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Zhang X, Zhao Y, Wang Y, Qian H, Xing J, Joseph A, Rene ER, Li J, Zhu N. The interplay of hematite and photic biofilm triggers the acceleration of biotic nitrate removal. CHEMOSPHERE 2024; 358:142136. [PMID: 38692363 DOI: 10.1016/j.chemosphere.2024.142136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/03/2024]
Abstract
The soil-water interface is replete with photic biofilm and iron minerals; however, the potential of how iron minerals promote biotic nitrate removal is still unknown. This study investigates the physiological and ecological responses of photic biofilm to hematite (Fe2O3), in order to explore a practically feasible approach for in-situ nitrate removal. The nitrate removal by photic biofilm was significantly higher in the presence of Fe2O3 (92.5%) compared to the control (82.8%). Results show that the presence of Fe2O3 changed the microbial community composition of the photic biofilm, facilitates the thriving of Magnetospirillum and Pseudomonas, and promotes the growth of photic biofilm represented by the extracellular polymeric substance (EPS) and the content of chlorophyll. The presence of Fe2O3 also induces oxidative stress (•O2-) in the photic biofilm, which was demonstrated by electron spin resonance spectrometry. However, the photic biofilm could improve the EPS productivity to prevent the entrance of Fe2O3 to cells in the biofilm matrix and mitigate oxidative stress. The Fe2O3 then promoted the relative abundance of Magnetospirillum and Pseudomonas and the activity of nitrate reductase, which accelerates nitrate reduction by the photic biofilm. This study provides an insight into the interaction between iron minerals and photic biofilm and demonstrates the possibility of combining biotic and abiotic methods to improve the in-situ nitrate removal rate.
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Affiliation(s)
- Xiguo Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Yanhui Zhao
- Changjiang Basin Ecology and Environment Monitoring and Scientific Research Center, Changjiang Basin Ecology and Environment Administration, Ministry of Ecology and Environment, Wuhan, 430010, China
| | - Yimin Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Haoliang Qian
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Jun Xing
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Akaninyene Joseph
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Eldon R Rene
- Department of Water Supply, Sanitation and Environmental Engineering, IHE Delft Institute for Water Education, Westvest 7, 2611AX, Delft, the Netherlands
| | - Jizhou Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Ningyuan Zhu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China; Institute of Soil Sciences, Chinese Academy of Sciences, 71 East Beijing Road, 210008, China.
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2
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Demkina A, Slonova D, Mamontov V, Konovalova O, Yurikova D, Rogozhin V, Belova V, Korostin D, Sutormin D, Severinov K, Isaev A. Benchmarking DNA isolation methods for marine metagenomics. Sci Rep 2023; 13:22138. [PMID: 38092853 PMCID: PMC10719357 DOI: 10.1038/s41598-023-48804-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023] Open
Abstract
Metagenomics is a powerful tool to study marine microbial communities. However, obtaining high-quality environmental DNA suitable for downstream sequencing applications is a challenging task. The quality and quantity of isolated DNA heavily depend on the choice of purification procedure and the type of sample. Selection of an appropriate DNA isolation method for a new type of material often entails a lengthy trial and error process. Further, each DNA purification approach introduces biases and thus affects the composition of the studied community. To account for these problems and biases, we systematically investigated efficiency of DNA purification from three types of samples (water, sea sediment, and digestive tract of a model invertebrate Magallana gigas) with eight commercially available DNA isolation kits. For each kit-sample combination we measured the quantity of purified DNA, extent of DNA fragmentation, the presence of PCR-inhibiting contaminants, admixture of eukaryotic DNA, alpha-diversity, and reproducibility of the resulting community composition based on 16S rRNA amplicons sequencing. Additionally, we determined a "kitome", e.g., a set of contaminating taxa inherent for each type of purification kit used. The resulting matrix of evaluated parameters allows one to select the best DNA purification procedure for a given type of sample.
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Affiliation(s)
- Alina Demkina
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Darya Slonova
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Viktor Mamontov
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Olga Konovalova
- Marine Research Center of Lomonosov Moscow State University, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Daria Yurikova
- Marine Research Center of Lomonosov Moscow State University, Moscow, Russia
- Shirshov Institute of Oceanology, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir Rogozhin
- Marine Research Center of Lomonosov Moscow State University, Moscow, Russia
- Shirshov Institute of Oceanology, Russian Academy of Sciences, Moscow, Russia
| | - Vera Belova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitriy Korostin
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitry Sutormin
- Skolkovo Institute of Science and Technology, Moscow, Russia.
| | | | - Artem Isaev
- Skolkovo Institute of Science and Technology, Moscow, Russia.
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3
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Tian H, Li Y, Chen H, Zhang J, Hui M, Xu X, Su Q, Smets BF. Aerobic biodegradation of quinoline under denitrifying conditions in membrane-aerated biofilm reactor. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 326:121507. [PMID: 36972812 DOI: 10.1016/j.envpol.2023.121507] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/10/2023] [Accepted: 03/22/2023] [Indexed: 06/18/2023]
Abstract
Aerobic denitrification is being investigated as a novel biological nitrogen removal process, yet the knowledge on aerobic denitrification is limited to pure culture isolations and its occurrence in bioreactors remains unclear. This study investigated the feasibility and capacity of applying aerobic denitrification in membrane aerated biofilm reactor (MABR) for biological treatment of quinoline-laden wastewater. Stable and efficient removals of quinoline (91.5 ± 5.2%) and nitrate (NO3-) (86.5 ± 9.3%) were obtained under different operational conditions. Enhanced formation and function of extracellular polymeric substances (EPS) were observed at increasing quinoline loadings. MABR biofilm was highly enriched with aerobic quinoline-degrading bacteria, with a predominance of Rhodococcus (26.9 ± 3.7%) and secondary abundance of Pseudomonas (1.7 ± 1.2%) and Comamonas (0.94 ± 0.9%). Metagenomic analysis indicated that Rhodococcus contributed significantly to both aromatic degradation (24.5 ± 21.3%) and NO3- reduction (4.5 ± 3.9%), indicating its key role in aerobic denitrifying quinoline biodegradation. At increasing quinoline loadings, abundances of aerobic quinoline degradation gene oxoO and denitrifying genes of napA, nirS and nirK increased; there was a significant positive correlation of oxoO with nirS and nirK (p < 0.05). Aerobic quinoline degradation was likely initiated by hydroxylation, encoded by oxoO, followed by stepwise oxidations through 5,6-dihydroxy-1H-2-oxoquinoline or 8-hydroxycoumarin pathway. The results advance our understanding of quinoline degradation during biological nitrogen removal, and highlight the potential implementation of aerobic denitrification driven quinoline biodegradation in MABR for simultaneous removal of nitrogen and recalcitrant organic carbon from coking, coal gasification and pharmaceutical wastewaters.
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Affiliation(s)
- Hailong Tian
- College of Bioengineering, Henan University of Technology, Zhengzhou 450001, PR China
| | - Yuanyuan Li
- College of Bioengineering, Henan University of Technology, Zhengzhou 450001, PR China
| | - Hui Chen
- College of Bioengineering, Henan University of Technology, Zhengzhou 450001, PR China
| | - Jisheng Zhang
- College of Bioengineering, Henan University of Technology, Zhengzhou 450001, PR China
| | - Ming Hui
- College of Bioengineering, Henan University of Technology, Zhengzhou 450001, PR China
| | - Xingjian Xu
- Hinggan League Academy of Agriculture and Animal Husbandry, Ulanhot, Inner Mongolia 137400, PR China
| | - Qingxian Su
- Center for Water Research, Advanced Institute of Natural Sciences, Beijing Normal University at Zhuhai, 519087, China; Department of Environmental and Resource Engineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
| | - Barth F Smets
- Department of Environmental and Resource Engineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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4
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Optimization of an approach to detect low-concentration MNV-1 and HAV from soil-rich or non-soil post-washing water containing various PCR inhibitory substances. Food Control 2023. [DOI: 10.1016/j.foodcont.2023.109735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
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5
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Tindale LC, Baticados W, Duan J, Coombe M, Jassem A, Tang P, Uyaguari-Diaz M, Moore R, Himsworth C, Hsiao W, Prystajecky N. Extraction and Detection of Avian Influenza Virus From Wetland Sediment Using Enrichment-Based Targeted Resequencing. Front Vet Sci 2020; 7:301. [PMID: 32548133 PMCID: PMC7273442 DOI: 10.3389/fvets.2020.00301] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 05/04/2020] [Indexed: 11/13/2022] Open
Abstract
Early virus detection and characterization is key to successful avian influenza virus (AIV) surveillance for the health of humans as well as domestic poultry. We explored a novel sampling approach and molecular strategy using sediment from wetlands and outdoor waterbodies on poultry farms as a population-level proxy of AIV activity in waterfowls. RNA was extracted using the MoBio RNA PowerSoil Total RNA isolation kit with additional chloroform extraction steps to reduce PCR inhibition. AIV matrix protein (MP) gene was detected in 42/345 (12.2%) samples by RT-qPCR; an additional 64 (18.6%) samples showed evidence of amplification below the threshold and were categorized as “suspect positive.” Enrichment-based targeted resequencing (TR) identified AIV sequences in 79/345 (22.9%) samples. TR probes were designed for MP, hemagglutinin (HA), and neuraminidase (NA), however PB2 and PA were also identified. Although RT-qPCR and TR only had fair-moderate agreement, RT-qPCR positivity was predictive of TR-positivity both when using only strictly positive RT-qPCR samples (OR = 11.29) and when coding suspect positives as positive (OR = 7.56). This indicates that RT-qPCR could be used as a screening tool to select samples for virus characterization by TR and that future studies should consider RT-qPCR suspect positives to be positive samples for subsequent resequencing when avoiding false negatives is the priority, for instance in a diagnostic test, and to consider suspect positives to be negative samples when cost efficiency over a large number of samples is the priority, for instance in a surveillance program. A total of 13 HA (H1-7, H9-13, H16) and 9 NA (N1-9) subtypes were identified, with a maximum of 8 HA and 8 NA subtypes detected in a single sample. The optimized RNA extraction and targeted resequencing methods provided increased virus detection and subtyping characterization that could be implemented in an AIV surveillance system.
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Affiliation(s)
- Lauren C Tindale
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada
| | - Waren Baticados
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada
| | - Jun Duan
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada
| | - Michelle Coombe
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada.,Animal Health Centre, British Columbia Ministry of Agriculture, Abbotsford, BC, Canada
| | - Agatha Jassem
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada
| | - Patrick Tang
- Department of Pathology, Sidra Medicine, Doha, Qatar
| | - Miguel Uyaguari-Diaz
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada
| | - Richard Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Chelsea Himsworth
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada.,Animal Health Centre, British Columbia Ministry of Agriculture, Abbotsford, BC, Canada
| | - William Hsiao
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada
| | - Natalie Prystajecky
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada
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6
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Zhu N, Wu Y, Tang J, Duan P, Yao L, Rene ER, Wong PK, An T, Dionysiou DD. A New Concept of Promoting Nitrate Reduction in Surface Waters: Simultaneous Supplement of Denitrifiers, Electron Donor Pool, and Electron Mediators. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:8617-8626. [PMID: 29966090 DOI: 10.1021/acs.est.8b01605] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The efficiency of biological nitrate reduction depends on the community composition of microorganisms, the electron donor pool, and the electron mediators participating in the biological reduction process. This study aims at creating an in situ system comprising of denitrifiers, electron donors, and electron mediators to reduce nitrate in surface waters. The ubiquitous periphytic biofilm in waters was employed to promote in situ nitrate reduction in the presence of titanium dioxide (TiO2) nanoparticles (NPs). The nitrate removal rate in the periphytic biofilm and TiO2 NPs system was significantly higher than the control (only periphytic biofilm or TiO2 NPs). TiO2 NPs optimized the community composition of periphytic biofilm for nitrate reduction by increasing the relative abundance of four dominant denitrifying bacteria. Periphytic biofilm showed a substantial increase in extracellular polymeric substance, especially the humic acid and protein content, due to the presence of TiO2 NPs. The synergistic action of humic acid, protein, denitrifying bacteria of the periphytic biofilm, and TiO2 NPs contributed to 80% of the nitrate reduction. The protein and humic acid, acting as electron mediators, facilitated the transfer of exogenous electrons from photoexcited TiO2 NPs to periphytic biofilm containing denitrifiers, which enhanced nitrate reduction in surface waters.
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Affiliation(s)
- Ningyuan Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Sciences , Chinese Academy of Sciences , 71 East Beijing Road , Nanjing 210008 , China
- College of Resource and Environment , University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Yonghong Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Sciences , Chinese Academy of Sciences , 71 East Beijing Road , Nanjing 210008 , China
| | - Jun Tang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Sciences , Chinese Academy of Sciences , 71 East Beijing Road , Nanjing 210008 , China
- College of Resource and Environment , University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Pengfei Duan
- Collaborative Innovation Center of Water Security for Water Source, Region of Mid-line of South-to-North Diversion Project , Nanyang Normal University , Nanyang 473061 , Henan , China
| | - Lunguang Yao
- Collaborative Innovation Center of Water Security for Water Source, Region of Mid-line of South-to-North Diversion Project , Nanyang Normal University , Nanyang 473061 , Henan , China
| | - Eldon R Rene
- Department of Environmental Engineering and Water Technology , IHE Delft Institute for Water Education , Westvest 7 , 2611 AX Delft , The Netherlands
| | - Po Keung Wong
- School of Life Sciences , The Chinese University of Hong Kong , Shatin, NT, Hong Kong , SAR , China
| | - Taicheng An
- Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control , Guangdong University of Technology , Guangzhou , 510006 , China
| | - Dionysios D Dionysiou
- Department of Chemical and Environmental Engineering (ChEE), 705 Engineering Research Center , University of Cincinnati , Cincinnati , Ohio 45221-0012 , United States
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7
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Responses of denitrifying bacterial communities to short-term waterlogging of soils. Sci Rep 2017; 7:803. [PMID: 28400580 PMCID: PMC5429771 DOI: 10.1038/s41598-017-00953-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 03/20/2017] [Indexed: 12/21/2022] Open
Abstract
Agricultural soil is often subjected to waterlogging after heavy rainfalls, resulting in sharp and explosive increases in the emission of nitrous oxide (N2O), an important greenhouse gas primarily released from agricultural soil ecosystems. Previous studies on waterlogged soil examined the abundance of denitrifiers but not the composition of denitrifier communities in soil. Also, the PCR primers used in those studies could only detect partial groups of denitrifiers. Here, we performed pyrosequencing analyses with the aid of recently developed PCR primers exhibiting high coverage for three denitrification genes, nirK, nirS, and nosZ to examine the effect of short-term waterlogging on denitrifier communities in soil. We found that microbial communities harboring denitrification genes in the top 5 cm of soil distributed according to soil depth, water-soluble carbon, and nitrate nitrogen. Short-term waterlogging scarcely affected abundance, richness, or the alpha-diversities of microbial communities harboring nirK, nirS, and nosZ genes, but significantly affected their composition, particularly in microbial communities at soil depths of 0 to 1 cm. Our results indicated that the composition of denitrifying microbial communities but not the abundance of denitrifiers in soil was responsive to short-term waterlogging of an agricultural soil ecosystem.
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8
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Humic substances cause fluorescence inhibition in real-time polymerase chain reaction. Anal Biochem 2015; 487:30-7. [DOI: 10.1016/j.ab.2015.07.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 07/01/2015] [Accepted: 07/03/2015] [Indexed: 11/18/2022]
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9
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An improved and reproducible protocol for the extraction of high quality fungal RNA from plant biomass substrates. Fungal Genet Biol 2014; 72:201-206. [PMID: 24951842 DOI: 10.1016/j.fgb.2014.06.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 05/20/2014] [Accepted: 06/08/2014] [Indexed: 11/23/2022]
Abstract
Isolation of high quantity and quality RNA is a crucial step in the detection of meaningful gene expression data. Obtaining intact fungal RNA from complex lignocellulosic substrates is often difficult, producing low integrity RNA which perform poorly in downstream applications. In this study we developed an RNA extraction method using CsCl centrifugation procedure, modified from previous reports and adapted for isolation of RNA from plant biomass. This method provided high level of integrity and good quantity of RNA which were suitable for reliable analyses of gene expression and produced consistent and reproducible results.
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10
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Pellicer-Nàcher C, Smets BF. Structure, composition, and strength of nitrifying membrane-aerated biofilms. WATER RESEARCH 2014; 57:151-161. [PMID: 24721662 DOI: 10.1016/j.watres.2014.03.026] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 03/03/2014] [Accepted: 03/13/2014] [Indexed: 06/03/2023]
Abstract
Membrane-aerated biofilm reactors (MABRs) are a novel technology based on the growth of biofilms on oxygen-permeable membranes. Hereby, MABRs combine all the advantages of biofilm growth with a more flexible and efficient control of the oxygen load. In the present work, MABR flow cells were operated to achieve full nitrification. MABR biofilms had a significantly different structure than co-diffusion biofilms reported in the literature. Different levels of shear stress and oxygen loading during MABR operation also affected the biofilm parameters. Furthermore, reactor operation at higher oxygen loads resulted in an increased biofilm cohesiveness, which depended on the EPS mass in the biofilms and the type of stress applied (more cohesive against normal than shear stresses). The EPS in the strongest biofilms had a higher content of proteins and a lower level of carbohydrates. Staining analyses revealed that the outermost EPS in the stronger biofilm regions was of hydrophilic nature and distributed around dense microbial aggregates, whereas it was homogeneously distributed in the weaker strata. Overall, the obtained results provide input parameters to future modelling efforts and operating conditions to support more robust autotrophic N conversions in MABRs.
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Affiliation(s)
- Carles Pellicer-Nàcher
- Department of Environmental Engineering, Technical University of Denmark, Miljøvej, Building 113, 2800 Kongens Lyngby, Denmark.
| | - Barth F Smets
- Department of Environmental Engineering, Technical University of Denmark, Miljøvej, Building 113, 2800 Kongens Lyngby, Denmark.
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11
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Pellicer-Nàcher C, Domingo-Félez C, Mutlu AG, Smets BF. Critical assessment of extracellular polymeric substances extraction methods from mixed culture biomass. WATER RESEARCH 2013; 47:5564-5574. [PMID: 23866135 DOI: 10.1016/j.watres.2013.06.026] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 06/09/2013] [Accepted: 06/16/2013] [Indexed: 06/02/2023]
Abstract
Extracellular polymeric substances (EPS) have a presumed determinant role in the structure, architecture, strength, filterability, and settling behaviour of microbial solids in biological wastewater treatment processes. Consequently, numerous EPS extraction protocols have recently been published that aim to optimize the trade off between high EPS recovery and low cell lysis. Despite extensive efforts, the obtained results are often contradictory, even when analysing similar biomass samples and using similar experimental conditions, which greatly complicates the selection of an extraction protocol. This study presents a rigorous and critical assessment of existing physical and chemical EPS extraction methods applied to mixed-culture biomass samples (nitrifying, nitritation-anammox, and activated sludge biomass). A novel fluorescence-based method was developed and calibrated to quantify the lysis potential of different EPS extraction protocols. We concluded that commonly used methods to assess cell lysis (DNA concentrations or G6PDH activities in EPS extracts) do not correlate with cell viability. Furthermore, we discovered that the presence of certain chemicals in EPS extracts results in severe underestimation of protein and carbohydrate concentrations by using standard analytical methods. Keeping both maximum EPS extraction yields and minimal biomass lysis as criteria, it was identified a sonication-based extraction method as the best to determine and compare tightly-bound EPS fractions in different biomass samples. Protein was consistently the main EPS component in all analysed samples. However, EPS from nitrifying enrichments was richer in DNA, the activated sludge EPS had a higher content in humic acids and carbohydrates, and the nitritation-anammox EPS, while similar in composition to the nitrifier EPS, had a lower fraction of hydrophobic biopolymers. In general, the easily-extractable EPS fraction was more abundant in carbohydrates and humic substances, while DNA could only be found in tightly bound EPS fractions. In conclusion, the methodology presented herein supports the rational selection of analytical tools and EPS extraction protocols in further EPS characterization studies.
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Affiliation(s)
- Carles Pellicer-Nàcher
- Department of Environmental Engineering, Technical University of Denmark, Miljøvej Building 113, 2800 Kongens Lyngby, Denmark.
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12
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Wang Y, Hayatsu M, Fujii T. Extraction of bacterial RNA from soil: challenges and solutions. Microbes Environ 2012; 27:111-21. [PMID: 22791042 PMCID: PMC4036013 DOI: 10.1264/jsme2.me11304] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Detection of bacterial gene expression in soil emerged in the early 1990s and provided information on bacterial responses in their original soil environments. As a key procedure in the detection, extraction of bacterial RNA from soil has attracted much interest, and many methods of soil RNA extraction have been reported in the past 20 years. In addition to various RT-PCR-based technologies, new technologies for gene expression analysis, such as microarrays and high-throughput sequencing technologies, have recently been applied to examine bacterial gene expression in soil. These technologies are driving improvements in RNA extraction protocols. In this mini-review, progress in the extraction of bacterial RNA from soil is summarized with emphasis on the major difficulties in the development of methodologies and corresponding strategies to overcome them.
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Affiliation(s)
- Yong Wang
- Environmental Biofunction Division, National Institute for Agro-Environmental Sciences, 3-1-3 Kannondai, Tsukuba, Ibaraki 305-8604, Japan.
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13
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A novel method for RNA extraction from Andosols using casein and its application to amoA gene expression study in soil. Appl Microbiol Biotechnol 2012; 96:793-802. [DOI: 10.1007/s00253-012-4342-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 07/25/2012] [Accepted: 07/26/2012] [Indexed: 11/27/2022]
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