolites in plants, has driven research efforts focusing on endophytes. However, limited information is available on the impacts of bacterial endophytes on plant secondary metabolism and signaling pathways involved. This work showed that an endophytic Acinetobacter sp. ALEB16, capable of activating accumulation of plant volatile oils, also induced abscisic acid (ABA) and salicylic acid (SA) production in Atractylodes lancea. Pre-treatment of plantlets with biosynthetic inhibitors of ABA or SA blocked the bacterium-induced volatile production. ABA inhibitors suppressed not only the bacterium-induced volatile accumulation but also the induced ABA and SA generation; nevertheless, SA inhibitors did not significantly inhibit the induced ABA biosynthesis, implying that SA acted downstream of ABA production. These results were confirmed by observations that exogenous ABA and SA reversed the inhibition of bacterium-induced volatile accumulation by inhibitors. Transcriptional activities of genes in sesquiterpenoid biosynthesis also increased significantly with bacterium, ABA and SA treatments. Mevalonate pathway proved to be the main source of isopentenyldiphosphate for bacterium-induced sesquiterpenoids, as assessed in experiments using specific terpene biosynthesis inhibitors. These results suggest that Acinetobacter sp. acts as an endophytic elicitor to stimulate volatile biosynthesis of A. lancea via an ABA/SA-dependent pathway, thereby yielding additional insight into the interconnection between ABA and SA in biosynthesis-related signaling pathways.

Pleural effusion as the initial clinical presentation in disseminated cryptococcosis and fungaemia: an unusual manifestation and a literature review.

BACKGROUND: Cryptococcus neoformans infection usually presents as chronic meningitis and is increasingly being recognized in immunocompromised patients. Presentation with pleural effusion is rare in cryptococcal disease; in fact, only 4 cases of pleural effusion as the initial clinical presentation in cryptococcosis have been reported in English-language literature to date. We report the first case of pleural effusion as the initial clinical presentation in a renal transplant recipient who was initially misdiagnosed with tuberculous pleuritis but who then developed fungaemia and disseminated cryptococcosis. The examination of this rare manifestation and the accompanying literature review will contribute to increased recognition of the disease and a reduction in misdiagnoses. CASE PRESENTATION: We describe a 63-year-old male renal transplant recipient on an immunosuppressive regimen who was admitted for left pleural effusion and fever. Cytological examinations and pleural fluid culture were nonspecific and negative. Thoracoscopy only found chronic, nonspecific inflammation with fibrosis in the pleura. After empirical anti-tuberculous therapy, the patient developed an elevated temperature, a severe headache and vomiting and fainted in the ward. Cryptococci were specifically found in the cerebrospinal fluid following lumbar puncture. Blood cultures were twice positive for C. neoformans one week later. He was transferred to the respiratory intensive care unit (RICU) immediately and was placed on non-invasive ventilation for respiratory failure for 2 days. He developed meningoencephalitis and fungaemia with C. neoformans during hospitalization. He was given amphotericin B liposome combined with 5-flucytosine and voriconazole for first 11 days, then amphotericin B liposome combined with 5-flucytosine sustained to 8 weeks, after that changed to fluconazole for maintenance. His condition improved after antifungal treatment, non-invasive ventilation and other support. Further pathological consultation and periodic acid-Schiff staining revealed Cryptococcus organisms in pleural sections, providing reliable evidence for cryptococcal pleuritis. CONCLUSION: Pleural effusion is an unusual manifestation of cryptococcosis. Cryptococcal infection must be considered in the case of patients on immunosuppressives, especially solid-organ transplant recipients, who present with pleural effusion, even if pleural fluid culture is negative. Close communication between the pathologist and the clinician, multiple special biopsy section stains and careful review are important and may contribute to decreasing misdiagnosis.

Consequences of antagonistic interactions between endophytic fungus and bacterium on plant growth and defense responses in Atractylodes lancea.

Many studies have examined pair-wise interactions between plants and endophytes, while overlooking the interplays among multiple endosymbionts and their combined impacts on hosts. In this study, Atractylodes lancea plantlets were inoculated with endophytic fungus Acremonium strictum AL16, or endophytic bacterium Acinetobacter sp., or both, to investigate the impacts of the three-way symbiosis on the host. Our results showed that defense-related responses of the co-inoculated plantlets were delayed and weakened relative to plantlets with single inoculants, but no detrimental effects on phyto-physiology (growth, photosynthesis) were observed after combined inoculations. Quantitative PCR analysis verified a decrease in AL16 colonization density within plants after co-inoculation with the endobacteria. An in vitro assay was then performed to elucidate the suppressed plant defense responses and reduced fungal colonization by dual inoculation. The data showed that the presence of Acinetobacter sp. reduced AL16 colony diameter and spore germination rate without negatively affecting fungal morphology. Additionally, direct hyphal attachment of the bacterium to AL16 in vitro was visualized by scanning electronic microscopy. Therefore, we propose that a balanced and compatible symbiosis might require constraints conferred by the antagonistic endophyte Acinetobacter sp. on the fungus AL16 in the tripartite endophytic bacterium-fungus-plant system.

Biohydrogen utilization in legume-rhizobium symbiosis reveals a novel mechanism of accelerated tetrachlorobiphenyl transformation.

Symbiosis between Glycine max and Bradyrhizobium diazoefficiens were used as a model system to investigate whether biohydrogen utilization promotes the transformation of the tetrachlorobiphenyl PCB77. Both a H2 uptake-positive (Hup+) strain (wild type) and a Hup- strain (a hupL deletion mutant) were inoculated into soybean nodules. Compared with Hup- nodules, Hup+ nodules increased dechlorination significantly by 61.1 % and reduced the accumulation of PCB77 in nodules by 37.7 % (p < 0.05). After exposure to nickel, an enhancer of uptake hydrogenase, dechlorination increased significantly by 2.2-fold, and the accumulation of PCB77 in nodules decreased by 54.4 % (p < 0.05). Furthermore, the tetrachlorobiphenyl transformation in the soybean root nodules was mainly testified to be mediated by nitrate reductase (encoded by the gene NR) for tetrachlorobiphenyl dechlorination and biphenyl-2,3-diol 1,2-dioxygenase (bphC) for biphenyl degradation. This study demonstrates for the first time that biohydrogen utilization has a beneficial effect on tetrachlorobiphenyl biotransformation in a legume-rhizobium symbiosis.

Enhancement of nitrogen fixation and diazotrophs by long-term polychlorinated biphenyl contamination in paddy soil.

Biological nitrogen fixation (BNF) driven by diazotrophs is a major means of increasing available nitrogen (N) in paddy soil, in addition to anthropogenic fertilization. However, the influence of long-term polychlorinated biphenyl (PCB) contamination on the diazotrophic community and nitrogen fixation in paddy soil is poorly understood. In this study, samples were collected from paddy soil subjected to > 30 years of PCB contamination, and the soil diazotrophic community and N2 fixation rate were evaluated by Illumina MiSeq sequencing and acetylene reduction assays, respectively. The results indicated that high PCB contamination increased diazotrophic abundance and the N2 fixation rate, and altered diazotrophic community structure in the paddy soil. The random forest model demonstrated that the ß-diversity of the diazotrophic community was the most significant predictor of the N2 fixation rate. Structure equation modeling identified a specialized keystone diazotrophic ecological cluster, predominated by Bradyrhizobium, Desulfomonile, and Cyanobacteria, as the key driver of N2 fixation. Overall, our findings indicated that long-term PCB contamination enhanced the N2 fixation rate by altering diazotrophic community abundance and structure, which may deepen our understanding of the ecological function of diazotrophs in organic-contaminated soil.

Endogenous biohydrogen from a rhizobium-legume association drives microbial biodegradation of polychlorinated biphenyl in contaminated soil.

Endogenous hydrogen (H2) is produced through rhizobium-legume associations in terrestrial ecosystems worldwide through dinitrogen fixation. In turn, this gas may alter rhizosphere microbial community structure and modulate biogeochemical cycles. However, very little is understood about the role that this H2 leaking to the rhizosphere plays in shaping the persistent organic pollutants degrading microbes in contaminated soils. Here, we combined DNA-stable isotope probing (DNA-SIP) with metagenomics to explore how endogenous H2 from the symbiotic rhizobium-alfalfa association drives the microbial biodegradation of tetrachlorobiphenyl PCB 77 in a contaminated soil. The results showed that PCB77 biodegradation efficiency increased significantly in soils treated with endogenous H2. Based on metagenomes of 13C-enriched DNA fractions, endogenous H2 selected bacteria harboring PCB degradation genes. Functional gene annotation allowed the reconstruction of several complete pathways for PCB catabolism, with different taxa conducting successive metabolic steps of PCB metabolism. The enrichment through endogenous H2 of hydrogenotrophic Pseudomonas and Magnetospirillum encoding biphenyl oxidation genes drove PCB biodegradation. This study proves that endogenous H2 is a significant energy source for active PCB-degrading communities and suggests that elevated H2 can influence the microbial ecology and biogeochemistry of the legume rhizosphere.

Nitrogen transfer and cross-feeding between Azotobacter chroococcum and Paracoccus aminovorans promotes pyrene degradation.

Nitrogen is a limiting nutrient for degraders function in hydrocarbon-contaminated environments. Biological nitrogen fixation by diazotrophs is a natural solution for supplying bioavailable nitrogen. Here, we determined whether the diazotroph Azotobacter chroococcum HN can provide nitrogen to the polycyclic aromatic hydrocarbon-degrading bacterium Paracoccus aminovorans HPD-2 and further explored the synergistic interactions that facilitate pyrene degradation in nitrogen-deprived environments. We found that A. chroococcum HN and P. aminovorans HPD-2 grew and degraded pyrene more quickly in co-culture than in monoculture. Surface-enhanced Raman spectroscopy combined with 15N stable isotope probing (SERS - 15N SIP) demonstrated that A. chroococcum HN provided nitrogen to P. aminovorans HPD-2. Metabolite analysis and feeding experiments confirmed that cross-feeding occurred between A. chroococcum HN and P. aminovorans HPD-2 during pyrene degradation. Transcriptomic and metabolomic analyses further revealed that co-culture significantly upregulated key pathways such as nitrogen fixation, aromatic compound degradation, protein export, and the TCA cycle in A. chroococcum HN and quorum sensing, aromatic compound degradation and ABC transporters in P. aminovorans HPD-2. Phenotypic and fluorescence in situ hybridization (FISH) assays demonstrated that A. chroococcum HN produced large amounts of biofilm and was located at the bottom of the biofilm in co-culture, whereas P. aminovorans HPD-2 attached to the surface layer and formed a bridge-like structure with A. chroococcum HN. This study demonstrates that distinct syntrophic interactions occur between A. chroococcum HN and P. aminovorans HPD-2 and provides support for their combined use in organic pollutant degradation in nitrogen-deprived environments.

Microbial diversity drives pyrene dissipation in soil.

Soil microbial diversity is an essential driver of multiple ecosystem functions and services. However, the role and mechanisms of microbial diversity in the dissipation of persistent organic pollutants in soil are largely unexplored. Here, a gradient of soil microbial diversity was constructed artificially by a dilution-to-extinction approach to assess the role of soil microbial diversity in the dissipation of pyrene, a high molecular weight polycyclic aromatic hydrocarbon (PAH), in a 42-day microcosm experiment. The results showed that pyrene dissipation (98.1%) and the abundances of pyrene degradation genes (the pyrene dioxygenase gene nidA and the gram-positive PAH-ring hydroxylating dioxygenase gene PAH-RHDα GP) were highest in soils with high microbial diversity. Random-forest machine learning was combined with linear regression analysis to identify a range of keystone taxa (order level) associated with pyrene dissipation, including Sphingobacteriales, Vampirovibrionales, Blastocatellales, Myxococcales, Micrococcales and Rhodobacterales. The diversity of these keystone taxa was significantly and positively correlated with the abundance of pyrene degradation genes and the removal rate of pyrene. According to (partial) Mantel tests, keystone taxa diversity was the dominant factor determining pyrene dissipation compared with total microbial diversity. Moreover, co-occurrence network analysis revealed that diverse keystone taxa may drive pyrene dissipation via more positive interactions between keystone species and with other species in soil. Taken together, these findings provide new insights on the regulation of keystone taxa diversity to promote the dissipation of PAH in soil.

Effects of combined pollution of organic pollutants and heavy metals on biodiversity and soil multifunctionality in e-waste contaminated soil.

Electronic waste (e-waste) is increasing globally, but the impact of this source of combined pollution on soil biodiversity and multiple soil functions (i.e., ecosystem multifunctionality) remains unclear. Here, we evaluated the effects of combined pollution on the biodiversity and soil multifunctionality using samples collected from upland and paddy soils chronically contaminated with e-waste. Overall biodiversity, as well as the relative abundance and biodiversity of key ecological clusters, as combined pollution concentrations increased in upland soil, while the opposite was true in paddy soil. Soil multifunctionality followed the same trend. Organic pollutants had significant negative effects on soil multifunctionality and were the main influencing factors in upland soil. Heavy metals had significant positive effects on soil multifunctionality in paddy soil. Moreover, driving soil multifunctionality was overall biodiversity in upland soil but key biodiversity in paddy soil. Importantly, a strong positive association between key organism biodiversity and soil multifunctionality was found in soil with low contamination. However, the relationship between key organism biodiversity and soil multifunctionality weakened or disappeared in highly contaminated soil, whereas overall biodiversity was significantly and positively correlated with multifunctionality. Our results emphasized that severe e-waste contamination would reduce soil biodiversity and soil multifunctionality and warrants high attention.

Variations of Bacterial and Diazotrophic Community Assemblies throughout the Soil Profile in Distinct Paddy Soil Types and Their Contributions to Soil Functionality.

Soil microbiota plays fundamental roles in maintaining ecosystem functions and services, including biogeochemical processes and plant productivity. Despite the ubiquity of soil microorganisms from the topsoil to deeper layers, their vertical distribution and contribution to element cycling in subsoils remain poorly understood. Here, nine soil profiles (0 to 135 cm) were collected at the local scale (within 300 km) from two canonical paddy soil types (Fe-accumuli and Hapli stagnic anthrosols), representing redoximorphic and oxidative soil types, respectively. Variations with depth in edaphic characteristics and soil bacterial and diazotrophic community assemblies and their associations with element cycling were explored. The results revealed that nitrogen and iron status were the most distinguishing edaphic characteristics of the two soil types throughout the soil profile. The acidic Fe-accumuli stagnic anthrosols were characterized by lower concentrations of free iron oxides and total iron in topsoil and ammonia in deeper layers compared with the Hapli stagnic anthrosols. The bacterial and diazotrophic community assemblies were mainly shaped by soil depth, followed by soil type. Random forest analysis revealed that nitrogen and iron cycling were strongly correlated in Fe-accumuli stagnic anthrosol, whereas in Hapli soil, available sulfur was the most important variable predicting both nitrogen and iron cycling. The distinctive biogeochemical processes could be explained by the differences in enrichment of microbial taxa between the two soil types. The main discriminant clades were the iron-oxidizing denitrifier Rhodanobacter, Actinobacteria, and diazotrophic taxa (iron-reducing Geobacter, Nitrospirillum, and Burkholderia) in Fe-accumuli stagnic anthrosol and the sulfur-reducing diazotroph Desulfobacca in Hapli stagnic anthrosol. IMPORTANCE Rice paddy ecosystems support nearly half of the global population and harbor remarkably diverse microbiomes and functions in a variety of soil types. Diazotrophs provide significant bioavailable nitrogen in paddy soil, priming nitrogen transformation and other biogeochemical processes. This study provides a novel perspective on the vertical distribution of bacterial and diazotrophic communities in two hydragric anthrosols. Microbiome analysis revealed divergent biogeochemical processes in the two paddy soil types, with a dominance of nitrogen-iron cycling processes in Fe-accumuli stagnic anthrosol and sulfur-nitrogen-iron coupling in Hapli stagnic anthrosol. This study advances our understanding of the multiple significant roles played by soil microorganisms, especially diazotrophs, in biogeochemical element cycles, which have important ecological and biogeochemical ramifications.

Soil bacterial diversity and functionality are driven by plant species for enhancing polycyclic aromatic hydrocarbons dissipation in soils.

Plant-microorganisms symbiosis has been widely used in developing strategies for the rhizoremediation of polycyclic aromatic hydrocarbon (PAHs) contaminated agricultural soils. However, understanding the potential mechanisms for using complex plant-microbe interactions to enhance rhizoremediation in contaminated soils is still limited. In this study, rhizosphere microbiomes were established by cultivating four types of cover crops for 15 months in a PAHs-contaminated field. The results showed that the PAHs removal rates were significantly higher in rhizosphere soils (55.2-82.3%) than the bare soils (20.5%). Of the four cover crops, the rhizosphere soils associated with the alfalfa and clover had higher removal rates for high molecular weight (HMW) PAHs (78.5-87.1%) than the grasses (39.0-46.2%). High-throughput sequencing analysis showed that bacterial community structure between the planted and bare soils, and among four cover crops rhizosphere soils were significantly different. The rhizosphere soils associated with the alfalfa and clover had more abundant degradation-related taxa. Correlation network analysis showed that bacterial communities with high removal rates have stronger interactions. Metagenome analysis indicated that the relative abundance of the key functional genes involved in PAHs degradation and nutrient metabolisms were significantly higher in rhizosphere soils, especially for alfalfa and clover. Overall, this study provides new insights for us to understand the mechanisms by different plants enhancing PAHs dissipation from the viewpoint of microbiology.

Changes in clover rhizosphere microbial community and diazotrophs in mercury-contaminated soils.

Little is known about the response of the soil microbiome (including bacteria in the rhizosphere of legumes such as clover) to mercury (Hg) despite the toxicity of Hg to soil microorganisms. Here, Hg-contaminated soils collected from Guizhou province, southwest China, were divided into three groups according to their Hg contents and were planted with clover. High-throughput sequencing of bacterial 16S rRNA and nitrogenase (nifH) genes and quantitative polymerase chain reaction (qPCR) were used to study the response of bacteria and diazotrophs to soil Hg stress and the effects of Hg on the abundance of functional genes in rhizosphere soils. High concentrations of soil Hg decreased bacterial community abundance and diversity and increased the abundance and diversity of nitrogen-fixing bacteria. LEfSe analysis indicates that Rhizobium was a biomarker at sites with high soil Hg contents and the co-occurrence network results indicate a positive relationship between the abundance of the dominant module (from the co-occurrence network analysis) of Rhizobiaceae and soil Hg concentration. Structural equation modeling (SEM) indicates that the Hg content in the clover shoots (ShootHg) was negatively correlated with the abundance of the mercury reductase (merA) gene (r = -0.26, P < 0.05) and the organomercury lyase (merB) gene (r = -0.23, P < 0.05) in rhizosphere soils. Moreover, correlation analysis and SEM indicate that soil total nitrogen (TN), nitrate­nitrogen (NO3-N), soil organic matter (SOM), and available molybdenum (Mo) contents were also important factors affecting the structure of the microbial community and the abundance of functional genes. The results provide a basis for further study of the mechanism(s) by which microorganisms may impart tolerance of clover to Hg in contaminated soils.

The inhibitory mechanism of natural soil colloids on the biodegradation of polychlorinated biphenyls by a degrading bacterium.

In spite of extensive studies of soil model components, the role of natural soil colloids in the biodegradation of organic pollutants remain poorly understood. Accordingly, the present study selected Mollisol colloids (MCs) and Ultisol colloids (UCs) to investigate their effects on the biodegradation of 3, 3', 4, 4'-tetrachlorobiphenyl (PCB77) by Bradyrhizobium diazoefficiens USDA 110. Results demonstrated that both natural soil colloids significantly decreased the biodegradation of PCB77, which partly resulted from the significant decrease in the bioaccessibility of PCB77. Furthermore, the activity of Bradyrhizobium diazoefficiens USDA 110 was remarkably inhibited under the exposure to the two types of soil colloids, which was mainly ascribed to the inhibition of cell reproduction but not the lethal effect of reactive oxygen species. The calculated results from Ex-DLVO theory further indicated that the repulsion between UCs and biodegrading bacteria retarded the effective contact of cells with adsorbed PCB77 from UCs, resulting in the decline of the rate of cell reproduction. In general, the inhibition of MCs was limited to PCB77 bioaccessibility, whereas the negative effect of UCs was controlled by PCB77 bioaccessibility and the effective contact of cells with colloids. This study could provide implication for the enhancement of microbial remediation in contaminated soil.

miR-30a-3p participates in the development of asthma by targeting CCR3.

This study aimed to investigate the role and relevant mechanism of miR-30a-3p action in asthma. The results of this study revealed that the expression levels of miR-30a-3p were significantly decreased in the peripheral blood of asthmatic patients. In addition, we found that the CC chemokine receptor (CCR3) was a target of miR-30a-3p. Subsequently, an asthma mouse model was established using ovalbumin (OVA). The results showed that the expression of miR-30a-3p and CCR3 was downregulated and upregulated, respectively, in the peripheral blood of asthmatic mice. Enzyme-linked immunosorbent assay (ELISA) in asthmatic mouse serum demonstrated that miR-30a-3p mimic treatment significantly decreased the secretion of OVA-specific IgE, eotaxin-1, interleukin (IL)-5, and IL-4. These results suggested that miR-30a-3p inhibited CCR3 signaling pathway and relieved the inflammatory response against asthma in vivo. Eosinophils have also been implicated in the asthmatic inflammatory response. Therefore, the in vitro effects of miR-30a-3p on eosinophil activity were determined. Findings suggested that miR-30a-3p mimic significantly reduced eosinophil viability and migration and induced apoptosis. In addition, CCR3 and eotaxin-1 downregulation were observed. The aforementioned results were significantly reversed following CCR3 overexpression. This study suggested that miR-30a-3p was involved in asthma by regulating eosinophil activity and targeting CCR3.