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Wang J, Yao H, Zhang X. The effect of the 13C abundance of soil microbial DNA on identifying labelled fractions after ultracentrifugation. Appl Microbiol Biotechnol 2024; 108:318. [PMID: 38700733 PMCID: PMC11068677 DOI: 10.1007/s00253-024-13151-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 01/17/2024] [Accepted: 04/16/2024] [Indexed: 05/06/2024]
Abstract
DNA-based stable isotope probing (DNA-SIP) technology has been widely employed to trace microbes assimilating target substrates. However, the fractions with labelled universal genes are sometimes difficult to distinguish when detected by quantitative real-time PCR. In this experiment, three paddy soils (AQ, CZ, and NB) were amended with 0.1% glucose containing 13C at six levels, and DNA was then extracted after a 7-day incubation and subjected to isopycnic gradient centrifugation. The results showed that the amount of labelled DNA was notably related to the 13C-glucose percentage, while the separation spans of 18S rRNA and 16S rRNA genes between labelled and unlabelled treatments became notably clearer when the δ13C values of the total DNA were 90.9, 61.6, and 38.9‰ and 256.2, 104.5 and 126.1‰ in the AQ, CZ, and NB soils, respectively. Moreover, fractionated DNA was also labelled by determining the δ13C values while adding only 5 atom% 13C-glucose to the soil. The results suggest that the optimal labelling fractions were not always those fractions with the maximal gene abundance, and detecting the δ13C values of the total and fractionated DNA was beneficial in estimating the results of DNA-SIP. KEY POINTS: • Appropriate 13C-DNA amount was needed for DNA-SIP. • Detecting the 13C ratio of fractionated DNA directly was an assistant method for identifying the labelled fractions. • Fractions with the maximal 18S or 16S rRNA gene abundance always were not labelled.
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Affiliation(s)
- Juan Wang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo, China
| | - Huaiying Yao
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, China.
| | - Xian Zhang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
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2
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Chen Y, Ren H, Kong X, Wu H, Lu Z. A multicomponent propane monooxygenase catalyzes the initial degradation of methyl tert-butyl ether in Mycobacterium vaccae JOB5. Appl Environ Microbiol 2023; 89:e0118723. [PMID: 37823642 PMCID: PMC10617536 DOI: 10.1128/aem.01187-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/30/2023] [Indexed: 10/13/2023] Open
Abstract
Methyl tert-butyl ether (MTBE) has been recognized as a groundwater contaminant due to its widespread distribution and potential threat to human health. The limited understanding of the enzymes catalyzing MTBE degradation restricts their application in MTBE bioremediation. In this study, an MTBE-degrading soluble di-iron monooxygenase that clusters phylogenetically with a known propane monooxygenase (PRM) encoded by the prmABCD gene cluster was identified and functionally characterized, revealing their role in MTBE metabolism by Mycobacterium vaccae JOB5. Transcriptome analysis demonstrated that the expression of prmABCD was upregulated when JOB5 was induced by MTBE. Escherichia coli Rosetta heterologously expressing prmABCD from JOB5 could transform MTBE, indicating that the PRM of JOB5 is capable of the initial degradation of MTBE. The loss of the gene encoding the oxygenase α-subunit or β-subunit, the coupling protein, or the reductase disrupted MTBE transformation by the recombinant E. coli Rosetta. In addition, the catalytic capacity of PRM is likely affected by residue G95 in the active site pocket and residues I84, P165, A269, and V270 in the substrate tunnel structure. Mutation of amino acids in the active site and substrate tunnel resulted in inefficiency or inactivation of MTBE degradation, and the activity in 1,4-dioxane (1,4-D) degradation was diminished less than that in MTBE degradation.IMPORTANCEMulticomponent monooxygenases catalyzing the initial hydroxylation of MTBE are important in MTBE biodegradation. Previous studies of MTBE degradation enzymes have focused on P450s, alkane monooxygenase and MTBE monooxygenase, but the vital role of soluble di-iron monooxygenases has rarely been reported. In this study, we deciphered the essential catalytic role of a PRM and revealed the key residues of the PRM in MTBE metabolism. Our findings provide new insight into the MTBE-degrading gene cluster and enzymes in bacteria. This characterization of the PRM associated with MTBE degradation expands our understanding of MTBE-degrading gene diversity and provides a novel candidate enzyme for the bioremediation of MTBE-contaminated sites.
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Affiliation(s)
- Yiyang Chen
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hao Ren
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiangyu Kong
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hao Wu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhenmei Lu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
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3
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Wang X, Xu T, Zhang X, Zhao N, Hu L, Liu H, Zhang Q, Geng Y, Kang S, Xu S. The Response of Ruminal Microbiota and Metabolites to Different Dietary Protein Levels in Tibetan Sheep on the Qinghai-Tibetan Plateau. Front Vet Sci 2022; 9:922817. [PMID: 35847641 PMCID: PMC9277223 DOI: 10.3389/fvets.2022.922817] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 05/31/2022] [Indexed: 11/13/2022] Open
Abstract
Ruminal microbiota and metabolites play crucial roles in animal health and productivity. Exploring the dynamic changes and interactions between microbial community composition and metabolites is important for understanding ruminal nutrition and metabolism. Tibetan sheep (Ovis aries) are an important livestock resource on the Qinghai-Tibetan Plateau (QTP), and the effects of various dietary protein levels on ruminal microbiota and metabolites are still unknown. The aim of this study was to investigate the response of ruminal microbiota and metabolites to different levels of dietary protein in Tibetan sheep. Three diets with different protein levels (low protein 10.1%, medium protein 12.1%, and high protein 14.1%) were fed to Tibetan sheep. 16S rRNA gene sequencing and gas chromatography coupled with time-of-flight mass spectrometry (GC-TOF-MS) were used to study the profile changes in each group of ruminal microbes and metabolites, as well as the potential interaction between them. The rumen microbiota in all groups was dominated by the phyla Bacteroidetes and Firmicutes regardless of the dietary protein level. At the genus level, Prevotella_1, Rikenellaceae_RC9_gut_group and Prevotellaceae_UCG-001 were dominant. Under the same forage-to-concentrate ratio condition, the difference in the dietary protein levels had no significant impact on the bacterial alpha diversity index and relative abundance of the major phyla and genera in Tibetan sheep. Rumen metabolomics analysis revealed that dietary protein levels altered the concentrations of ruminal amino acids, carbohydrates and organic acids, and significantly affected tryptophan metabolism (p < 0.05). Correlation analysis of the microbiota and metabolites revealed positive and negative regulatory mechanisms. Overall, this study provides detailed information on rumen microorganisms and ruminal metabolites under different levels of dietary protein, which could be helpful in subsequent research for regulating animal nutrition and metabolism through nutritional interventions.
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Affiliation(s)
- Xungang Wang
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Tianwei Xu
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Xiaoling Zhang
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Na Zhao
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Linyong Hu
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Hongjin Liu
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Qian Zhang
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yuanyue Geng
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Shengping Kang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Shixiao Xu
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
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4
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Host genetics and gut microbiota cooperatively contribute to azoxymethane-induced acute toxicity in Collaborative Cross mice. Arch Toxicol 2021; 95:949-958. [PMID: 33458792 DOI: 10.1007/s00204-021-02972-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/04/2021] [Indexed: 12/19/2022]
Abstract
Azoxymethane (AOM) is a widely used carcinogen to study chemical-induced colorectal carcinogenesis and is an agent for studying fulminant hepatic failure. The inter-strain susceptibility to acute toxicity by AOM has been reported, but its association with host genetics or gut microbiota remains largely unexplored. Here a cohort of genetically diverse Collaborative Cross (CC) mice was used to assess the contribution of host genetics and the gut microbiome to AOM-induced acute toxicity. We observed variation in AOM-induced acute liver failure across CC strains. Quantitative trait loci (QTL) analysis revealed three chromosome regions significantly associated with AOM toxicity. Genes located within these QTL, including peroxisome proliferator-activated receptor alpha (Ppara), were enriched for enzyme activator and nucleoside-triphosphatase regulator activity. We further demonstrated that the protein level of PPARα in liver tissues from sensitive strains was remarkably lower compared to levels in resistant strains, consistent with protective role of PPAR family in liver injury. We discovered that the abundance levels of gut microbial families Anaeroplasmataceae, Ruminococcaceae, Lactobacillaceae, Akkermansiaceae and Clostridiaceae were significantly higher in the sensitive strains compared to the resistant strains. Using a random forest classifier method, we determined that the relative abundance levels of these microbial families predicted AOM toxicity with the area under the receiver-operating curve (AUC) of 0.75. Combining the three genetic loci and five microbial families increased the predictive accuracy of AOM toxicity (AUC of 0.99). Moreover, we found that Ruminococcaceae and Lactobacillaceae acted as mediators between host genetics and AOM toxicity. In conclusion, this study shows that host genetics and specific microbiome members play a critical role in AOM-induced acute toxicity, which provides a framework for analysis of the health effects from environmental toxicants.
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5
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Hidalgo KJ, Saito T, Silva RS, Delforno TP, Duarte ICS, de Oliveira VM, Okada DY. Microbiome taxonomic and functional profiles of two domestic sewage treatment systems. Biodegradation 2020; 32:17-36. [PMID: 33230597 DOI: 10.1007/s10532-020-09921-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 11/17/2020] [Indexed: 11/26/2022]
Abstract
Anaerobic systems for domestic sewage treatment, like septic tanks and anaerobic filters, are used in developing countries due to favorable economic and functional features. The anaerobic filter is used for the treatment of the septic tank effluent, to improve the COD removal efficiency of the system. The microbial composition and diversity of the microbiome from two wastewater treatment systems (factory and rural school) were compared through 16S rRNA gene sequencing using MiSeq 2 × 250 bp Illumina sequencing platform. Additionally, 16S rRNA data were used to predict the functional profile of the microbial communities using PICRUSt2. Results indicated that hydrogenotrophic methanogens, like Methanobacterium, were found in higher abundance in both systems compared to acetotrophic methanogens belonging to Methanosaeta genus. Also, important syntrophic microorganisms (Smithella, Syntrophus, Syntrophobacter) were found in the factory and rural school wastewater treatment systems. Microbial communities were also compared between stages (septic tank and anaerobic filter) of each wastewater treatment stage, revealing that, in the case of the rural school, both microbial communities were quite similar most likely due to hydraulic short-circuit issues. Meanwhile, in the factory, microbial communities from the septic tank and anaerobic filter were different. The school system showed lower COD removal rates (2-30%), which were probably related to a higher abundance of Firmicutes members in addition to the hydraulic short-circuit and low abundance of Chloroflexi members. On the other hand, the fiberglass factory presented higher COD removal rates (60-83%), harboring phyla reported as the core microbiome of anaerobic digesters (Bacteroidetes, Chloroflexi, and Proteobacteria phyla). The knowledge of the structure and composition of wastewater treatment systems may provide support for the improvement of the pollutant removal in anaerobic process.
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Affiliation(s)
- K J Hidalgo
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), Campinas University - UNICAMP, Campinas, SP, CEP 13081-970, Brazil.
| | - T Saito
- Division of Technology in Environment Sanitation, School of Technology, Campinas University - UNICAMP, Limeira, SP, CEP 13484-332, Brazil
| | - R S Silva
- Division of Technology in Environment Sanitation, School of Technology, Campinas University - UNICAMP, Limeira, SP, CEP 13484-332, Brazil
| | - Tiago P Delforno
- Department of Biology (DBio), Federal University of São Carlos (UFSCar), Sorocaba, Brazil
| | - Iolanda C S Duarte
- Department of Biology (DBio), Federal University of São Carlos (UFSCar), Sorocaba, Brazil
| | - V M de Oliveira
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), Campinas University - UNICAMP, Campinas, SP, CEP 13081-970, Brazil
| | - Dagoberto Y Okada
- Division of Technology in Environment Sanitation, School of Technology, Campinas University - UNICAMP, Limeira, SP, CEP 13484-332, Brazil
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Dam HT, Sun W, McGuinness L, Kerkhof LJ, Häggblom MM. Identification of a Chlorodibenzo- p-dioxin Dechlorinating Dehalococcoides mccartyi by Stable Isotope Probing. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:14409-14419. [PMID: 31765134 DOI: 10.1021/acs.est.9b05395] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Polychlorinated dibenzo-p-dioxins (PCDDs) are released into the environment from a variety of both anthropogenic and natural sources. While highly chlorinated dibenzo-p-dioxins are persistent under oxic conditions, in anoxic environments, these organohalogens can be reductively dechlorinated to less chlorinated compounds that are then more amenable to subsequent aerobic degradation. Identifying the microorganisms responsible for dechlorination is an important step in developing bioremediation approaches. In this study, we demonstrated the use of a DNA-stable isotope probing (SIP) approach to identify the bacteria active in dechlorination of PCDDs in river sediments, with 1,2,3,4-tetrachlorodibenzo-p-dioxin (1,2,3,4-TeCDD) as a model. In addition, pyrosequencing of reverse transcribed 16S rRNA of TeCDD dechlorinating enrichment cultures was used to reveal active members of the bacterial community. A set of operational taxonomic units (OTUs) responded positively to the addition of 1,2,3,4-TeCDD in SIP microcosms assimilating 13C-acetate as the carbon source. Analysis of bacterial community profiles of the 13C labeled heavy DNA fraction revealed that an OTU corresponding to Dehalococcoides mccartyi accounted for a significantly greater abundance in cultures amended with 1,2,3,4-TeCDD than in cultures without 1,2,3,4-TeCDD. This implies the involvement of this Dehalococcoides mccartyi strain in the reductive dechlorination of 1,2,3,4-TeCDD and suggests the applicability of SIP for a robust assessment of the bioremediation potential of organohalogen contaminated sites.
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Affiliation(s)
- Hang T Dam
- Department of Biochemistry and Microbiology, Rutgers , The State University of New Jersey , New Brunswick , New Jersey 08901 , United States
- Institute for Biological Interfaces 5 (IBG 5) , Karlsruhe Institute of Technology (KIT) , Eggenstein-Leopoldshafen 76344 , Germany
| | - Weimin Sun
- Department of Biochemistry and Microbiology, Rutgers , The State University of New Jersey , New Brunswick , New Jersey 08901 , United States
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management , Guangdong Institute of Eco-Environmental Science & Technology , Guangzhou 510650 , China
| | - Lora McGuinness
- Department of Marine and Coastal Sciences, Rutgers , The State University of New Jersey , New Brunswick , New Jersey 08901 , United States
| | - Lee J Kerkhof
- Department of Marine and Coastal Sciences, Rutgers , The State University of New Jersey , New Brunswick , New Jersey 08901 , United States
| | - Max M Häggblom
- Department of Biochemistry and Microbiology, Rutgers , The State University of New Jersey , New Brunswick , New Jersey 08901 , United States
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7
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Tian Y, Zhang H, Zheng L, Li S, Hao H, Huang H. Effect of Zn Addition on the Cd-Containing Anaerobic Fermentation Process: Biodegradation and Microbial Communities. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16162998. [PMID: 31434308 PMCID: PMC6720270 DOI: 10.3390/ijerph16162998] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/14/2019] [Accepted: 08/16/2019] [Indexed: 12/20/2022]
Abstract
Anaerobic fermentation is considered as a cost-effective way of biomass waste disposal. However, the compound heavy metals contained in the biomass may induce complex effects on anaerobic fermentation, which limit the utilization of metal-contaminated biowaste. In this study, the impacts of Cd and Zn addition on biogas properties, process stability, substrate biodegradation, enzyme activity, and microbial properties were studied. The results showed that the addition of Cd together with Zn (Cd+Zn) increased the maximum daily and cumulative biogas yields, and brought forward the gas production peak compared with the Cd-added group. Taking the whole fermentation process into account, the promotion effects of adding Zn into the Cd-containing fermentation system on biogas yields were mainly attributable to better process stability, higher average NH4+-N concentration in the later stage of fermentation, reduced COD (p < 0.05), and increased biodegradability of lignocelluloses (p < 0.01), especially cellulose (p < 0.05) and lignin (p < 0.01). Meanwhile, the addition of Zn promoted the coenzyme M activity (p < 0.05), and increased the absolute abundance of Methanothermobacter. The bacteria communities during the fermentation process were responsible for the degradation of lignocelluloses. The results demonstrated that the addition of appropriate Zn into the Cd-containing fermentation system enhanced the efficiency of anaerobic fermentation and utilization of biowaste.
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Affiliation(s)
- Yonglan Tian
- Research Center for Engineering Ecology and Nonlinear Science, North China Electric Power University, Beijing 102206, China
| | - Huayong Zhang
- Research Center for Engineering Ecology and Nonlinear Science, North China Electric Power University, Beijing 102206, China.
| | - Lei Zheng
- Research Center for Engineering Ecology and Nonlinear Science, North China Electric Power University, Beijing 102206, China
| | - Shusen Li
- Research Center for Engineering Ecology and Nonlinear Science, North China Electric Power University, Beijing 102206, China
| | - He Hao
- Research Center for Engineering Ecology and Nonlinear Science, North China Electric Power University, Beijing 102206, China
| | - Hai Huang
- Research Center for Engineering Ecology and Nonlinear Science, North China Electric Power University, Beijing 102206, China
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8
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Zhan YY, Wan YF, Su MJ, Luo Y, Chu GW, Zhang LL, Chen JF. Spent Caustic Regeneration in a Rotating Packed Bed: Reaction and Separation Process Intensification. Ind Eng Chem Res 2019. [DOI: 10.1021/acs.iecr.9b02664] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuan-Yuan Zhan
- State Key Laboratory of Organic−Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029, P.R. China
- Research Center of the Ministry of Education for High Gravity Engineering and Technology, Beijing University of Chemical Technology, Beijing 100029, P.R. China
| | - Yuan-Fang Wan
- College of Mechanical and Electrical Engineering, Beijing University of Chemical Technology, Beijing 100029, P.R. China
| | - Meng-Jun Su
- State Key Laboratory of Organic−Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029, P.R. China
- Research Center of the Ministry of Education for High Gravity Engineering and Technology, Beijing University of Chemical Technology, Beijing 100029, P.R. China
| | - Yong Luo
- State Key Laboratory of Organic−Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029, P.R. China
- Research Center of the Ministry of Education for High Gravity Engineering and Technology, Beijing University of Chemical Technology, Beijing 100029, P.R. China
| | - Guang-Wen Chu
- State Key Laboratory of Organic−Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029, P.R. China
- Research Center of the Ministry of Education for High Gravity Engineering and Technology, Beijing University of Chemical Technology, Beijing 100029, P.R. China
| | - Liang-Liang Zhang
- State Key Laboratory of Organic−Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029, P.R. China
- Research Center of the Ministry of Education for High Gravity Engineering and Technology, Beijing University of Chemical Technology, Beijing 100029, P.R. China
| | - Jian-Feng Chen
- State Key Laboratory of Organic−Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029, P.R. China
- Research Center of the Ministry of Education for High Gravity Engineering and Technology, Beijing University of Chemical Technology, Beijing 100029, P.R. China
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9
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Process Analysis of Anaerobic Fermentation Exposure to Metal Mixtures. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16142458. [PMID: 31295944 PMCID: PMC6678117 DOI: 10.3390/ijerph16142458] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/08/2019] [Accepted: 07/08/2019] [Indexed: 01/23/2023]
Abstract
Anaerobic fermentation is a cost-effective biowaste disposal approach. During fermentation, microorganisms require a trace amount of metals for optimal growth and performance. This study investigated the effects of metal mixtures on biogas properties, process stability, substrate degradation, enzyme activity, and microbial communities during anaerobic fermentation. The addition of iron (Fe), nickel (Ni), and zinc (Zn) into a copper (Cu)-stressed fermentation system resulted in higher cumulative biogas yields, ammonia nitrogen (NH4+-N) concentrations and coenzyme F420 activities. Ni and Zn addition enhanced process stability and acetate utilization. The addition of these metals also improved and brought forward the peak daily biogas yields as well as increased CH4 content to 88.94 and 86.58%, respectively. Adding Zn into the Cu-stressed system improved the abundance of Defluviitoga, Fibrobacter and Methanothermobacter, the degradation of cellulose, and the transformation of CO2 to CH4. The bacterial and archaeal communities were responsible for the degradation of lignocelluloses and CH4 production during the fermentation process. This study supports the reutilization of heavy metal-contaminated biowaste and provides references for further research on heavy metals impacted anaerobic fermentation.
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Cupit C, Lomstein BA, Kjeldsen KU. Contrasting community composition of endospores and vegetative Firmicutes in a marine sediment suggests both endogenous and exogenous sources of endospore accumulation. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:352-360. [PMID: 30043505 DOI: 10.1111/1758-2229.12679] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 07/09/2018] [Accepted: 07/12/2018] [Indexed: 06/08/2023]
Abstract
Bacterial endospores are highly abundant in marine sediments, but their taxonomic identity and ecology is largely unknown. We selectively extracted DNA from endospores and vegetative cells and sequenced 16S rRNA genes to characterize the composition of the endospore and vegetative Firmicutes communities in the sediment and water column of Aarhus Bay (Denmark). The endospore community in the sediment was dominated by the families Bacillaceae, Lachnospiraceae, Clostridiaceae and Ruminoccocaceae. These families were also represented in the vegetative community in the sediment and the endospore community in the water column. OTUs of high relative abundance in the endospore community were also represented in the vegetative Firmicutes community. Other OTUs were exclusively found in the endospore communities. This suggests that endospores accumulate in marine sediments due to passive deposition from the water column and sporulation of vegetative cells in the sediment. Some OTUs were detected in the endospore community of the water column and the vegetative community the sediment indicating that endospores deposited from the water column may germinate upon burial/deposition in the sediment. We provide novel insight into the composition of endospore communities in marine sediments and highlight their role in microbial dispersal and as a seed bank in subsurface sediments.
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Affiliation(s)
- Carina Cupit
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Bente Aagaard Lomstein
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Kasper Urup Kjeldsen
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
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11
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Zhang B, Xu X, Zhu L. Activated sludge bacterial communities of typical wastewater treatment plants: distinct genera identification and metabolic potential differential analysis. AMB Express 2018; 8:184. [PMID: 30430271 PMCID: PMC6236004 DOI: 10.1186/s13568-018-0714-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 11/07/2018] [Indexed: 12/26/2022] Open
Abstract
To investigate the differences in activated sludge microbial communities of different wastewater treatment plants (WWTPs) and understand their metabolic potentials, we sampled sludge from every biological treatment unit of 5 full-scale waste water treatment systems in 3 typical Chinese municipal WWTPs. The microbial communities and overall metabolic patterns were not only affected by influent characteristics but also varied between different biological treatment units. Distinct genera in different wastewater treatment systems were identified. The important microorganisms in domestic sewage treatment systems were unclassified SHA-20, Caldilinea, Dechloromonas, and unclassified genera from Rhodospirilaceae and Caldilineaceae. The important microorganisms in dyeing wastewater treatment systems were Nitrospira, Sphingobacteriales, Thiobacillus, Sinobacteraceae and Comamonadaceae. Compared with the obvious differences in microbial community composition, the metabolic potential showed no significant differences.
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12
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van der Waals MJ, Pijls C, Sinke AJC, Langenhoff AAM, Smidt H, Gerritse J. Anaerobic degradation of a mixture of MtBE, EtBE, TBA, and benzene under different redox conditions. Appl Microbiol Biotechnol 2018; 102:3387-3397. [PMID: 29478141 PMCID: PMC5852185 DOI: 10.1007/s00253-018-8853-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 02/08/2018] [Accepted: 02/10/2018] [Indexed: 11/30/2022]
Abstract
The increasing use of biobased fuels and fuel additives can potentially change the typical fuel-related contamination in soil and groundwater. Anaerobic biotransformation of the biofuel additive ethyl tert-butyl ether (EtBE), as well as of methyl tert-butyl ether (MtBE), benzene, and tert-butyl alcohol (TBA, a possible oxygenate metabolite), was studied at an industrially contaminated site and in the laboratory. Analysis of groundwater samples indicated that in the field MtBE was degraded, yielding TBA as major product. In batch microcosms, MtBE was degraded under different conditions: unamended control, with medium without added electron acceptors, or with ferrihydrite or sulfate (with or without medium) as electron acceptor, respectively. Degradation of EtBE was not observed under any of these conditions tested. TBA was partially depleted in parallel with MtBE. Results of microcosm experiments with MtBE substrate analogues, i.e., syringate, vanillate, or ferulate, were in line with the hypothesis that the observed TBA degradation is a cometabolic process. Microcosms with ferulate, syringate, isopropanol, or diethyl ether showed EtBE depletion up to 86.5% of the initial concentration after 83 days. Benzene was degraded in the unamended controls, with medium without added electron acceptors and with ferrihydrite, sulfate, or chlorate as electron acceptor, respectively. In the presence of nitrate, benzene was only degraded after addition of an anaerobic benzene-degrading community. Nitrate and chlorate hindered MtBE, EtBE, and TBA degradation.
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Affiliation(s)
- Marcelle J van der Waals
- Deltares, Subsurface and Groundwater Systems, Daltonlaan 600, 3584 BK, Utrecht, the Netherlands. .,Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, the Netherlands.
| | - Charles Pijls
- Tauw, Handelskade 37, 7400 AC, Deventer, the Netherlands
| | - Anja J C Sinke
- BP International Limited, Sunbury on Thames, Middlesex, TW167BP, UK
| | - Alette A M Langenhoff
- Department of Environmental Technology, Wageningen University & Research, Bornse Weilanden 9, 6708 WG, Wageningen, the Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, the Netherlands
| | - Jan Gerritse
- Deltares, Subsurface and Groundwater Systems, Daltonlaan 600, 3584 BK, Utrecht, the Netherlands
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13
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Sun W, Krumins V, Dong Y, Gao P, Ma C, Hu M, Li B, Xia B, He Z, Xiong S. A Combination of Stable Isotope Probing, Illumina Sequencing, and Co-occurrence Network to Investigate Thermophilic Acetate- and Lactate-Utilizing Bacteria. MICROBIAL ECOLOGY 2018; 75:113-122. [PMID: 28669057 DOI: 10.1007/s00248-017-1017-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 06/12/2017] [Indexed: 06/07/2023]
Abstract
Anaerobic digestion is a complicated microbiological process that involves a wide diversity of microorganisms. Acetate is one of the most important intermediates, and interactions between acetate-oxidizing bacteria and archaea could play an important role in the formation of methane in anoxic environments. Anaerobic digestion at thermophilic temperatures is known to increase methane production, but the effects on the microbial community are largely unknown. In the current study, stable isotope probing was used to characterize acetate- and lactate-oxidizing bacteria in thermophilic anaerobic digestion. In microcosms fed 13C-acetate, bacteria related to members of Clostridium, Hydrogenophaga, Fervidobacterium, Spirochaeta, Limnohabitans, and Rhodococcus demonstrated elevated abundances of 13C-DNA fractions, suggesting their activities in acetate oxidation. In the treatments fed 13C-lactate, Anaeromyxobacter, Desulfobulbus, Syntrophus, Cystobacterineae, and Azospira were found to be the potential thermophilic lactate utilizers. PICRUSt predicted that enzymes related to nitrate and nitrite reduction would be enriched in 13C-DNA fractions, suggesting that the acetate and lactate oxidation may be coupled with nitrate and/or nitrite reduction. Co-occurrence network analysis indicated bacterial taxa not enriched in 13C-DNA fractions that may also play a critical role in thermophilic anaerobic digestion.
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Affiliation(s)
- Weimin Sun
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environment Science and Technology, Guangzhou, 510650, China.
| | - Valdis Krumins
- Department of Environmental Sciences, Rutgers University, New Brunswick, NJ, USA
| | - Yiran Dong
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL, USA
| | - Pin Gao
- College of Environmental Science and Engineering, State Environmental Protection Engineering Center for Pollution Treatment and Control in Textile Industry, Donghua University, Shanghai, 201620, China.
| | - Chunyan Ma
- College of Environmental Science and Engineering, State Environmental Protection Engineering Center for Pollution Treatment and Control in Textile Industry, Donghua University, Shanghai, 201620, China
| | - Min Hu
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environment Science and Technology, Guangzhou, 510650, China
| | - Baoqin Li
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environment Science and Technology, Guangzhou, 510650, China
| | - Bingqing Xia
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environment Science and Technology, Guangzhou, 510650, China
| | - Zijun He
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environment Science and Technology, Guangzhou, 510650, China
| | - Shangling Xiong
- Biological and Environmental College, Zhejiang Wanli University, Ningbo, 315211, China
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14
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Najdegerami IH, Maghami P, Sheikh-Hasani V, Hosseinzadeh G, Sheibani N, Moosavi-Movahedi AA. Antichaperone activity and heme degradation effect of methyl tert-butyl ether (MTBE) on normal and diabetic hemoglobins. J Mol Recognit 2016; 30. [PMID: 27917590 DOI: 10.1002/jmr.2596] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 10/29/2016] [Accepted: 10/31/2016] [Indexed: 01/17/2023]
Abstract
Because of the extensive use of methyl tert-butyl ether (MTBE) as an additive to increase the octane quality of gasoline, the environmental pollution by this compound has increased in recent decades. Environmental release of MTBE may lead to its entry to the blood stream through inhalation or drinking of contaminated water, and its interactions with biological molecules such as proteins. The present study was proposed to comparatively investigate the interactions of MTBE with hemoglobin (Hb) from diabetic and nondiabetic individuals using various spectroscopic methods including UV-visible, fluorescence, chemiluminescence, and circular dichroism. These results demonstrated the effects of MTBE on heme degradation of Hb and the reaction of these degradation products with water generating reactive oxygen species. Interaction of Hb with MTBE enhanced its aggregation rate and decreased lag time, indicating the antichaperone activity of MTBE upon interaction with Hb. Furthermore, the diabetic Hb showed more severe effects of MTBE, including heme degradation, reactive oxygen species production, unfolding, and antichaperone behavior than the nondiabetic Hb. The results from molecular docking suggested that the special interaction site of MTBE in the vicinity of Hb heme group is responsible for heme degradation.
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Affiliation(s)
- Ismaeil Hossein Najdegerami
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.,Center of Excellence in Biothermodynamics, University of Tehran, Tehran, Iran
| | - Parvaneh Maghami
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Vahid Sheikh-Hasani
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.,Center of Excellence in Biothermodynamics, University of Tehran, Tehran, Iran
| | - Ghader Hosseinzadeh
- Department of Physical Chemistry, School of Chemistry, College of Science, University of Tehran, Tehran, Iran
| | - Nader Sheibani
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.,Department of Biomedical Engineering, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Ali A Moosavi-Movahedi
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.,Center of Excellence in Biothermodynamics, University of Tehran, Tehran, Iran
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15
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Fischer A, Manefield M, Bombach P. Application of stable isotope tools for evaluating natural and stimulated biodegradation of organic pollutants in field studies. Curr Opin Biotechnol 2016; 41:99-107. [PMID: 27314918 DOI: 10.1016/j.copbio.2016.04.026] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 04/15/2016] [Accepted: 04/29/2016] [Indexed: 11/25/2022]
Abstract
Stable isotope tools are increasingly applied for in-depth evaluation of biodegradation of organic pollutants at contaminated field sites. They can be divided into three methods i) determination of changes in natural abundance of stable isotopes using compound-specific stable isotope analysis (CSIA), ii) detection of incorporation of stable-isotope label from a stable-isotope labelled target compound into degradation and/or mineralisation products and iii) determination of stable-isotope label incorporation into biomarkers using stable isotope probing (SIP). Stable isotope tools have been applied as key monitoring tools for multiple-line-of-evidence-approaches (MLEA) for sensitive evaluation of pollutant biodegradation. This review highlights the application of CSIA, SIP and MLEA including stable isotope tools for assessing natural and stimulated biodegradation of organic pollutants in field studies dealing with soil and groundwater contaminations.
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Affiliation(s)
- Anko Fischer
- Isodetect GmbH, Deutscher Platz 5b, 04103 Leipzig, Germany.
| | - Mike Manefield
- Micronovo Py Ltd, 18 Mason St, Maroubra, NSW, 2035, Australia
| | - Petra Bombach
- Isodetect GmbH, Deutscher Platz 5b, 04103 Leipzig, Germany
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