Frontiers in Microbiology
·
2021
·
IF 5.64
Law Kai P.,He Wei,Tao Jianchang,Zhang Chuanlun
Marine Thaumarchaeota (formerly known as the marine group I archaea) have received much research interest in recent years since these chemolithoautotrophic organisms are abundant in the subsurface ocean and oxidize ammonium to nitrite, which makes them a major contributor to the marine carbon and nitrogen cycles. However, few studies have investigated the chemical composition of their exometabolome and their contributions to the pool of dissolved organic matter (DOM) in seawater. This study exploits the recent advances in ion mobility mass spectrometry (IM-MS) and integrates this instrumental capability with bioinformatics to reassess the exometabolome of a model ammonia-oxidizing archaeon, Nitrosopumilus maritimus strain SCM1. Our method has several advantages over the conventional approach using an Orbitrap or ion cyclotron resonance mass analyzer and allows assignments or annotations of spectral features to known metabolites confidently and indiscriminately, as well as distinction of biological molecules from background organics. Consistent with the results of a previous report, the SPE-extracted exometabolome of N. maritimus is dominated by biologically active nitrogen-containing metabolites, in addition to peptides secreted extracellularly. Cobalamin and associated intermediates, including α-ribazole and α-ribazole 5′-phosphate, are major components of the SPE-extracted exometabolome of N. maritimus. This supports the proposition that Thaumarchaeota have the capacity of de novo biosynthesizing cobalamin. Other biologically significant metabolites, such as agmatidine and medicagenate, predicted by genome screening are also detected, which indicates that Thaumarchaeota have remarkable metabolic potentials, underlining their importance in driving elemental cycles critical to biological processes in the ocean.
研究领域:
微生物学
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海洋生物学
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分析化学
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环境科学
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DOI
PubMed
高影响因子
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
·
2022
·Vol. 23
·期 7
·4012
·
IF 6.208
Jiacheng Yu,Changqian Cao,Fengjiao Fang,Yongxin Pan
Iron oxide nanoparticles have attracted a great deal of research interest in recent years for magnetic hyperthermia therapy owing to their biocompatibility and superior thermal conversion efficiency. Magnetoferritin is a type of biomimetic superparamagnetic iron oxide nanoparticle in a ferritin cage with good monodispersity, biocompatibility, and natural hydrophilicity. However, the magnetic hyperthermic efficiency of this kind of nanoparticle is limited by the small size of the mineral core as well as its low synthesis temperature. Here, we synthesized a novel magnetoferritin particle by using a recombinant ferritin from the hyperthermophilic archaeonPyrococcus furiosusas a template with high iron atom loading of 9517 under a designated temperature of 90 °C. Compared with the magnetoferritins synthesized at 45 and 65 °C, the one synthesized at 90 °C displays a larger average magnetite and/or maghemite core size of 10.3 nm. This yields an increased saturation magnetization of up to 49.6 emu g−1and an enhanced specific absorption rate (SAR) of 805.3 W g−1in an alternating magnetic field of 485.7 kHz and 49 kA m−1. The maximum intrinsic loss power (ILP) value is 1.36 nHm2kg−1. These results provide new insights into the biomimetic synthesis of magnetoferritins with enhanced hyperthermic efficiency and demonstrate the potential application of magnetoferritin in the magnetic hyperthermia of tumors.Keywords:hyperthermophilic archaeon;iron oxide nanoparticle;magnetic hyperthermia;magnetoferritin;biomineralization
研究领域:
纳米技术
·
生物材料
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癌症治疗
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生物物理学
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产品关联
DOI
PubMed
高影响因子
BIORESOURCE TECHNOLOGY
·
2021
·
IF 9.642
Yu-Xi Gao,Xing Li,Jun-Ru Zhao,Zhong-Xing Zhang,Xiao-Yan Fan
The responses of microbial communities and antibiotic resistance genes (ARGs) to azithromycin and copper combined pollution under gradient increasing (from 0.5 to 10 mg/L) and decreasing exposure (from 10 to 0.5 mg/L) modes were investigated. Nitrification was inhibited more obviously under gradient increasing exposure mode. Responses of archaeal community and function structure were more obvious than bacteria under both exposure modes. The dominant bacterial and archaeal compositions ( Hyphomicrobium , Euryarchaeota , etc.) were affected by two exposure modes, except some rare archaea ( Methanoregula and Methanosarcina ). There were more positive correlations between bacteria and archaea, and Nitrospira was keystone genus. Ammonia-oxidizing archaea (0.37–3.06%) and complete ammonia oxidizers ( Nitrospira_ENR4 ) were enriched, and Nitrososphaera_viennensis was closely related to denitrifying genes ( napA/B , nosZ , etc.). 50 ARG subtypes were detected and specific ARG subtypes ( aac , ImrA , etc.) proliferated in two exposure modes. Bacteria and archaea were common hosts for 24 ARGs and contributed to their shifts.
研究领域:
环境科学
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微生物学
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废水处理
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生态毒理学
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产品关联
DOI
PubMed
高影响因子
CHEMOSPHERE
·
2024
·
IF 8.1
Lingchao Kong,Yi Wang,Dongyu Cui,Wei He,Chuanlun Zhang,Chunmiao Zheng
Antimicrobial resistance (AMR) in oceans poses a significant threat to human health through the seafood supply chain. Ammonia-oxidizing archaea (AOA) are important marine microorganisms and play a key role in the biogeochemical nitrogen cycle around the world. However, the AMR of marine AOA to aquicultural antibiotics is poorly explored. Here, Raman-deuterium isotope probing (Raman-DIP), a single-cell tool, was developed to reveal the AMR of a typical marine species of AOA, Nitrosopumilus maritimus (designated SCM1), against six antibiotics, including erythromycin , tetracycline , novobiocin , neomycin , bacitracin , and vancomycin . The D 2 O concentration (30% v/v) and culture period (9 days) were optimized for the precise detection of metabolic activity in SCM1 cells through Raman-DIP. The relative metabolic activity of SCM1 upon exposure to antibiotics was semi-quantitatively calculated based on single-cell Raman spectra. SCM1 exhibited high resistance to erythromycin, tetracycline, novobiocin, neomycin , and vancomycin , with minimum inhibitory concentration (MIC) values between 100 and 400 mg/L, while SCM1 is very sensitive to bacitracin (MIC: 0.8 mg/L). Notably, SCM1 cells were completely inactive under the metabolic activity minimum inhibitory concentration conditions (MA-MIC: 1.6–800 mg/L) for the six antibiotics. Further genomic analysis revealed the antibiotic resistance genes (ARGs) of SCM1, including 14 types categorized into 33 subtypes. This work increases our knowledge of the AMR of marine AOA by linking the resistant phenome to the genome, contributing to the risk assessment of AMR in the underexplored ocean environment. As antibiotic resistance in marine microorganisms is significantly affected by the concentration of antibiotics in coastal environments, we encourage more studies concentrating on both the phenotypic and genotypic antibiotic resistance of marine archaea . This may facilitate a comprehensive evaluation of the capacity of marine microorganisms to spread AMR and the implementation of suitable control measures to protect environmental safety and human health.
研究领域:
微生物学
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环境科学
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海洋生物学
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DOI
PubMed
高影响因子
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
·
2023
·Vol. 30
·期 19
·56108-56120
·
IF 5.8
Zhou Changrui,Gao Yun,Ma Qiang,Xia Zhuqing,Zhu Mengmeng,Zhang Xinhui,An Siyu,Li Shuailin,Yu Wantai
The coexistence of antibiotics and heavy metals in soil has attracted increasing attention due to their negative effects on microorganisms. However, how antibiotics and heavy metals affect functional microorganisms related to nitrogen cycle remains unclear. The goals of this work were to explore the individual and combined effects of sulfamethazine (SMT) and cadmium (Cd), selected as target pollutants in soil, on potential nitrification rates (PNR) and ammonia oxidizers (ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB)) structure and diversity by 56-day cultivation experiment. Results showed that PNR in Cd- or SMT-treated soil decreased at the beginning of the experiment and then increased over time. PNR was significantly correlated with AOA and AOB- amoA relative abundance ( P < 0.01). SMT addition (10 and 100 mg kg −1 ) significantly improved AOA activity by 13.93% and 17.93%, respectively, and had no effect on AOB at day 1. Conversely, Cd at 10 mg kg −1 significantly inhibited AOA and AOB by 34.34% and 37.39%, respectively. Moreover, the relative abundance of AOA and AOB in combined SMT and Cd addition clearly higher relative to single Cd at 1 day. The single and combined Cd and SMT increased and reduced the community richness of AOA and AOB, respectively, but reduced the diversity of both after 56 days. Cd and SMT treatments significantly changed the relative abundance of AOA phylum levels and AOB genus levels in the soil. It was mainly manifested in reducing the relative abundance of AOA Thaumarchaeota , and increasing the relative abundance of AOB Nitrosospira. Besides, AOB Nitrosospira was more tolerant to the compound addition of both than single application. Graphical abstract
研究领域:
环境科学
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微生物学
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土壤学
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产品关联
DOI
PubMed
高影响因子
BIOLOGY AND FERTILITY OF SOILS
·
2021
·Vol. 57
·期 3
·399-407
·
IF 6.432
Li Yaying,Zhang Yang,Chapman Stephen James,Yao Huaiying
Sorghum has a great capacity to release biological nitrification inhibitors (BNIs), but the inhibitory effect on nitrification and ammonia oxidizer populations under planted soil conditions is unclear. A pot experiment with three nitrogen (N) application rates (0, 50, and 200 mg N kg −1 ) was set up to detect the influence of sorghum growth on soil nitrification and investigate the function of blocking the activity of ammonia oxidizers. A 15 N-labeled experiment was also conducted to detect the N form absorbed by sorghum. Sorghum root exudates were collected at 30 days after transplanting to hydroponic culture and added into cultured soil to determine the shifts in the populations of nitrifiers. The 15 N labeling experiment showed that the uptake rate by sorghum of ammonium N fertilizer was 24% and that of nitrate N fertilizer was 9%, indicating that sorghum was an ammonium using plant. Compared with unplanted soil, sorghum planting had a significant inhibitory effect on the nitrification process even at the high-N fertilizer rates. Autotrophic nitrification was the prevailing process, and sorghum root exudation inhibited this process as much as dicyandiamide (DCD, 10 mg kg −1 ). Root exudates had a significant inhibitory effect on ammonia-oxidizing bacteria (AOB) but had no effect on ammonia-oxidizing archaea (AOA).
研究领域:
土壤微生物学
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植物生理学
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环境科学
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农学
✓ 已验证
DOI
高影响因子
ENVIRONMENTAL MICROBIOLOGY
·
2019
·Vol. 22
·期 1
·329-342
·
IF 5.147
Wei-Wei Liu,Jie Pan,Xiaoyuan Feng,Meng Li,Ying Xu,Fengping Wang,Ning-Yi Zhou
Summary Thermoprofundales (Marine Benthic Group D archaea, MBG-D) is a newly proposed archaeal order and widely distributed in global marine sediment, and the members in the order may play a vital role in carbon cycling. However, the lack of pure cultures of these oeganisms has hampered the recognition of their catabolic roles. Here, by constructing high-quality metagenome-assembled genomes (MAGs) of two new subgroups of Thermoprofundales from hydrothermal sediment and predicting their catabolic pathways, we here provide genomic evidences that Thermoprofundales are capable of degrading aromatics via the phenylacetic acid (PAA) pathway. Then, the gene sequences of phenylacetyl-CoA ligase (PCL), a key enzyme for the PAA pathway, were searched in reference genomes. The widespread distribution of PCL genes among 14.9% of archaea and 75.9% of Thermoprofundales further supports the importance of the PAA pathway in archaea, particularly in Thermoprofundales where no ring-cleavage dioxygenases were found. Two PCLs from Thermoprofundales MAGs, PCL M8-3 and PCL M10-15 , were able to convert PAA to phenylacetyl-CoA (PA-CoA) in vitro , demonstrating the involvement of Thermoprofundales in aromatics degradation through PAA via CoA activation. Their acid tolerance (pH 5–7), high-optimum temperatures (60°C and 80°C), thermostability (stable at 60°C and 50°C for 48 h) and broad substrate spectra imply that Thermoprofundales are capable of transforming aromatics under extreme conditions. Together with the evidence of in situ transcriptional activities for most genes related to the aromatics pathway in Thermoprofundales, these genomic, and biochemical evidences highlight the essential role of this ubiquitous and abundant archaeal order in the carbon cycle of marine sediments.
研究领域:
微生物学
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环境科学
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基因组学
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产品关联
DOI
PubMed
高影响因子
Environmental Technology & Innovation
·
2024
·
IF 6.7
Hanjie Zhang,Zhuang Ye,Xiuping Gu,Baowei Hu,Steve A. Wakelin,Guixin Chu
Di-(2-ethylhexyl) phthalate (DEHP) has increasingly accumulated in soils due to DEHP-containing plastic film has been extensively used in agriculture. However, the exposure of DEHP on calcareous soil nitrification potential, ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are poorly investigated. Here, an incubation experiment was established containing four treatments:(ⅰ) unfertilized blank control, (ⅱ) urea addition alone, (ⅲ) urea plus DEHP (10 mg kg -1 ), (ⅳ) urea plus DEHP (100 mg kg -1 ). The influences of DEHP exposure on soil NH 4 + -N, NO 3 - -N, soil potential nitrification rate (PNR), ammonia monooxygenase (AMO) activity, AOA and AOB were analyzed. We found that DEHP exposure (10 and 100 mg kg -1 ) lowered NO 3 - -N in the treatments of urea plus DEHP 10 and urea plus DEHP 100 , and it significantly decreased soil PNR and AMO activity. Also, the exposure of DEHP reduced the numbers of AOA and AOB gene copies, and decreased AOB community’s α-diversity. Moreover, DEHP exposure destabilized AOB community’s co-occurrence network and decreased key module abundance, but its influences on AOA community was not significant. Taken together, the exposure of DEHP inhibited PNR in a calcareous soil through decreasing AOB gene copies and weakening the co-occurrence network of AOB community. Our findings provide a novel insights into microbial mechanisms about the detrimental effects of DEHP pollution on soil PNR and nitrification process in calcareous soil.
研究领域:
环境科学
·
土壤微生物学
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生态毒理学
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产品关联
DOI
高影响因子
SCIENCE OF THE TOTAL ENVIRONMENT
·
2023
·
IF 9.8
Sai Xu,Xinyi Zhang,Yuxiang Zhu
Anaerobic oxidation of methane coupled to nitrous oxide reduction (N 2 O-AOM) is an important microbial pathway for mitigating greenhouse gases. However, it remains largely unknown whether this process could occur in landfills, which are important anthropogenic sources of greenhouse gases emissions. Here, 13 CH 4 was supplied in microcosm incubations to track potential rates for the N 2 O-AOM process in landfill cover soils (LCS). The highest rates for the N 2 O-AOM process were observed in the bottom layers of LCS and it could be remarkably promoted by the addition of electron shuttles. In addition, 2-bromoethanesulfonic sodium inhibited the N 2 O-AOM process and reduced the expression of the mcr A gene, showing that ANME archaea/methanogens might be the methane oxidizers for the N 2 O-AOM process. Our results implied that the N 2 O-AOM process was an overlooked process for synchronous control of methane and nitrous oxide and may contribute to the future management of greenhouse gases emissions from landfills.
研究领域:
环境微生物学
·
土壤学
·
气候变化研究
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产品关联
DOI
PubMed
高影响因子
ENVIRONMENTAL RESEARCH
·
2024
·
IF 7.7
HeLang Huang,CaiYun Xie,ZiYuan Xia,ZhaoYong Sun,YaTing Chen,Min Gou,YueQin Tang,HengLin Cui,XiaoLei Wu
Haloarchaea with the capacity to degrade alkanes is promising to deal with petroleum pollution in hypersaline environments. However, only a limited number of haloarchaeal species are investigated, and their pathway and mechanism for alkane degradation remain unclear. In this study, Halogranum rubrum RO2-11, a haloarchaeal strain, verified the ability to degrade kerosene and hexadecane in 184 g/L NaCl, with a 53% degradation rate after 9 and 4 days, respectively. Genome sequencing and gene annotation indicated that strain RO2-11 possesses a complete potential alkane-degrading pathway, of which alkane hydroxylases may include CYP450, AlmA, and LadA. Transcriptome and metabolome analyses revealed that the upregulation of related genes in TCA cycle, lysine biosynthesis, and acetylation may help improve hexadecane degradation. Additionally, an alternative degrading pathway of hexadecane based on dual-terminal β -oxidation may occur in strain RO2-11. It is likely to be the first report of alkane degradation by the genus Halogranum , which may be helpful for applications of oil-pollution bioremediation under high-salt conditions.
研究领域:
微生物学
·
环境科学
·
基因组学
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转录组学
·
代谢组学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
CHEMICAL ENGINEERING JOURNAL
·
2024
·
IF 13.3
Jie Ma,Linhui Lei,Zhiwei Gong,Zongping Wang,Hui Liu,Guanghao Chen,Gang Guo
The efficacy of in-situ bioremediation of chlorinated ethenes (CEs)-contaminated groundwater is heavily contingent upon the provision of exogenous electron donors to facilitate reductive dechlorination by dechlorinating bacteria. Nonetheless, methanogenic archaea have been reported to engender competition for the limited electron donor supply, thereby diminishing dechlorination efficiency. This study proposes a novel strategy to enhance reductive dechlorination by reducing the particle size of polyhydroxyalkanoate (PHA) to the micrometer scale, thereby inhibiting methanogenic competition for electron donors. The results demonstrate that trichloroethylene (TCE) biodegradation efficiency peaked at a PHA particle size of 500 μm, significantly surpassing the efficiency observed in groups with particle sizes of 50 and 2000 μm. Furthermore, the electron utilization efficiency of dechlorinating bacteria (represented by Geobacter , Dehalobacter , Anaerolinea , etc in this study) was as high as 94.82 % over methanogenic archaea (represented by Methanobacterium ) in the 500 μm group. Mechanistic analyses revealed that the 500 μm PHA particles activated dark oxygen, leading to the generation of reactive oxygen species that decreased the abundance of the methanogenic functional gene McrA and increased the abundance of dechlorinating functional gene TceA relative to the total microbial genome gene (in terms of 16S rRNA). In contrast, PHA particles of 50 μm exhibited lower TCE biodegradation efficiency due to particle aggregation, while particles of 2000 μm exhibited reduced efficiency due to lower specific surface area. This study moves a step for the in-situ microbial remediation of CEs-contaminated groundwater.
研究领域:
环境科学
·
生物修复
·
微生物学
·
化学工程
✓ 已验证
产品关联
DOI
高影响因子
CHEMICAL ENGINEERING JOURNAL
·
2023
·
IF 15.1
Xiangyu Yang,Fucheng Guo,Tao Liu,Qiang He,Jan Vymazal,Yi Chen
Ammonia-oxidizing microorganisms (AOMs, archaea (AOA) and bacteria (AOB)) are primarily responsible for the ammoxidation in constructed wetlands (CWs). However, little is known about evaluating the response of AOA and AOB to engineered nanomaterials (ENMs) and quantifying the shift of their contribution to ammoxidation. Herein, we operated a series of CWs exposing to silver nanoparticles (Ag-NPs), single-walled carbon nanotubes (SWCNTs), and polystyrene nano-sized plastics (PS-NPs) with the wastewater-accumulating concentration of ENMs for 180 days. The results showed that the abundance of AOA amo A gene in situ was far lower than that of AOB, while the abundance ratio of AOA to AOB increased by 15 folds after 180-day experiment. Using DNA stable isotope probing (DNA-SIP) experiment, we found that the active AOB microbiota varied substantially but the AOA was more stable across different groups. Furthermore, the co-occurrence analysis proved that ENMs stress increased the negative coexistence pattern of AOA and AOB; predictive functional profiling showed that the ENMs enhanced the functional advantage of AOA by inhibiting AOB (mainly hydroxylamine oxidation process). Finally, the contribution of AOA increased under exposing to SWCNTs (18.35%), PS-NPs (24.92%), and Ag-NPs (32.14%) compared with control group (0.03%) for 180 days. Despite this, AOB was still the primary executant of ammoxidation in CWs. Overall, in our study, the differences in activities and contributions of AOMs were quantified in CWs, and a significantly negative coexistence relationship between AOA and AOB was revealed when exposed to emerging nanomaterials.
研究领域:
环境微生物学
·
生态毒理学
·
废水处理
·
纳米技术
✓ 已验证
DOI
高影响因子
危险品化学品经营许可证（带存储）