101
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Treu L, Kougias PG, de Diego-Díaz B, Campanaro S, Bassani I, Fernández-Rodríguez J, Angelidaki I. Two-year microbial adaptation during hydrogen-mediated biogas upgrading process in a serial reactor configuration. BIORESOURCE TECHNOLOGY 2018; 264:140-147. [PMID: 29800774 DOI: 10.1016/j.biortech.2018.05.070] [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: 04/03/2018] [Revised: 05/17/2018] [Accepted: 05/18/2018] [Indexed: 05/07/2023]
Abstract
Microbial dynamics in an upgrading biogas reactor system undergoing a more than two years-period at stable operating conditions were explored. The carbon dioxide generated during biomass degradation in the first reactor of the system was converted to methane into the secondary reactor by addition of external hydrogen. Considering the overall efficiency, the long-term operation period resulted in an improved biogas upgrading performance (99% methane content). However, a remarkable accumulation of acetate was revealed, indicating the enhancement of homoacetogenic activity. For this reason, a shift in the anaerobic digestion microbiome was expected and evaluated by 16S rRNA amplicon analysis. Results demonstrated that the most abundant archaeal species identified in the first time point, Candidatus Methanoculleus thermohydrogenotrophicum, was replaced by Methanothermobacter thermautotrophicus, becoming dominant after the community adaptation. The most interesting taxonomic units were clustered by relative abundance and six main long-term adaptation trends were found, characterizing functionally related microbes (e.g. homoacetogens).
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Affiliation(s)
- L Treu
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark
| | - P G Kougias
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark.
| | - B de Diego-Díaz
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark; Department of Chemistry, University of Navarra, Spain
| | - S Campanaro
- Department of Biology, University of Padua, Via U. Bassi 58/b, 35131 Padova, Italy
| | - I Bassani
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark
| | | | - I Angelidaki
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark
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102
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Theuerl S, Klang J, Heiermann M, De Vrieze J. Marker microbiome clusters are determined by operational parameters and specific key taxa combinations in anaerobic digestion. BIORESOURCE TECHNOLOGY 2018; 263:128-135. [PMID: 29738975 DOI: 10.1016/j.biortech.2018.04.111] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/24/2018] [Accepted: 04/27/2018] [Indexed: 05/10/2023]
Abstract
In this study, microbiomes of 36 full-scale anaerobic digesters originated from 22 different biogas plants were compared by terminal restriction fragment length polymorphism (TRFLP) analysis. Regarding the differences in microbial community composition, a weighting of the environmental parameters could be derived from higher to lower importance as follows: (i) temperature, (ii) TAN and NH3 concentrations and conductivity, and (iii) the chemical composition of the supplied feedstocks. Biotic interactions between specific bacterial and archaeal community arrangements were revealed, whereby members of the phyla Bacteroidetes and Cloacimonetes combined with the archaeal genus Methanothrix dominated the conversion of homogeneous feedstocks, such as waste water sludge or industrial waste. As most of the detected TRFs were only found in a certain number of anaerobic digestion plants, each plant develops its unique microbiome. The putative rare species, the specialists, are potentially hidden drivers of microbiome functioning as they provide necessary traits under, e.g., process-inconvenient conditions.
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Affiliation(s)
- Susanne Theuerl
- Leibniz Institute for Agricultural Engineering and Bioeconomy e.V. (ATB), Department Bioengineering, Max-Eyth-Allee 100, D-14469 Potsdam, Germany.
| | - Johanna Klang
- Leibniz Institute for Agricultural Engineering and Bioeconomy e.V. (ATB), Department Bioengineering, Max-Eyth-Allee 100, D-14469 Potsdam, Germany
| | - Monika Heiermann
- Leibniz Institute for Agricultural Engineering and Bioeconomy e.V. (ATB), Department Technology Assessment and Substance Cycles, Max-Eyth-Allee 100, D-14469 Potsdam, Germany
| | - Jo De Vrieze
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000 Gent, Belgium
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103
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Zheng B, Zhu Y, Sardans J, Peñuelas J, Su J. QMEC: a tool for high-throughput quantitative assessment of microbial functional potential in C, N, P, and S biogeochemical cycling. SCIENCE CHINA-LIFE SCIENCES 2018; 61:1451-1462. [DOI: 10.1007/s11427-018-9364-7] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 07/26/2018] [Indexed: 02/07/2023]
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104
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Designing Reactor Microbiomes for Chemical Production from Organic Waste. Trends Biotechnol 2018; 36:747-750. [DOI: 10.1016/j.tibtech.2018.01.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 01/05/2018] [Accepted: 01/08/2018] [Indexed: 01/31/2023]
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105
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Tijani H, Yuzir A, Abdullah N. Producing desulfurized biogas using two-stage domesticated shear-loop anaerobic contact stabilization system. WASTE MANAGEMENT (NEW YORK, N.Y.) 2018; 78:770-780. [PMID: 32559969 DOI: 10.1016/j.wasman.2018.06.045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 05/10/2018] [Accepted: 06/23/2018] [Indexed: 06/11/2023]
Abstract
In this study, a two-stage domesticated shear-loop anaerobic contact stabilization (SLACS) system is introduced as a new reactor design to enhance methane productivity with significant reduction in hydrogen sulphide (H2S) synthesis. Due to the rich sulfate content in industrial wastewaters, the initial fermentation phase of anaerobic digestion is highly acidifying and often leads to severe performance losses, digester's instability, and even culture crash. The SLACS system functions as a dissimilatory sulfate reduction - methanogenic reactor consisting of two compartments, a shear-loop anaerobic bed (SLAB) unit and an anaerobic plug flow (APF) unit. The functional role of the SLAB unit is not limited to acidogenesis but also sulfidogenic processes, which curtails H2S generation in the APF unit (methanogenic stage). Experimental observations indicated that pH serves a critical role in the cohabitation of acidogenic and sulfidogenic microbes in the SLAB unit. Although acidogenesis was not influenced by pH within the range of 4.5-6.0, it is vital to stabilize the pH of this unit at 5.4 to establish a steady sulfate reduction of above 75%. The highest desulfurization achieved in this compartment was 88% under a hydraulic retention time (HRT) of 4 h. With an average methane productivity of 256 mL g-1 VS, the methanogenic performance of the two-stage domesticated SLACS system shows a 32% methanogenic proficiency higher than that of the one-stage digestion system. Microbial community structure within the system carried out via Next Generation Sequencing (NGS) provided qualitative data on the sludge's sulfidogenic and methanogenic performance.
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Affiliation(s)
- Hamzat Tijani
- Algal Biomass iKohza, Malaysia-Japan International Institute of Technology (MJIIT), Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, 54100 Kuala Lumpur, Malaysia
| | - Ali Yuzir
- Department of Environmental Engineering & Green Technology, Malaysia-Japan International Institute of Technology (MJIIT), Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, 54100 Kuala Lumpur, Malaysia.
| | - Norhayati Abdullah
- Department of Environmental Engineering & Green Technology, Malaysia-Japan International Institute of Technology (MJIIT), Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, 54100 Kuala Lumpur, Malaysia
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106
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Zamorano-López N, Moñino P, Borrás L, Aguado D, Barat R, Ferrer J, Seco A. Influence of food waste addition over microbial communities in an Anaerobic Membrane Bioreactor plant treating urban wastewater. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2018; 217:788-796. [PMID: 29660704 DOI: 10.1016/j.jenvman.2018.04.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 03/22/2018] [Accepted: 04/04/2018] [Indexed: 06/08/2023]
Abstract
Notorious changes in microbial communities were observed during and after the joint treatment of wastewater with Food Waste (FW) in an Anaerobic Membrane Bioreactor (AnMBR) plant. The microbial population was analysed by high-throughput sequencing of the 16S rRNA gene and dominance of Chloroflexi, Firmicutes, Synergistetes and Proteobacteria phyla was found. The relative abundance of these potential hydrolytic phyla increased as a higher fraction of FW was jointly treated. Moreover, whereas Specific Methanogenic Activity (SMA) rose from 10 to 51 mL CH4 g-1 VS, Methanosarcinales order increased from 34.0% over 80.0% of total Archaea, being Methanosaeta the dominant genus. The effect of FW over AnMBR biomass was observed during the whole experience, as methane production rose from 49.2 to 144.5 L CH4 · kg-1 influent COD. Furthermore, biomethanization potential was increased over 82% after the experience. AnMBR technology allows the established microbial community to remain in the bioreactor even after the addition of FW, improving the anaerobic digestion of urban wastewater.
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Affiliation(s)
- N Zamorano-López
- CALAGUA - Unidad Mixta UV-UPV, Departament d'Enginyeria Química, Universitat de València, Avinguda de la Universitat s/n, Burjassot, Valencia, 46100, Spain.
| | - P Moñino
- CALAGUA - Unidad Mixta UV-UPV, Institut Universitari d'Investigació d'Enginyeria de l'Aigua i Medi Ambient - IIAMA, Universitat Politècnica de Valencia, Camí de Vera s/n, Valencia, 46022, Spain
| | - L Borrás
- CALAGUA - Unidad Mixta UV-UPV, Departament d'Enginyeria Química, Universitat de València, Avinguda de la Universitat s/n, Burjassot, Valencia, 46100, Spain
| | - D Aguado
- CALAGUA - Unidad Mixta UV-UPV, Institut Universitari d'Investigació d'Enginyeria de l'Aigua i Medi Ambient - IIAMA, Universitat Politècnica de Valencia, Camí de Vera s/n, Valencia, 46022, Spain
| | - R Barat
- CALAGUA - Unidad Mixta UV-UPV, Institut Universitari d'Investigació d'Enginyeria de l'Aigua i Medi Ambient - IIAMA, Universitat Politècnica de Valencia, Camí de Vera s/n, Valencia, 46022, Spain
| | - J Ferrer
- CALAGUA - Unidad Mixta UV-UPV, Institut Universitari d'Investigació d'Enginyeria de l'Aigua i Medi Ambient - IIAMA, Universitat Politècnica de Valencia, Camí de Vera s/n, Valencia, 46022, Spain
| | - A Seco
- CALAGUA - Unidad Mixta UV-UPV, Departament d'Enginyeria Química, Universitat de València, Avinguda de la Universitat s/n, Burjassot, Valencia, 46100, Spain
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107
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Keating C, Hughes D, Mahony T, Cysneiros D, Ijaz UZ, Smith CJ, O'Flaherty V. Cold adaptation and replicable microbial community development during long-term low-temperature anaerobic digestion treatment of synthetic sewage. FEMS Microbiol Ecol 2018; 94:5004848. [PMID: 29846574 PMCID: PMC5995215 DOI: 10.1093/femsec/fiy095] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 05/24/2018] [Indexed: 11/12/2022] Open
Abstract
The development and activity of a cold-adapting microbial community was monitored during low-temperature anaerobic digestion (LtAD) treatment of wastewater. Two replicate hybrid anaerobic sludge bed-fixed-film reactors treated a synthetic sewage wastewater at 12°C, at organic loading rates of 0.25-1.0 kg chemical oxygen demand (COD) m-3 d-1, over 889 days. The inoculum was obtained from a full-scale anaerobic digestion reactor, which was operated at 37°C. Both LtAD reactors readily degraded the influent with COD removal efficiencies regularly exceeding 78% for both the total and soluble COD fractions. The biomass from both reactors was sampled temporally and tested for activity against hydrolytic and methanogenic substrates at 12°C and 37°C. Data indicated that significantly enhanced low-temperature hydrolytic and methanogenic activity developed in both systems. For example, the hydrolysis rate constant (k) at 12°C had increased 20-30-fold by comparison to the inoculum by day 500. Substrate affinity also increased for hydrolytic substrates at low temperature. Next generation sequencing demonstrated that a shift in a community structure occurred over the trial, involving a 1-log-fold change in 25 SEQS (OTU-free approach) from the inoculum. Microbial community structure changes and process performance were replicable in the LtAD reactors.
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Affiliation(s)
- C Keating
- Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland, Galway, Ireland
| | - D Hughes
- Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland, Galway, Ireland
| | - T Mahony
- Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland, Galway, Ireland
| | - D Cysneiros
- Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland, Galway, Ireland
| | - U Z Ijaz
- Infrastructure and Environment, School of Engineering, University of Glasgow, Rankine Building, 79-85 Oakfield Avenue, Glasgow, G12 8LT, UK
| | - C J Smith
- Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland, Galway, Ireland
| | - V O'Flaherty
- Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland, Galway, Ireland
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108
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Córdova O, Chamy R, Guerrero L, Sánchez-Rodríguez A. Assessing the Effect of Pretreatments on the Structure and Functionality of Microbial Communities for the Bioconversion of Microalgae to Biogas. Front Microbiol 2018; 9:1388. [PMID: 29997601 PMCID: PMC6028723 DOI: 10.3389/fmicb.2018.01388] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 06/06/2018] [Indexed: 11/23/2022] Open
Abstract
Microalgae biomethanization is driven by anaerobic sludge associated microorganisms and is generally limited by the incomplete hydrolysis of the microalgae cell wall, which results in a low availability of microalgal biomass for the methanogenic community. The application of enzymatic pretreatments, e.g., with hydrolytic enzymes, is among the strategies used to work around the incomplete hydrolysis of the microalgae cell wall. Despite the proven efficacy of these pretreatments in increasing biomethanization, the changes that a given pretreatment may cause to the anaerobic sludge associated microorganisms during biomethanization are still unknown. This study evaluated the changes in the expression of the metatranscriptome of anaerobic sludge associated microorganisms during Chlorella sorokiniana biomethanization without pretreatment (WP) (control) and pretreated with commercial cellulase in order to increase the solubilization of the microalgal organic matter. Pretreated microalgal biomass experienced significant increases in biogas the production. The metatranscriptomic analysis of control samples showed functionally active microalgae cells, a bacterial community dominated by γ- and δ-proteobacteria, and a methanogenic community dominated by Methanospirillum hungatei. In contrast, pretreated samples were characterized by the absence of active microalgae cells and a bacteria population dominated by species of the Clostridia class. These differences are also related to the differential activation of metabolic pathways e.g., those associated with the degradation of organic matter during its biomethanization.
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Affiliation(s)
- Olivia Córdova
- Laboratorio de Biotecnología Ambiental, Escuela de Ingeniería Bioquímica, Facultad de Ingeniería, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Rolando Chamy
- Laboratorio de Biotecnología Ambiental, Escuela de Ingeniería Bioquímica, Facultad de Ingeniería, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Lorna Guerrero
- Department of Chemical and Environmental Engineering, Universidad Técnica Federico Santa, Valparaíso, Chile
| | - Aminael Sánchez-Rodríguez
- Microbial Systems Ecology and Evolution, Department of Biological Sciences, Universidad Técnica Particular de Loja, Loja, Ecuador
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109
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De Vrieze J, De Waele M, Boeckx P, Boon N. Isotope Fractionation in Biogas Allows Direct Microbial Community Stability Monitoring in Anaerobic Digestion. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:6704-6713. [PMID: 29432683 DOI: 10.1021/acs.est.8b00723] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Process monitoring of anaerobic digestion is typically based on operational parameters, such as pH and volatile fatty acid concentration, that are lagging on actual microbial community performance. In this study, 13C isotope fractionation in CH4 and CO2 in the biogas was used to monitor process stability of anaerobic digestion in response to salt stress. A gradual and pulsed increase in salt concentration resulted in a decrease in methane production. No clear shift in δ13CH4 was observed in response to the gradual increase in salt concentration, and δ13CO2 of the biogas showed only a clear shift after process failure, compared with the control. In contrast, both δ13CH4 and δ13CO2 in the biogas changed in response to the pulsed increase in salt concentration. This change preceded the decrease in methane production. A significantly different bacterial and archaeal community profile was observed between the DNA and RNA level, which was also reflected in a different relation with the δ13CH4 and δ13CO2 values. This shows that isotope fractionation in the biogas can predict process stability in anaerobic digestion, as it directly reflects shifts in the total and active microbial community, yet, due to its temporal character, further validation is needed.
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Affiliation(s)
- Jo De Vrieze
- Center for Microbial Ecology and Technology (CMET) , Ghent University , Coupure Links 653 , B-9000 Gent , Belgium
| | - Michiel De Waele
- Center for Microbial Ecology and Technology (CMET) , Ghent University , Coupure Links 653 , B-9000 Gent , Belgium
| | - Pascal Boeckx
- Isotope Bioscience Laboratory - ISOFYS , Ghent University , Coupure Links 653 , B-9000 Gent , Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET) , Ghent University , Coupure Links 653 , B-9000 Gent , Belgium
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110
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Morris L, O'Brien A, Natera SHA, Lutz A, Roessner U, Long SM. Structural and functional measures of marine microbial communities: An experiment to assess implications for oil spill management. MARINE POLLUTION BULLETIN 2018; 131:525-529. [PMID: 29886978 DOI: 10.1016/j.marpolbul.2018.04.054] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 04/16/2018] [Accepted: 04/22/2018] [Indexed: 06/08/2023]
Abstract
Microbial communities are ecologically important in aquatic environments and impacts on microbes have the potential to affect a number of functional processes. We have amended seawater with a crude oil and assessed changes in species composition as well as a measure of functional diversity (the ability of the community to utilise different carbon sources) and the community level metabolic signature. We found that there was a degree of functional redundancy in the community we tested. Oiled assemblages became less diverse and more dominated by specialist hydrocarbon degraders, carbon source utilisation increased initially but there was no change in metabolic signature in this small scale laboratory experiment. This study supports the decision framework around management of oil spills. This package of methods has the potential to be used in the testing and selection of new dispersants for use in oil spill response.
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Affiliation(s)
- Liz Morris
- Centre for Aquatic Pollution Identification and Management (CAPIM), School of Biosciences, University of Melbourne, Parkville 3010, Victoria, Australia.
| | - Allyson O'Brien
- School of Biosciences, University of Melbourne, Parkville 3010, Victoria, Australia
| | - Siria H A Natera
- Metabolomics Australia, School of Biosciences, University of Melbourne, Parkville 3010, Victoria, Australia
| | - Adrian Lutz
- Metabolomics Australia, School of Biosciences, University of Melbourne, Parkville 3010, Victoria, Australia
| | - Ute Roessner
- Metabolomics Australia, School of Biosciences, University of Melbourne, Parkville 3010, Victoria, Australia
| | - Sara M Long
- Centre for Aquatic Pollution Identification and Management (CAPIM), School of Biosciences, University of Melbourne, Parkville 3010, Victoria, Australia
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111
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Zhang L, Li L, Pan X, Shi Z, Feng X, Gong B, Li J, Wang L. Enhanced Growth and Activities of the Dominant Functional Microbiota of Chicken Manure Composts in the Presence of Maize Straw. Front Microbiol 2018; 9:1131. [PMID: 29896185 PMCID: PMC5986910 DOI: 10.3389/fmicb.2018.01131] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 05/14/2018] [Indexed: 12/05/2022] Open
Abstract
As a consequence of intensive feeding, the bulk deposition of livestock manure causes severe environmental problems. Composting is a promising method for waste disposal, and the fermentation process is driven by microbial communities. However, chicken manure contains diverse gut microbes, mainly species derived from Proteobacteria, which may include pathogens that threaten human health. To evaluate composting as a harmless treatment of livestock manure, the dynamics of the microbiota in two chicken manure composts were studied, and the influences of adding maize straw on the compost microbiota were compared. The results revealed that microbes from Firmicutes including Bacillus and Lentibacillus are the most dominant degraders with a strong amino acid metabolism, and they secrete a diverse array of proteases as revealed in metaproteomics data. The addition of maize straw to the chicken manure compost accelerated species succession at the initial stage, and stimulated carbohydrate metabolism in the dominant microbiota. Besides, under the resulting high temperature (>70°C) conditions, the relative abundance of Proteobacteria was reduced by 78% in composts containing maize straw by day 4, which was faster than in compost without added maize straw, in which the abundance was reduced by 66%. Adding maize straw to chicken manure composts can therefore increase the fermentation temperature and inhibit the growth of Proteobacteria. In general, these findings provide increased insight into the dynamic changes among the dominant functional microbiota in chicken manure composts, and may contribute to the optimization of livestock manure composting on an industrial scale.
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Affiliation(s)
- Lili Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China.,School of Computer Science and Technology, Shandong University, Jinan, China
| | - Lijuan Li
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Xiaoguang Pan
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Zelu Shi
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | | | - Bin Gong
- School of Computer Science and Technology, Shandong University, Jinan, China
| | - Jian Li
- Laboratory of Antimicrobial Systems Pharmacology, Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Melbourne, VIC, Australia
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
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112
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New concepts in anaerobic digestion processes: recent advances and biological aspects. Appl Microbiol Biotechnol 2018; 102:5065-5076. [DOI: 10.1007/s00253-018-9039-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/16/2018] [Accepted: 04/16/2018] [Indexed: 10/17/2022]
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113
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Ziels RM, Svensson BH, Sundberg C, Larsson M, Karlsson A, Yekta SS. Microbial rRNA gene expression and co-occurrence profiles associate with biokinetics and elemental composition in full-scale anaerobic digesters. Microb Biotechnol 2018; 11:694-709. [PMID: 29633555 PMCID: PMC6011980 DOI: 10.1111/1751-7915.13264] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 03/05/2018] [Accepted: 03/07/2018] [Indexed: 11/29/2022] Open
Abstract
This study examined whether the abundance and expression of microbial 16S rRNA genes were associated with elemental concentrations and substrate conversion biokinetics in 20 full-scale anaerobic digesters, including seven municipal sewage sludge (SS) digesters and 13 industrial codigesters. SS digester contents had higher methane production rates from acetate, propionate and phenyl acetate compared to industrial codigesters. SS digesters and industrial codigesters were distinctly clustered based on their elemental concentrations, with higher concentrations of NH3 -N, Cl, K and Na observed in codigesters. Amplicon sequencing of 16S rRNA genes and reverse-transcribed 16S rRNA revealed divergent grouping of microbial communities between mesophilic SS digesters, mesophilic codigesters and thermophilic digesters. Higher intradigester distances between Archaea 16S rRNA and rRNA gene profiles were observed in mesophilic codigesters, which also had the lowest acetate utilization biokinetics. Constrained ordination showed that microbial rRNA and rRNA gene profiles were significantly associated with maximum methane production rates from acetate, propionate, oleate and phenyl acetate, as well as concentrations of NH3 -N, Fe, S, Mo and Ni. A co-occurrence network of rRNA gene expression confirmed the three main clusters of anaerobic digester communities based on active populations. Syntrophic and methanogenic taxa were highly represented within the subnetworks, indicating that obligate energy-sharing partnerships play critical roles in stabilizing the digester microbiome. Overall, these results provide new evidence showing that different feed substrates associate with different micronutrient compositions in anaerobic digesters, which in turn may influence microbial abundance, activity and function.
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Affiliation(s)
- Ryan M Ziels
- Department of Civil Engineering, The University of British Columbia, Vancouver, BC, Canada
| | - Bo H Svensson
- Department of Thematic Studies-Environmental Change, Linköping University, Linköping, Sweden.,Biogas Research Center, Linköping University, Linköping, Sweden
| | - Carina Sundberg
- Department of Thematic Studies-Environmental Change, Linköping University, Linköping, Sweden
| | - Madeleine Larsson
- Department of Thematic Studies-Environmental Change, Linköping University, Linköping, Sweden.,Biogas Research Center, Linköping University, Linköping, Sweden
| | | | - Sepehr Shakeri Yekta
- Department of Thematic Studies-Environmental Change, Linköping University, Linköping, Sweden.,Biogas Research Center, Linköping University, Linköping, Sweden
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114
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De Vrieze J, Pinto AJ, Sloan WT, Ijaz UZ. The active microbial community more accurately reflects the anaerobic digestion process: 16S rRNA (gene) sequencing as a predictive tool. MICROBIOME 2018; 6:63. [PMID: 29609653 PMCID: PMC5879801 DOI: 10.1186/s40168-018-0449-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 03/16/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND Amplicon sequencing methods targeting the 16S rRNA gene have been used extensively to investigate microbial community composition and dynamics in anaerobic digestion. These methods successfully characterize amplicons but do not distinguish micro-organisms that are actually responsible for the process. In this research, the archaeal and bacterial community of 48 full-scale anaerobic digestion plants were evaluated on DNA (total community) and RNA (active community) level via 16S rRNA (gene) amplicon sequencing. RESULTS A significantly higher diversity on DNA compared with the RNA level was observed for archaea, but not for bacteria. Beta diversity analysis showed a significant difference in community composition between the DNA and RNA of both bacteria and archaea. This related with 25.5 and 42.3% of total OTUs for bacteria and archaea, respectively, that showed a significant difference in their DNA and RNA profiles. Similar operational parameters affected the bacterial and archaeal community, yet the differentiating effect between DNA and RNA was much stronger for archaea. Co-occurrence networks and functional prediction profiling confirmed the clear differentiation between DNA and RNA profiles. CONCLUSIONS In conclusion, a clear difference in active (RNA) and total (DNA) community profiles was observed, implying the need for a combined approach to estimate community stability in anaerobic digestion.
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Affiliation(s)
- Jo De Vrieze
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
- Infrastructure and Environment Research Division, School of Engineering, University of Glasgow, Rankine Building, Oakfield Avenue, Glasgow, G12 8LT UK
| | - Ameet J. Pinto
- Northeastern University, 360 Huntington Avenue, Boston, MA 02115 USA
| | - William T. Sloan
- Infrastructure and Environment Research Division, School of Engineering, University of Glasgow, Rankine Building, Oakfield Avenue, Glasgow, G12 8LT UK
| | - Umer Zeeshan Ijaz
- Infrastructure and Environment Research Division, School of Engineering, University of Glasgow, Rankine Building, Oakfield Avenue, Glasgow, G12 8LT UK
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Tashiro Y, Kanda K, Asakura Y, Kii T, Cheng H, Poudel P, Okugawa Y, Tashiro K, Sakai K. A Unique Autothermal Thermophilic Aerobic Digestion Process Showing a Dynamic Transition of Physicochemical and Bacterial Characteristics from the Mesophilic to the Thermophilic Phase. Appl Environ Microbiol 2018; 84:e02537-17. [PMID: 29305505 PMCID: PMC5835747 DOI: 10.1128/aem.02537-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 12/20/2017] [Indexed: 01/01/2023] Open
Abstract
A unique autothermal thermophilic aerobic digestion (ATAD) process has been used to convert human excreta to liquid fertilizer in Japan. This study investigated the changes in physicochemical and bacterial community characteristics during the full-scale ATAD process operated for approximately 3 weeks in 2 different years. After initiating simultaneous aeration and mixing using an air-inducing circulator (aerator), the temperature autothermally increased rapidly in the first 1 to 2 days with exhaustive oxygen consumption, leading to a drastic decrease and gradual increase in oxidation-reduction potential in the first 2 days, reached >50°C in the middle 4 to 6 days, and remained steady in the final phase. Volatile fatty acids were rapidly consumed and diminished in the first 2 days, whereas the ammonia nitrogen concentration was relatively stable during the process, despite a gradual pH increase to 9.3. Principal-coordinate analysis of 16S rRNA gene amplicons using next-generation sequencing divided the bacterial community structures into distinct clusters corresponding to three phases, and they were similar in the final phase in both years despite different transitions in the middle phase. The predominant phyla (closest species, dominancy) in the initial, middle, and final phases were Proteobacteria (Arcobacter trophiarum, 19 to 43%; Acinetobacter towneri, 6.3 to 30%), Bacteroidetes (Moheibacter sediminis, 43 to 54%), and Firmicutes (Thermaerobacter composti, 11 to 28%; Heliorestis baculata, 2.1 to 16%), respectively. Two predominant operational taxonomic units (OTUs) in the final phase showed very low similarities to the closest species, indicating that the process is unique compared with previously published ones. This unique process with three distinctive phases would be caused by the aerator with complete aeration.IMPORTANCE Although the autothermal thermophilic aerobic digestion (ATAD) process has several advantages, such as a high degradation capacity, a short treatment period, and inactivation of pathogens, one of the factors limiting its broad application is the high electric power consumption for aerators with a full-scale bioreactor. We elucidated the dynamics of the bacterial community structures, as well as the physicochemical characteristics, in the ATAD process with a full-scale bioreactor from human excreta for 3 weeks. Our results indicated that this unique process can be divided into three distinguishable phases by an aerator with complete aeration and showed a possibility of shortening the digestion period to approximately 10 days. This research not only helps to identify which bacteria play significant roles and how the process can be improved and controlled but also demonstrates an efficient ATAD process with less electric power consumption for worldwide application.
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Affiliation(s)
- Yukihiro Tashiro
- Laboratory of Soil and Environmental Microbiology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School of Bioresources and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
- Laboratory of Microbial Environmental Protection, Tropical Microbiology Unit, Center for International Education and Research of Agriculture, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Kosuke Kanda
- Laboratory of Soil and Environmental Microbiology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School of Bioresources and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Yuya Asakura
- Laboratory of Soil and Environmental Microbiology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School of Bioresources and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Toshihiko Kii
- Laboratory of Soil and Environmental Microbiology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School of Bioresources and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Huijun Cheng
- Laboratory of Soil and Environmental Microbiology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School of Bioresources and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Pramod Poudel
- Laboratory of Soil and Environmental Microbiology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School of Bioresources and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Yuki Okugawa
- Laboratory of Soil and Environmental Microbiology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School of Bioresources and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Kosuke Tashiro
- Laboratory of Molecular Gene Technology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka, Japan
| | - Kenji Sakai
- Laboratory of Soil and Environmental Microbiology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School of Bioresources and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
- Laboratory of Microbial Environmental Protection, Tropical Microbiology Unit, Center for International Education and Research of Agriculture, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
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State of the art on granular sludge by using bibliometric analysis. Appl Microbiol Biotechnol 2018; 102:3453-3473. [PMID: 29497798 DOI: 10.1007/s00253-018-8844-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 02/02/2018] [Accepted: 02/05/2018] [Indexed: 02/07/2023]
Abstract
With rapid industrialization and urbanization in the nineteenth century, the activated sludge process (ASP) has experienced significant steps forward in the face of greater awareness of and sensitivity toward water-related environmental problems. Compared with conventional flocculent ASP, the major advantages of granular sludge are characterized by space saving and resource recovery, where the methane and hydrogen recovery in anaerobic granular and 50% more space saving, 30-50% of energy consumption reduction, 75% of footprint cutting, and even alginate recovery in aerobic granular. Numerous engineers and scientists have made great efforts to explore the superiority over the last 40 years. Therefore, a bibliometric analysis was desired to trace the global trends of granular sludge research from 1992 to 2016 indexed in the SCI-EXPANDED. Articles were published in 276 journals across 44 subject categories spanning 1420 institutes across 68 countries. Bioresource Technology (293, 11.9%), Water Research (235, 9.6%), and Applied Microbiology and Biotechnology (127, 5.2%) dominated in top three journals. The Engineering (991, 40.3%), China (906, 36.9%), and Harbin Inst Technol, China (114, 4.6%) were the most productive subject category, country, and institution, respectively. The hotspot is the emerging techniques depended on granular reactors in response to the desired removal requirements and bio-energy production (primarily in anaerobic granular sludge). In view of advanced and novel bio-analytical methods, the characteristics, functions, and mechanisms for microbial granular were further revealed in improving and innovating the granulation techniques. Therefore, a promising technique armed with strengthened treatment efficiency and efficient resource and bio-energy recovery can be achieved.
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Wang X, Ye C, Zhang Z, Guo Y, Yang R, Chen S. Effects of temperature shock on N 2O emissions from denitrifying activated sludge and associated active bacteria. BIORESOURCE TECHNOLOGY 2018; 249:605-611. [PMID: 29091844 DOI: 10.1016/j.biortech.2017.10.070] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 10/15/2017] [Accepted: 10/18/2017] [Indexed: 06/07/2023]
Abstract
To investigate the effects of temperature shock on N2O emissions, four treatments with rapidly changing incubation temperature from the control (20 °C) to 4, 12, 25, or 34 °C were conducted. Results showed that higher N2O emissions (0.023-0.37%) were observed when reactor contents received temperature shocks. N2O emissions increased as the temperature interval increased. Nitrate, nitrite, and nitrous oxide reduction rates generally followed the order: 34 °C > 25 °C > 20 °C > 12 °C > 4°C. Overall, the low-temperature shocks down-regulated and high-temperature shocks up-regulated the expression of denitrifying genes. However, the transcription rate of norB/nosZ and nirS/nosZ could not explain higher N2O emission. The increased N2O emissions might be more related to post-transcriptional regulation and enzyme activity (Q10 value). The results of cDNA sequencing showed that the active microbial community was relatively stable. Among the members of top 15 genera with active transcripts, Flavobacterium, Comamonadaceae and Xanthomonadales were the dominant denitrifying bacteria.
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Affiliation(s)
- Xiaojun Wang
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Chengsong Ye
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Zhaoji Zhang
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yan Guo
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Ruili Yang
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Shaohua Chen
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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118
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Wang S, Zuo X, Zhao X, Awada T, Luo Y, Li Y, Qu H. Dominant plant species shape soil bacterial community in semiarid sandy land of northern China. Ecol Evol 2018; 8:1693-1704. [PMID: 29435244 PMCID: PMC5792618 DOI: 10.1002/ece3.3746] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 11/04/2017] [Accepted: 11/26/2017] [Indexed: 01/22/2023] Open
Abstract
Plant species affect soil bacterial diversity and compositions. However, little is known about the role of dominant plant species in shaping the soil bacterial community during the restoration of sandy grasslands in Horqin Sandy Land, northern China. We established a mesocosm pots experiment to investigate short-term responses of soil bacterial diversity and composition, and the related soil properties in degraded soils without vegetation (bare sand as the control, CK) to restoration with five plant species that dominate across restoration stages: Agriophyllum squarrosum (AS), Artemisia halodendron (AH), Setaria viridis (SV), Chenopodium acuminatum (CA), and Corispermum macrocarpum (CM). We used redundancy analysis (RDA) to analyze the association between soil bacterial composition and soil properties in different plant species. Our results indicated that soil bacterial diversity was significantly lower in vegetated soils independent of plant species than in the CK. Specifically, soil bacterial species richness and diversity were lower under the shrub AH and the herbaceous plants AS, SV, and CA, and soil bacterial abundance was lower under AH compared with the CK. A field investigation confirmed the same trends where soil bacteria diversity was lower under AS and AH than in bare sand. The high-sequence annotation analysis showed that Proteobacteria, Actinobacteria, and Bacteroidetes were the most common phyla in sandy land irrespective of soil plant cover. The OTUs (operational taxonomic units) indicated that some bacterial species were specific to the host plants. Relative to bare sand (CK), soils with vegetative cover exhibited lower soil water content and temperature, and higher soil carbon and nitrogen contents. The RDA result indicated that, in addition to plant species, soil water and nitrogen contents were the most important factors shaping soil bacterial composition in semiarid sandy land. Our study from the pot and field investigations clearly demonstrated that planting dominant species in bare sand impacts bacterial diversity. In semiarid ecosystems, changes in the dominant plant species during vegetation restoration efforts can affect the soil bacterial diversity and composition through the direct effects of plants and the indirect effects of soil properties that are driven by plant species.
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Affiliation(s)
- Shaokun Wang
- Urat Desert‐grassland Research StationNorthwest Institute of Eco‐Environment and ResourcesChinese Academy of SciencesLanzhouChina
- Naiman Desertification Research StationNorthwest Institute of Eco‐Environment and ResourcesChinese Academy of SciencesLanzhouChina
- School of Natural Resources and Agricultural Research DivisionUniversity of Nebraska‐LincolnLincolnNEUSA
| | - Xiaoan Zuo
- Urat Desert‐grassland Research StationNorthwest Institute of Eco‐Environment and ResourcesChinese Academy of SciencesLanzhouChina
- Naiman Desertification Research StationNorthwest Institute of Eco‐Environment and ResourcesChinese Academy of SciencesLanzhouChina
| | - Xueyong Zhao
- Urat Desert‐grassland Research StationNorthwest Institute of Eco‐Environment and ResourcesChinese Academy of SciencesLanzhouChina
- Naiman Desertification Research StationNorthwest Institute of Eco‐Environment and ResourcesChinese Academy of SciencesLanzhouChina
| | - Tala Awada
- School of Natural Resources and Agricultural Research DivisionUniversity of Nebraska‐LincolnLincolnNEUSA
| | - Yongqing Luo
- Urat Desert‐grassland Research StationNorthwest Institute of Eco‐Environment and ResourcesChinese Academy of SciencesLanzhouChina
| | - Yuqiang Li
- Urat Desert‐grassland Research StationNorthwest Institute of Eco‐Environment and ResourcesChinese Academy of SciencesLanzhouChina
- Naiman Desertification Research StationNorthwest Institute of Eco‐Environment and ResourcesChinese Academy of SciencesLanzhouChina
| | - Hao Qu
- Urat Desert‐grassland Research StationNorthwest Institute of Eco‐Environment and ResourcesChinese Academy of SciencesLanzhouChina
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Calusinska M, Goux X, Fossépré M, Muller EEL, Wilmes P, Delfosse P. A year of monitoring 20 mesophilic full-scale bioreactors reveals the existence of stable but different core microbiomes in bio-waste and wastewater anaerobic digestion systems. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:196. [PMID: 30038663 PMCID: PMC6052691 DOI: 10.1186/s13068-018-1195-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 07/06/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND Anaerobic digestion (AD) is a microbe-driven process of biomass decomposition to CH4 and CO2. In addition to renewable and cost-effective energy production, AD has emerged in the European Union as an environmentally friendly model of bio-waste valorisation and nutrient recycling. Nevertheless, due to the high diversity of uncharacterised microbes, a typical AD microbiome is still considered as "dark matter". RESULTS Using the high-throughput sequencing of small rRNA gene, and a monthly monitoring of the physicochemical parameters for 20 different mesophilic full-scale bioreactors over 1 year, we generated a detailed view of AD microbial ecology towards a better understanding of factors that influence and shape these communities. By studying the broadly distributed OTUs present in over 80% of analysed samples, we identified putatively important core bacteria and archaea to the AD process that accounted for over 70% of the whole microbial community relative abundances. AD reactors localised at the wastewater treatment plants were shown to operate with distinct core microbiomes than the agricultural and bio-waste treating biogas units. We also showed that both the core microbiomes were composed of low (with average community abundance ≤ 1%) and highly abundant microbial populations; the vast majority of which remains yet uncharacterised, e.g. abundant candidate Cloacimonetes. Using non-metric multidimensional scaling, we observed microorganisms grouping into clusters that well reflected the origin of the samples, e.g. wastewater versus agricultural and bio-waste treating biogas units. The calculated diversity patterns differed markedly between the different community clusters, mainly due to the presence of highly diverse and dynamic transient species. Core microbial communities appeared relatively stable over the monitoring period. CONCLUSIONS In this study, we characterised microbial communities in different AD systems that were monitored over a 1-year period. Evidences were shown to support the concept of a core community driving the AD process, whereas the vast majority of dominant microorganisms remain yet to be characterised.
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Affiliation(s)
- Magdalena Calusinska
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, 41 rue du Brill, 4422 Belvaux, Luxembourg
| | - Xavier Goux
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, 41 rue du Brill, 4422 Belvaux, Luxembourg
| | - Marie Fossépré
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, 41 rue du Brill, 4422 Belvaux, Luxembourg
| | - Emilie E. L. Muller
- Eco-Systems Biology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 avenue des Hauts-Fourneaux, 4362 Esch-sur-Alzette, Luxembourg
- Department of Microbiology, Genomics and the Environment, Université de Strasbourg, CNRS, GMGM, UMR 7156, Strasbourg, France
| | - Paul Wilmes
- Eco-Systems Biology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 avenue des Hauts-Fourneaux, 4362 Esch-sur-Alzette, Luxembourg
| | - Philippe Delfosse
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, 41 rue du Brill, 4422 Belvaux, Luxembourg
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120
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Dennehy C, Lawlor PG, McCabe MS, Cormican P, Sheahan J, Jiang Y, Zhan X, Gardiner GE. Anaerobic co-digestion of pig manure and food waste; effects on digestate biosafety, dewaterability, and microbial community dynamics. WASTE MANAGEMENT (NEW YORK, N.Y.) 2018; 71:532-541. [PMID: 29113838 DOI: 10.1016/j.wasman.2017.10.047] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 10/26/2017] [Accepted: 10/27/2017] [Indexed: 06/07/2023]
Abstract
This study assessed the effect of varying pig manure (PM)/food waste (FW) mixing ratio and hydraulic retention time (HRT) on methane yields, digestate dewaterability, enteric indicator bacteria and microbial communities during anaerobic co-digestion. Three 10 L digesters were operated at 39 °C, each with a PM/FW feedstock composition of 85%/15%, 63%/37% and 40%/60% (volatile solids basis). While the PM/FW ratio was different among reactors, the organic loading rate applied was equal, and increased stepwise with reducing HRT. The effects of three different HRTs were studied: 41, 29, and 21 days. Increasing the proportion of FW in the feedstock significantly increased methane yields, but had no significant effect on counts of enteric indicator bacteria in the digestate or specific resistance to filtration, suggesting that varying the PM/FW feedstock composition at the mixing ratios studied should not have major consequences for digestate disposal. Decreasing HRT significantly increased volumetric methane yields, increased digestate volatile solids concentrations and increased the proportion of particles >500 µm in the digestate, indicating that decreasing HRT to 21 days reduced methane conversion efficiency High throughput 16S rRNA sequencing data revealed that microbial communities were just slightly affected by changes in digester operating conditions. These results would provide information useful when optimizing the start-up and operation of biogas plants treating these substrates.
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Affiliation(s)
- C Dennehy
- Civil Engineering, College of Engineering and Informatics, National University of Ireland, Galway, Ireland
| | - P G Lawlor
- Teagasc Pig Development Department, Animal and Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - M S McCabe
- Teagasc Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Grange, Dunsany, Co. Meath, Ireland
| | - P Cormican
- Teagasc Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Grange, Dunsany, Co. Meath, Ireland
| | - J Sheahan
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, Ireland
| | - Y Jiang
- Civil Engineering, College of Engineering and Informatics, National University of Ireland, Galway, Ireland
| | - X Zhan
- Civil Engineering, College of Engineering and Informatics, National University of Ireland, Galway, Ireland.
| | - G E Gardiner
- Department of Science, Waterford Institute of Technology, Ireland
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121
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Jia Y, Ng SK, Lu H, Cai M, Lee PKH. Genome-centric metatranscriptomes and ecological roles of the active microbial populations during cellulosic biomass anaerobic digestion. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:117. [PMID: 29713376 PMCID: PMC5911951 DOI: 10.1186/s13068-018-1121-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/16/2018] [Indexed: 05/13/2023]
Abstract
BACKGROUND Although anaerobic digestion for biogas production is used worldwide in treatment processes to recover energy from carbon-rich waste such as cellulosic biomass, the activities and interactions among the microbial populations that perform anaerobic digestion deserve further investigations, especially at the population genome level. To understand the cellulosic biomass-degrading potentials in two full-scale digesters, this study examined five methanogenic enrichment cultures derived from the digesters that anaerobically digested cellulose or xylan for more than 2 years under 35 or 55 °C conditions. RESULTS Metagenomics and metatranscriptomics were used to capture the active microbial populations in each enrichment culture and reconstruct their meta-metabolic network and ecological roles. 107 population genomes were reconstructed from the five enrichment cultures using a differential coverage binning approach, of which only a subset was highly transcribed in the metatranscriptomes. Phylogenetic and functional convergence of communities by enrichment condition and phase of fermentation was observed for the highly transcribed populations in the metatranscriptomes. In the 35 °C cultures grown on cellulose, Clostridium cellulolyticum-related and Ruminococcus-related bacteria were identified as major hydrolyzers and primary fermenters in the early growth phase, while Clostridium leptum-related bacteria were major secondary fermenters and potential fatty acid scavengers in the late growth phase. While the meta-metabolism and trophic roles of the cultures were similar, the bacterial populations performing each function were distinct between the enrichment conditions. CONCLUSIONS Overall, a population genome-centric view of the meta-metabolism and functional roles of key active players in anaerobic digestion of cellulosic biomass was obtained. This study represents a major step forward towards understanding the microbial functions and interactions at population genome level during the microbial conversion of lignocellulosic biomass to methane. The knowledge of this study can facilitate development of potential biomarkers and rational design of the microbiome in anaerobic digesters.
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Affiliation(s)
- Yangyang Jia
- B5423-AC1, School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Siu-Kin Ng
- B5423-AC1, School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Hongyuan Lu
- B5423-AC1, School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Mingwei Cai
- B5423-AC1, School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Patrick K. H. Lee
- B5423-AC1, School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
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Free A, McDonald MA, Pagaling E. Diversity-Function Relationships in Natural, Applied, and Engineered Microbial Ecosystems. ADVANCES IN APPLIED MICROBIOLOGY 2018; 105:131-189. [PMID: 30342721 DOI: 10.1016/bs.aambs.2018.07.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The connection between ecosystem function and taxonomic diversity has been of interest and relevance to macroecologists for decades. After many years of lagging behind due to the difficulty of assigning both taxonomy and function to poorly distinguishable microscopic cells, microbial ecology now has access to a suite of powerful molecular tools which allow its practitioners to generate data relating to diversity and function of a microbial community on an unprecedented scale. Instead, the problem facing today's microbial ecologists is coupling the ease of generation of these datasets with the formulation and testing of workable hypotheses relating the diversity and function of environmental, host-associated, and engineered microbial communities. Here, we review the current state of knowledge regarding the links between taxonomic alpha- and beta-diversity and ecosystem function, comparing our knowledge in this area to that obtained by macroecologists who use more traditional techniques. We consider the methodologies that can be applied to study these properties and how successful they are at linking function to diversity, using examples from the study of model microbial ecosystems, methanogenic bioreactors (anaerobic digesters), and host-associated microbiota. Finally, we assess ways in which our newly acquired understanding might be used to manipulate diversity in ecosystems of interest in order to improve function for the benefit of us or the environment in general through the provision of ecosystem services.
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Affiliation(s)
- Andrew Free
- School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Michael A McDonald
- School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Eulyn Pagaling
- The James Hutton Institute, Craigiebuckler, Aberdeen, United Kingdom
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Amha YM, Anwar MZ, Brower A, Jacobsen CS, Stadler LB, Webster TM, Smith AL. Inhibition of anaerobic digestion processes: Applications of molecular tools. BIORESOURCE TECHNOLOGY 2018; 247:999-1014. [PMID: 28918349 DOI: 10.1016/j.biortech.2017.08.210] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 08/30/2017] [Accepted: 08/31/2017] [Indexed: 05/25/2023]
Abstract
Inhibition of anaerobic digestion (AD) due to perturbation caused by substrate composition and/or operating conditions can significantly reduce performance. Such perturbations could be limited by elucidating microbial community response to inhibitors and devising strategies to increase community resilience. To this end, advanced molecular methods are increasingly being applied to study the AD microbiome, a diverse community of microbial populations with complex interactions. This literature review of AD inhibition studies indicates that inhibitory concentrations are highly variable, likely stemming from differences in community structure or activity profile and previous exposure to inhibitors. More recent molecular methods such as 'omics' tools, substrate mapping, and real-time sequencing are helping to unravel the complexity of AD inhibition by elucidating physiological and ecological significance of key microbial populations. The AD community must strive towards developing predictive abilities to avoid system failure (e.g., real-time tracking of an indicator species) to improve resilience of AD systems.
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Affiliation(s)
- Yamrot M Amha
- Astani Department of Civil and Environmental Engineering, University of Southern California, 3620 South Vermont Avenue, Los Angeles, CA 90089, USA
| | - Muhammad Zohaib Anwar
- mBioInform ApS, Ole Maaloes Vej 3, 2200 Copenhagen N, Denmark; Department of Environmental Sciences, Aarhus University, Frederiksborgvej, 399, 4000 Roskilde, Denmark
| | - Andrew Brower
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, TX 77005, USA
| | - Carsten S Jacobsen
- mBioInform ApS, Ole Maaloes Vej 3, 2200 Copenhagen N, Denmark; Department of Environmental Sciences, Aarhus University, Frederiksborgvej, 399, 4000 Roskilde, Denmark
| | - Lauren B Stadler
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, TX 77005, USA
| | - Tara M Webster
- Soil and Crop Sciences Section, Cornell University, 306 Tower Road, Ithaca, NY 14853, USA
| | - Adam L Smith
- Astani Department of Civil and Environmental Engineering, University of Southern California, 3620 South Vermont Avenue, Los Angeles, CA 90089, USA.
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Li L, Peng X, Wang X, Wu D. Anaerobic digestion of food waste: A review focusing on process stability. BIORESOURCE TECHNOLOGY 2018; 248:20-28. [PMID: 28711296 DOI: 10.1016/j.biortech.2017.07.012] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 06/30/2017] [Accepted: 07/04/2017] [Indexed: 06/07/2023]
Abstract
Food waste (FW) is rich in biomass energy, and increasing numbers of national programs are being established to recover energy from FW using anaerobic digestion (AD). However process instability is a common operational issue for AD of FW. Process monitoring and control as well as microbial management can be used to control instability and increase the energy conversion efficiency of anaerobic digesters. Here, we review research progress related to these methods and identify existing limitations to efficient AD; recommendations for future research are also discussed. Process monitoring and control are suitable for evaluating the current operational status of digesters, whereas microbial management can facilitate early diagnosis and process optimization. Optimizing and combining these two methods are necessary to improve AD efficiency.
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Affiliation(s)
- Lei Li
- Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Xuya Peng
- Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China.
| | - Xiaoming Wang
- Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Di Wu
- Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
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125
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Ziels RM, Sousa DZ, Stensel HD, Beck DAC. DNA-SIP based genome-centric metagenomics identifies key long-chain fatty acid-degrading populations in anaerobic digesters with different feeding frequencies. THE ISME JOURNAL 2018; 12:112-123. [PMID: 28895946 PMCID: PMC5737908 DOI: 10.1038/ismej.2017.143] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 06/22/2017] [Accepted: 07/22/2017] [Indexed: 12/14/2022]
Abstract
Fats, oils and greases (FOG) are energy-dense wastes that can be added to anaerobic digesters to substantially increase biomethane recovery via their conversion through long-chain fatty acids (LCFAs). However, a better understanding of the ecophysiology of syntrophic LCFA-degrading microbial communities in anaerobic digesters is needed to develop operating strategies that mitigate inhibitory LCFA accumulation from FOG. In this research, DNA stable isotope probing (SIP) was coupled with metagenomic sequencing for a genome-centric comparison of oleate (C18:1)-degrading populations in two anaerobic codigesters operated with either a pulse feeding or continuous-feeding strategy. The pulse-fed codigester microcosms converted oleate into methane at over 20% higher rates than the continuous-fed codigester microcosms. Differential coverage binning was demonstrated for the first time to recover population genome bins (GBs) from DNA-SIP metagenomes. About 70% of the 13C-enriched GBs were taxonomically assigned to the Syntrophomonas genus, thus substantiating the importance of Syntrophomonas species to LCFA degradation in anaerobic digesters. Phylogenetic comparisons of 13C-enriched GBs showed that phylogenetically distinct Syntrophomonas GBs were unique to each codigester. Overall, these results suggest that syntrophic populations in anaerobic digesters can have different adaptive capacities, and that selection for divergent populations may be achieved by adjusting reactor operating conditions to maximize biomethane recovery.
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Affiliation(s)
- Ryan M Ziels
- Department of Civil Engineering, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - H David Stensel
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - David A C Beck
- eScience Institute, University of Washington, Seattle, WA, USA
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
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126
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Koch C, Korth B, Harnisch F. Microbial ecology-based engineering of Microbial Electrochemical Technologies. Microb Biotechnol 2018; 11:22-38. [PMID: 28805354 PMCID: PMC5743830 DOI: 10.1111/1751-7915.12802] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 07/11/2017] [Accepted: 07/12/2017] [Indexed: 11/27/2022] Open
Abstract
Microbial ecology is devoted to the understanding of dynamics, activity and interaction of microorganisms in natural and technical ecosystems. Bioelectrochemical systems represent important technical ecosystems, where microbial ecology is of highest importance for their function. However, whereas aspects of, for example, materials and reactor engineering are commonly perceived as highly relevant, the study and engineering of microbial ecology are significantly underrepresented in bioelectrochemical systems. This shortfall may be assigned to a deficit on knowledge and power of these methods as well as the prerequisites for their thorough application. This article discusses not only the importance of microbial ecology for microbial electrochemical technologies but also shows which information can be derived for a knowledge-driven engineering. Instead of providing a comprehensive list of techniques from which it is hard to judge the applicability and value of information for a respective one, this review illustrates the suitability of selected techniques on a case study. Thereby, best practice for different research questions is provided and a set of key questions for experimental design, data acquisition and analysis is suggested.
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Affiliation(s)
- Christin Koch
- Department of Environmental MicrobiologyHelmholtz Centre for Environmental Research GmbH ‐ UFZPermoserstraße 1504318LeipzigGermany
| | - Benjamin Korth
- Department of Environmental MicrobiologyHelmholtz Centre for Environmental Research GmbH ‐ UFZPermoserstraße 1504318LeipzigGermany
| | - Falk Harnisch
- Department of Environmental MicrobiologyHelmholtz Centre for Environmental Research GmbH ‐ UFZPermoserstraße 1504318LeipzigGermany
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127
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Świątczak P, Cydzik-Kwiatkowska A. Performance and microbial characteristics of biomass in a full-scale aerobic granular sludge wastewater treatment plant. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:1655-1669. [PMID: 29101689 PMCID: PMC5766719 DOI: 10.1007/s11356-017-0615-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 10/24/2017] [Indexed: 05/27/2023]
Abstract
By modification of the operational conditions of batch reactors, a municipal wastewater treatment plant was upgraded from activated sludge to aerobic granular sludge (AGS) technology. After upgrading, the volume of the biological reactors was reduced by 30%, but the quality of the effluent substantially improved. The concentration of biomass in the reactors increased twofold; the average biomass yield was 0.6 g MLVSS/g COD, and excess granular sludge was efficiently stabilized in aerobic conditions. Canonical correspondence analysis based on the results of next-generation sequencing showed that the time of adaptation significantly influenced the microbial composition of the granules. In mature granules, the abundance of ammonium-oxidizing bacteria was very low, while the abundance of the nitrite-oxidizing bacteria Nitrospira sp. was 0.5 ± 0.1%. The core genera were Tetrasphaera, Sphingopyxis, Dechloromonas, Flavobacterium, and Ohtaekwangia. Bacteria belonging to these genera produce extracellular polymeric substances, which stabilize granule structure and accumulate phosphorus. The results of this study will be useful for designers of AGS wastewater treatment plants, and molecular data given here provide insight into the ecology of mature aerobic granules from a full-scale facility.
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Affiliation(s)
- Piotr Świątczak
- Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, Sloneczna 45G, 10-709, Olsztyn, Poland
| | - Agnieszka Cydzik-Kwiatkowska
- Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, Sloneczna 45G, 10-709, Olsztyn, Poland.
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128
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Zamanzadeh M, Hagen LH, Svensson K, Linjordet R, Horn SJ. Biogas production from food waste via co-digestion and digestion- effects on performance and microbial ecology. Sci Rep 2017; 7:17664. [PMID: 29247239 PMCID: PMC5732306 DOI: 10.1038/s41598-017-15784-w] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 11/02/2017] [Indexed: 12/13/2022] Open
Abstract
In this work, performance and microbial structure of a digestion (food waste-only) and a co-digestion process (mixture of cow manure and food waste) were studied at mesophilic (37 °C) and thermophilic (55 °C) temperatures. The highest methane yield (480 mL/g VS) was observed in the mesophilic digester (MDi) fed with food waste alone. The mesophilic co-digestion of food waste and manure (McoDi) yielded 26% more methane than the sum of individual digestions of manure and food waste. The main volatile fatty acid (VFA) in the mesophilic systems was acetate, averaging 93 and 172 mg/L for McoDi and MDi, respectively. Acetate (2150 mg/L) and propionate (833 mg/L) were the main VFAs in the thermophilic digester (TDi), while propionate (163 mg/L) was the major VFA in the thermophilic co-digester (TcoDi). The dominant bacteria in MDi was Chloroflexi (54%), while Firmicutes was dominant in McoDi (60%). For the mesophilic reactors, the dominant archaea was Methanosaeta in MDi, while Methanobacterium and Methanosaeta had similar abundance in McoDi. In the thermophilic systems, the dominant bacteria were Thermotogae, Firmicutes and Synergistetes in both digesters, however, the relative abundance of these phyla were different. For archaea, the genus Methanothermobacter were entirely dominant in both TDi and TcoDi.
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Affiliation(s)
- Mirzaman Zamanzadeh
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P. O. Box 5003, N-1432, Ås, Norway
- Department of Environmental Health Engineering, School of Public Health, Tehran University of Medical Sciences, P.O. Box 14155-6446, Tehran, Iran
- Department of Civil and Environmental Engineering, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Live Heldal Hagen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P. O. Box 5003, N-1432, Ås, Norway
| | - Kine Svensson
- Nibio, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Roar Linjordet
- Nibio, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Svein Jarle Horn
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P. O. Box 5003, N-1432, Ås, Norway.
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129
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Xu D, Liu S, Chen Q, Ni J. Microbial community compositions in different functional zones of Carrousel oxidation ditch system for domestic wastewater treatment. AMB Express 2017; 7:40. [PMID: 28205101 PMCID: PMC5311017 DOI: 10.1186/s13568-017-0336-y] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Accepted: 01/31/2017] [Indexed: 11/10/2022] Open
Abstract
The microbial community diversity in anaerobic-, anoxic- and oxic-biological zones of a conventional Carrousel oxidation ditch system for domestic wastewater treatment was systematically investigated. The monitored results of the activated sludge sampled from six full-scale WWTPs indicated that Proteobacteria, Chloroflexi, Bacteroidetes, Actinobacteria, Verrucomicrobia, Acidobacteria and Nitrospirae were dominant phyla, and Nitrospira was the most abundant and ubiquitous genus across the three biological zones. The anaerobic-, anoxic- and oxic-zones shared approximately similar percentages across the 50 most abundant genera, and three genera (i.e. uncultured bacterium PeM15, Methanosaeta and Bellilinea) presented statistically significantly differential abundance in the anoxic-zone. Illumina high-throughput sequences related to ammonium oxidizer organisms and denitrifiers with top50 abundance in all samples were Nitrospira, uncultured Nitrosomonadaceae, Dechloromonas, Thauera, Denitratisoma, Rhodocyclaceae (norank) and Comamonadaceae (norank). Moreover, environmental variables such as water temperature, water volume, influent ammonium nitrogen, influent chemical oxygen demand (COD) and effluent COD exhibited significant correlation to the microbial community according to the Monte Carlo permutation test analysis (p < 0.05). The abundance of Nitrospira, uncultured Nitrosomonadaceae and Denitratisoma presented strong positive correlations with the influent/effluent concentration of COD and ammonium nitrogen, while Dechloromonas, Thauera, Rhodocyclaceae (norank) and Comamonadaceae (norank) showed positive correlations with water volume and temperature. The established relationship between microbial community and environmental variables in different biologically functional zones of the six representative WWTPs at different geographical locations made the present work of potential use for evaluation of practical wastewater treatment processes.
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130
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Jia X, Xi B, Li M, Liu D, Hou J, Hao Y, Meng F. Metaproteomic analysis of the relationship between microbial community phylogeny, function and metabolic activity during biohydrogen-methane coproduction under short-term hydrothermal pretreatment from food waste. BIORESOURCE TECHNOLOGY 2017; 245:1030-1039. [PMID: 28946205 DOI: 10.1016/j.biortech.2017.08.180] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/25/2017] [Accepted: 08/29/2017] [Indexed: 06/07/2023]
Abstract
Short-term hydrothermal pretreatment (SHP) is an attractive method for food waste anaerobic digestion, which facilitates the solubilisation of recalcitrant particles. This study employed metaproteomic method to evaluate the relationships among microbial community phylogeny, function, and metabolic activity during two-stage anaerobic digestion under SHP (SHPT) from food waste. The presence of 651 bacterial proteins and 477 archaeal protein has been detected by liquid chromatography online linked to mass spectrometry, revealing a high metabolic heterogeneity during SHPT. The different stages of SHPT highlighted important roles for the bacterial proteins from Gammaproteobacteria, Bacilli, and Clostridia and the archaeal proteins from Methanosarcinales. The identified proteins related to biohydrogen production come from pyruvic acid decarboxylase and formic acid decomposition pathway in carbohydrate metabolism and methanogenesis from acetate, CO2 and a methylotrophic pathway during energy metabolism. This could provide functional evidence of the metabolic activities and biogas production during SHPT.
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Affiliation(s)
- Xuan Jia
- Key Laboratory of Cleaner Production and Integrated Resource Utilization of China National Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Beidou Xi
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Mingxiao Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Dongming Liu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Jiaqi Hou
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Yan Hao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Fanhua Meng
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
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131
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McIlroy SJ, Kirkegaard RH, McIlroy B, Nierychlo M, Kristensen JM, Karst SM, Albertsen M, Nielsen PH. MiDAS 2.0: an ecosystem-specific taxonomy and online database for the organisms of wastewater treatment systems expanded for anaerobic digester groups. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2017; 2017:3074787. [PMID: 28365734 PMCID: PMC5467571 DOI: 10.1093/database/bax016] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 02/13/2017] [Indexed: 11/13/2022]
Abstract
Wastewater is increasingly viewed as a resource, with anaerobic digester technology being routinely implemented for biogas production. Characterising the microbial communities involved in wastewater treatment facilities and their anaerobic digesters is considered key to their optimal design and operation. Amplicon sequencing of the 16S rRNA gene allows high-throughput monitoring of these systems. The MiDAS field guide is a public resource providing amplicon sequencing protocols and an ecosystem-specific taxonomic database optimized for use with wastewater treatment facility samples. The curated taxonomy endeavours to provide a genus-level-classification for abundant phylotypes and the online field guide links this identity to published information regarding their ecology, function and distribution. This article describes the expansion of the database resources to cover the organisms of the anaerobic digester systems fed primary sludge and surplus activated sludge. The updated database includes descriptions of the abundant genus-level-taxa in influent wastewater, activated sludge and anaerobic digesters. Abundance information is also included to allow assessment of the role of emigration in the ecology of each phylotype. MiDAS is intended as a collaborative resource for the progression of research into the ecology of wastewater treatment, by providing a public repository for knowledge that is accessible to all interested in these biotechnologically important systems. Database URL http://www.midasfieldguide.org.
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Affiliation(s)
- Simon Jon McIlroy
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg DK-9220, Denmark
| | - Rasmus Hansen Kirkegaard
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg DK-9220, Denmark
| | - Bianca McIlroy
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg DK-9220, Denmark
| | - Marta Nierychlo
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg DK-9220, Denmark
| | - Jannie Munk Kristensen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg DK-9220, Denmark
| | - Søren Michael Karst
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg DK-9220, Denmark
| | - Mads Albertsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg DK-9220, Denmark
| | - Per Halkjær Nielsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg DK-9220, Denmark
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Doloman A, Soboh Y, Walters AJ, Sims RC, Miller CD. Qualitative Analysis of Microbial Dynamics during Anaerobic Digestion of Microalgal Biomass in a UASB Reactor. Int J Microbiol 2017; 2017:5291283. [PMID: 29259629 PMCID: PMC5702946 DOI: 10.1155/2017/5291283] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 09/04/2017] [Accepted: 09/10/2017] [Indexed: 11/18/2022] Open
Abstract
Anaerobic digestion (AD) is a microbiologically coordinated process with dynamic relationships between bacterial players. Current understanding of dynamic changes in the bacterial composition during the AD process is incomplete. The objective of this research was to assess changes in bacterial community composition that coordinates with anaerobic codigestion of microalgal biomass cultivated on municipal wastewater. An upflow anaerobic sludge blanket reactor was used to achieve high rates of microalgae decomposition and biogas production. Samples of the sludge were collected throughout AD and extracted DNA was subjected to next-generation sequencing using methanogen mcrA gene specific and universal bacterial primers. Analysis of the data revealed that samples taken at different stages of AD had varying bacterial composition. A group consisting of Bacteroidales, Pseudomonadales, and Enterobacteriales was identified to be putatively responsible for the hydrolysis of microalgal biomass. The methanogenesis phase was dominated by Methanosarcina mazei. Results of observed changes in the composition of microbial communities during AD can be used as a road map to stimulate key bacterial species identified at each phase of AD to increase yield of biogas and rate of substrate decomposition. This research demonstrates a successful exploitation of methane production from microalgae without any biomass pretreatment.
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Affiliation(s)
- Anna Doloman
- Department of Biological Engineering, Utah State University, Old Main Hill 4105, Logan, UT 84322-4105, USA
| | - Yousef Soboh
- Department of Food Processing, Palestine Technical Colleges, Arroub, P.O. Box 14, West Bank, State of Palestine
| | - Andrew J. Walters
- Department of Biological Engineering, Utah State University, Old Main Hill 4105, Logan, UT 84322-4105, USA
| | - Ronald C. Sims
- Department of Biological Engineering, Utah State University, Old Main Hill 4105, Logan, UT 84322-4105, USA
| | - Charles D. Miller
- Department of Biological Engineering, Utah State University, Old Main Hill 4105, Logan, UT 84322-4105, USA
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133
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Mei R, Nobu MK, Narihiro T, Kuroda K, Muñoz Sierra J, Wu Z, Ye L, Lee PKH, Lee PH, van Lier JB, McInerney MJ, Kamagata Y, Liu WT. Operation-driven heterogeneity and overlooked feed-associated populations in global anaerobic digester microbiome. WATER RESEARCH 2017; 124:77-84. [PMID: 28750287 DOI: 10.1016/j.watres.2017.07.050] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Revised: 07/18/2017] [Accepted: 07/19/2017] [Indexed: 05/11/2023]
Abstract
Anaerobic digester (AD) microbiomes harbor complex, interacting microbial populations to achieve biomass reduction and biogas production, however how they are influenced by operating conditions and feed sludge microorganisms remain unclear. These were addressed by analyzing the microbial communities of 90 full-scale digesters at 51 municipal wastewater treatment plants from five countries. Heterogeneity detected in community structures suggested that no single AD microbiome could be defined. Instead, the AD microbiomes were classified into eight clusters driven by operating conditions (e.g., pretreatment, temperature range, and salinity), whereas geographic location of the digesters did not have significant impacts. Comparing digesters populations with those present in the corresponding feed sludge led to the identification of a hitherto overlooked feed-associated microbial group (i.e., the residue populations). They accounted for up to 21.4% of total sequences in ADs operated at low temperature, presumably due to ineffective digestion, and as low as 0.8% in ADs with pretreatment. Within each cluster, a core microbiome was defined, including methanogens, syntrophic metabolizers, fermenters, and the newly described residue populations. Our work provides insights into the key factors shaping full-scale AD microbiomes in a global scale, and draws attentions to the overlooked residue populations.
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Affiliation(s)
- Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Masaru K Nobu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Kyohei Kuroda
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Environmental Systems Engineering, Nagaoka University of Technology, Kami-tomioka, Niigata, Japan
| | - Julian Muñoz Sierra
- Section Sanitary Engineering, Department of Water Management, Delft University of Technology, Delft, The Netherlands
| | - Zhuoying Wu
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Lin Ye
- School of the Environment, Nanjing University, Nanjing, Jiangsu, China
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong
| | - Po-Heng Lee
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Jules B van Lier
- Section Sanitary Engineering, Department of Water Management, Delft University of Technology, Delft, The Netherlands
| | - Michael J McInerney
- Department of Botany and Microbiology, University of Oklahoma, Norman, OK, USA
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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134
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Xu R, Yang ZH, Zheng Y, Zhang HB, Liu JB, Xiong WP, Zhang YR, Ahmad K. Depth-resolved microbial community analyses in the anaerobic co-digester of dewatered sewage sludge with food waste. BIORESOURCE TECHNOLOGY 2017; 244:824-835. [PMID: 28841787 DOI: 10.1016/j.biortech.2017.07.056] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 07/08/2017] [Accepted: 07/10/2017] [Indexed: 06/07/2023]
Abstract
This study evaluated the impacts of FW addition on co-digestion in terms of microbial community. Anaerobic co-digestion (AcoD) reactors were conducted at gradually increased addition of food waste (FW) from 0 to 4kg-VSm-3d-1 for 220days. Although no markable acidification was found at an OLR of 4kg-VSm-3d-1, the unhealthy operation was observed in aspect of an inhibited methane yield (185mLg-1VSadded), which was restricted by 40% when compared with its peak value. Deterioration of digestion process was timely indicated by the dramatic decrease of archaeal population and microbial biodiversity. Furthermore, the cooperation network showed a considerable number of rare species (<1%) were strongly correlated with methane production, which were frequently overlooked due to the limits of detecting resolution or analysis methods before. Advances in the analysis of sensitive microbial community enable us to detect the early disturbances in AcoD reactors.
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Affiliation(s)
- Rui Xu
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Zhao-Hui Yang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China.
| | - Yue Zheng
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195, United States
| | - Hai-Bo Zhang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Jian-Bo Liu
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Wei-Ping Xiong
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Yan-Ru Zhang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Kito Ahmad
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
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135
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Wang X, Yang T, Lin B, Tang Y. Effects of salinity on the performance, microbial community, and functional proteins in an aerobic granular sludge system. CHEMOSPHERE 2017; 184:1241-1249. [PMID: 28672723 DOI: 10.1016/j.chemosphere.2017.06.047] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Revised: 06/07/2017] [Accepted: 06/13/2017] [Indexed: 06/07/2023]
Abstract
The response mechanism of aerobic granular sludge (AGS) systems to salt stress in high-salinity wastewater treatment processes has not been fully elucidated in current studies. The aim of this study was to reveal the comprehensive effects of salinity on AGS characteristics using microbial community and metaproteomics analyses. The results showed that the removal efficiency of COD, TN and TP decreased significantly with increasing salinity. Under salt stress, the Na+ content in AGS decreased, while the K+ and Ca2+ contents increased. This was because the salt-tolerant mechanism of the microorganisms was dependent on the uptake of K+ and ejection of Na+via K+/Na+ pumps, Na+/H+ reversed transport proteins, and K+ channels. Compared with the salt-free condition, 14 of 25 different protein spots were identified successfully by metaproteomic analysis, including porin, periplasmic-binding protein, and ATP-binding cassette-type for phosphonate transporter, which were expressed mainly by members of γ-Proteobacteria and α-Proteobacteria. The variations in functional proteins and microbial community revealed that α- and γ-Proteobacteria had disproportionally active and the metabolic activity of β-Proteobacteria was inhibited by increasing salinity. Additionally, Psychrobacter sp. was confirmed to be a predominant bacterium at 15 g/L NaCl, as the porin was strongly expressed.
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Affiliation(s)
- Xingang Wang
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212018, PR China.
| | - Tongyi Yang
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212018, PR China.
| | - Bing Lin
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212018, PR China.
| | - Yubin Tang
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212018, PR China.
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136
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The microbiome as engineering tool: Manufacturing and trading between microorganisms. N Biotechnol 2017; 39:206-214. [DOI: 10.1016/j.nbt.2017.07.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 04/21/2017] [Accepted: 07/01/2017] [Indexed: 11/24/2022]
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137
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Dong X, Kleiner M, Sharp CE, Thorson E, Li C, Liu D, Strous M. Fast and Simple Analysis of MiSeq Amplicon Sequencing Data with MetaAmp. Front Microbiol 2017; 8:1461. [PMID: 28824589 PMCID: PMC5540949 DOI: 10.3389/fmicb.2017.01461] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 07/20/2017] [Indexed: 11/18/2022] Open
Abstract
Microbial community profiling by barcoded 16S rRNA gene amplicon sequencing currently has many applications in microbial ecology. The low costs of the parallel sequencing of multiplexed samples, combined with the relative ease of data processing and interpretation (compared to shotgun metagenomes) have made this an entry-level approach. Here we present the MetaAmp pipeline for processing of SSU rRNA gene and other non-coding or protein-coding amplicon sequencing data by investigators that are inexperienced with bioinformatics procedures. It accepts single-end or paired-end sequences in fasta or fastq format from various sequencing platforms. It includes read quality control, and merging of forward and reverse reads of paired-end reads. It makes use of UPARSE, Mothur, and the SILVA database for clustering, removal of chimeric reads, taxonomic classification, and generation of diversity metrics. The pipeline has been validated with a mock community of known composition. MetaAmp provides a convenient web interface as well as command line interface. It is freely available at: http://ebg.ucalgary.ca/metaamp. Since its launch 2 years ago, MetaAmp has been used >2,800 times, by many users worldwide.
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Affiliation(s)
- Xiaoli Dong
- Department of Geoscience, University of CalgaryCalgary, AB, Canada
| | - Manuel Kleiner
- Department of Geoscience, University of CalgaryCalgary, AB, Canada
| | | | - Erin Thorson
- Department of Geoscience, University of CalgaryCalgary, AB, Canada
| | - Carmen Li
- Department of Biological Sciences, University of CalgaryCalgary, AB, Canada
| | - Dan Liu
- Department of Geoscience, University of CalgaryCalgary, AB, Canada
| | - Marc Strous
- Department of Geoscience, University of CalgaryCalgary, AB, Canada
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138
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Bio-methane from an-aerobic digestion using activated carbon adsorption. Anaerobe 2017; 46:33-40. [DOI: 10.1016/j.anaerobe.2017.05.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 03/06/2017] [Accepted: 05/04/2017] [Indexed: 11/22/2022]
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139
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Guo J, Ni BJ, Han X, Chen X, Bond P, Peng Y, Yuan Z. Unraveling microbial structure and diversity of activated sludge in a full-scale simultaneous nitrogen and phosphorus removal plant using metagenomic sequencing. Enzyme Microb Technol 2017; 102:16-25. [DOI: 10.1016/j.enzmictec.2017.03.009] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 03/19/2017] [Accepted: 03/20/2017] [Indexed: 12/25/2022]
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140
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McIlroy SJ, Kirkegaard RH, Dueholm MS, Fernando E, Karst SM, Albertsen M, Nielsen PH. Culture-Independent Analyses Reveal Novel Anaerolineaceae as Abundant Primary Fermenters in Anaerobic Digesters Treating Waste Activated Sludge. Front Microbiol 2017; 8:1134. [PMID: 28690595 PMCID: PMC5481317 DOI: 10.3389/fmicb.2017.01134] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 06/06/2017] [Indexed: 11/13/2022] Open
Abstract
Anaerobic digestion for biogas production is reliant on the tightly coupled synergistic activities of complex microbial consortia. Members of the uncultured A6 phylotype, within the phylum Chloroflexi, are among the most abundant genus-level-taxa of mesophilic anaerobic digester systems treating primary and surplus sludge from wastewater treatment plants, yet are known only by their 16S rRNA gene sequence. This study applied metagenomics to obtain a complete circular genome (2.57 Mbp) from a representative of the A6 taxon. Preliminary annotation of the genome indicates these organisms to be anaerobic chemoorganoheterotrophs with a fermentative metabolism. Given their observed abundance, they are likely important primary fermenters in digester systems. Application of fluorescence in situ hybridisation probes designed in this study revealed their morphology to be short filaments present within the flocs. The A6 were sometimes co-located with the filamentous Archaea Methanosaeta spp. suggesting potential undetermined synergistic relationships. Based on its genome sequence and morphology we propose the species name Brevefilum fermentans gen. nov. sp. nov.
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Affiliation(s)
- Simon J McIlroy
- The Centre for Microbial Communities, Department of Chemistry and Bioscience, Aalborg UniversityAalborg, Denmark
| | - Rasmus H Kirkegaard
- The Centre for Microbial Communities, Department of Chemistry and Bioscience, Aalborg UniversityAalborg, Denmark
| | - Morten S Dueholm
- The Centre for Microbial Communities, Department of Chemistry and Bioscience, Aalborg UniversityAalborg, Denmark
| | - Eustace Fernando
- The Centre for Microbial Communities, Department of Chemistry and Bioscience, Aalborg UniversityAalborg, Denmark
| | - Søren M Karst
- The Centre for Microbial Communities, Department of Chemistry and Bioscience, Aalborg UniversityAalborg, Denmark
| | - Mads Albertsen
- The Centre for Microbial Communities, Department of Chemistry and Bioscience, Aalborg UniversityAalborg, Denmark
| | - Per H Nielsen
- The Centre for Microbial Communities, Department of Chemistry and Bioscience, Aalborg UniversityAalborg, Denmark
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141
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Ziels RM, Beck DAC, Stensel HD. Long-chain fatty acid feeding frequency in anaerobic codigestion impacts syntrophic community structure and biokinetics. WATER RESEARCH 2017; 117:218-229. [PMID: 28402870 DOI: 10.1016/j.watres.2017.03.060] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/28/2017] [Accepted: 03/29/2017] [Indexed: 05/23/2023]
Abstract
This study investigated the impacts of long-chain fatty acid (LCFA) feeding frequencies on microbial community structure, bioconversion kinetics, and process stability during anaerobic codigestion. Parallel laboratory-scale anaerobic codigesters fed with dairy cattle manure were either pulse-fed every two days or continuously-fed daily, respectively, with oleate (C18:1) in incremental step increases over 200 days up to 64% of the influent chemical oxygen demand (COD). The effluent acetate concentration exceeded 3000 mg/L in the continuous-fed codigester at the highest oleate loading rate, but remained below 100 mg/L in the pulse-fed codigester at the end of its 48-hr oleate feed cycle. Maximum substrate conversion rates of oleate (qmax, oleate) and acetate (qmax, acetate) were significantly higher in the pulse-fed codigester compared to the continuous-fed codigester. 16S rRNA gene amplicon sequencing showed that Bacteria and Archaea community profiles diverged based on the codigester LCFA feeding pattern and loading rate. LCFA-degrading Syntrophomonas bacteria were significantly enriched in both LCFA codigesters relative to the control digester. The pulse-fed codigester had the highest community fraction of Syntrophomonas 16S rRNA genes by the end of the experiment with 43% of Bacteria amplicon sequences. qmax, oleate and qmax, acetate values were both significantly correlated to absolute concentrations of Syntrophomonas and Methanosaeta 16S rRNA genes, respectively. Multiple-linear regression models based on the absolute abundance of Syntrophomonas and Methanosaeta taxa provided improved predictions of oleate and acetate bioconversion kinetics, respectively. These results collectively suggest that pulse feeding rather than continuous feeding LCFA during anaerobic codigestion selected for higher microbial bioconversion kinetics and functional stability, which were related to changes in the physiological diversity and adaptive capacity of syntrophic and methanogenic communities.
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Affiliation(s)
- Ryan M Ziels
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA; Department of Civil Engineering, University of British Columbia, Vancouver, Canada.
| | - David A C Beck
- eScience Institute, University of Washington, Seattle, WA, USA; Department of Chemical Engineering, University of Washington, Seattle, WA, USA
| | - H David Stensel
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
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142
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Drennan DM, Almstrand R, Ladderud J, Lee I, Landkamer L, Figueroa L, Sharp JO. Spatial impacts of inorganic ligand availability and localized microbial community structure on mitigation of zinc laden mine water in sulfate-reducing bioreactors. WATER RESEARCH 2017; 115:50-59. [PMID: 28259814 DOI: 10.1016/j.watres.2017.02.037] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 02/17/2017] [Accepted: 02/17/2017] [Indexed: 06/06/2023]
Abstract
Sulfate-reducing bioreactors (SRBRs) represent a passive, sustainable, and long-term option for mitigating mining influenced water (MIW) during release. Here we investigate spatial zinc precipitation profiles as influenced by substrate differentiation, inorganic ligand availability (inorganic carbon and sulfide), and microbial community structure in pilot-scale SRBR columns fed with sulfate and zinc-rich MIW. Through a combination of aqueous sampling, geochemical digests, electron microscopy and energy-dispersive x-ray spectroscopy, we were able to delineate zones of enhanced zinc removal, identify precipitates of varying stability, and discern the temporal and spatial evolution of zinc, sulfur, and calcium associations. These geochemical insights revealed spatially variable immobilization regimes between SRBR columns that could be further contrasted as a function of labile (alfalfa-dominated) versus recalcitrant (woodchip-dominated) solid-phase substrate content. Both column subsets exhibited initial zinc removal as carbonates; however precipitation in association with labile substrates was more pronounced and dominated by metal-sulfide formation in the upper portions of the down flow columns with micrographs visually suggestive of sphalerite (ZnS). In contrast, a more diffuse and lower mass of zinc precipitation in the presence of gypsum-like precipitates occurred within the more recalcitrant column systems. While removal and sulfide-associated precipitation were spatially variable, whole bacterial community structure (ANOSIM) and diversity estimates were comparatively homogeneous. However, two phyla exhibited a potentially selective relationship with a significant positive correlation between the ratio of Firmicutes to Bacteroidetes and sulfide-bound zinc. Collectively these biogeochemical insights indicate that depths of maximal zinc sulfide precipitation are temporally dynamic, influenced by substrate composition and broaden our understanding of bio-immobilized zinc species, microbial interactions and potential operational and monitoring tools in these types of passive bioreactors.
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Affiliation(s)
- Dina M Drennan
- Colorado School of Mines, Department of Civil and Environmental Engineering, 1500 Illinois St., Golden, CO 80401, USA
| | - Robert Almstrand
- Colorado School of Mines, Department of Civil and Environmental Engineering, 1500 Illinois St., Golden, CO 80401, USA; Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Box 7026, 75007 Uppsala, Sweden
| | - Jeffrey Ladderud
- Colorado School of Mines, Hydrologic Science and Engineering Program, 1500 Illinois St., Golden, CO 80401, USA; Freeport McMoRan Inc., 1600 Hanley Blvd., Oro Valley, AZ 85737, USA
| | - Ilsu Lee
- Freeport McMoRan Inc., 1600 Hanley Blvd., Oro Valley, AZ 85737, USA
| | - Lee Landkamer
- Colorado School of Mines, Department of Civil and Environmental Engineering, 1500 Illinois St., Golden, CO 80401, USA
| | - Linda Figueroa
- Colorado School of Mines, Department of Civil and Environmental Engineering, 1500 Illinois St., Golden, CO 80401, USA
| | - Jonathan O Sharp
- Colorado School of Mines, Department of Civil and Environmental Engineering, 1500 Illinois St., Golden, CO 80401, USA; Colorado School of Mines, Hydrologic Science and Engineering Program, 1500 Illinois St., Golden, CO 80401, USA.
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143
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Kouzuma A, Tsutsumi M, Ishii S, Ueno Y, Abe T, Watanabe K. Non-autotrophic methanogens dominate in anaerobic digesters. Sci Rep 2017; 7:1510. [PMID: 28473726 PMCID: PMC5431450 DOI: 10.1038/s41598-017-01752-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 04/03/2017] [Indexed: 12/12/2022] Open
Abstract
Anaerobic digesters are man-made habitats for fermentative and methanogenic microbes, and are characterized by extremely high concentrations of organics. However, little is known about how microbes adapt to such habitats. In the present study, we report phylogenetic, metagenomic, and metatranscriptomic analyses of microbiomes in thermophilic packed-bed digesters fed acetate as the major substrate, and we have shown that acetoclastic and hydrogenotrophic methanogens that utilize acetate as a carbon source dominate there. Deep sequencing and precise binning of the metagenomes reconstructed complete genomes for two dominant methanogens affiliated with the genera Methanosarcina and Methanothermobacter, along with 37 draft genomes. The reconstructed Methanosarcina genome was almost identical to that of a thermophilic acetoclastic methanogen Methanosarcina thermophila TM-1, indicating its cosmopolitan distribution in thermophilic digesters. The reconstructed Methanothermobacter (designated as Met2) was closely related to Methanothermobacter tenebrarum, a non-autotrophic hydrogenotrophic methanogen that grows in the presence of acetate. Met2 lacks the Cdh complex required for CO2 fixation, suggesting that it requires organic molecules, such as acetate, as carbon sources. Although the metagenomic analysis also detected autotrophic methanogens, they were less than 1% in abundance of Met2. These results suggested that non-autotrophic methanogens preferentially grow in anaerobic digesters containing high concentrations of organics.
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Affiliation(s)
- Atsushi Kouzuma
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, 192-0392, Japan.
| | - Maho Tsutsumi
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, 192-0392, Japan
| | - Shun'ichi Ishii
- R&D Center for Submarine Resources, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi, 783-8502, Japan
| | - Yoshiyuki Ueno
- Kajima Technical Research Institute, Chofu, Tokyo, 182-0036, Japan
| | - Takashi Abe
- Graduate School of Science and Technology, Niigata University, Niigata, Niigata, 950-2181, Japan
| | - Kazuya Watanabe
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, 192-0392, Japan
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144
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Microbial Community Ability to Adapt to Altered Temperature Conditions Influences Operating Stability in Anaerobic Digestion. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.egypro.2017.03.408] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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145
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Ju F, Lau F, Zhang T. Linking Microbial Community, Environmental Variables, and Methanogenesis in Anaerobic Biogas Digesters of Chemically Enhanced Primary Treatment Sludge. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:3982-3992. [PMID: 28240534 DOI: 10.1021/acs.est.6b06344] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Understanding the influences of biotic and abiotic factors on microbial community structure and methanogenesis are important for its engineering and ecological significance. In this study, four biogas digesters were supplied with the same inoculum and feeding sludge but operated at different sludge retention time (7 to 16 days) and organic loading rates for 90 days to determine the relative influence of biotic and environmental factors on the microbial community assembly and methanogenic performance. Despite different operational parameters, all digester communities were dominated by Bacteroidales, Clostridiales, and Thermotogales and followed the same trend of population dynamics over time. Network and multivariate analyses suggest that deterministic factors, including microbial competition (involving Bacteroidales spp.), niche differentiation (e.g., within Clostridiales spp.), and periodic microbial immigration (from feed sludge), are the key drivers of microbial community assembly and dynamics. A yet-to-be-cultured phylotype of Bacteroidales (GenBank ID: GU389558.1 ) is implicated as a strong competitor for carbohydrates. Moreover, biogas-producing rate and methane content were significantly related with the abundances of functional populations rather than any operational or physicochemical parameter, revealing microbiological mediation of methanogenesis. Combined, this study enriches our understandings of biological and environmental drivers of microbial community assembly and performance in anaerobic digesters.
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Affiliation(s)
- Feng Ju
- Environmental Biotechnology Lab, The University of Hong Kong , Hong Kong SAR, China
| | - Frankie Lau
- Drainage Services Department, The Government of the Hong Kong Special Administrative Region , Hong Kong SAR, China
| | - Tong Zhang
- Environmental Biotechnology Lab, The University of Hong Kong , Hong Kong SAR, China
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146
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Wu LH, Lu ZM, Zhang XJ, Wang ZM, Yu YJ, Shi JS, Xu ZH. Metagenomics reveals flavour metabolic network of cereal vinegar microbiota. Food Microbiol 2017; 62:23-31. [DOI: 10.1016/j.fm.2016.09.010] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 06/11/2016] [Accepted: 09/15/2016] [Indexed: 01/28/2023]
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147
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Krakat N, Anjum R, Demirel B, Schröder P. Methodological flaws introduce strong bias into molecular analysis of microbial populations. J Appl Microbiol 2017; 122:364-377. [PMID: 27914209 DOI: 10.1111/jam.13365] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 11/08/2016] [Accepted: 11/24/2016] [Indexed: 11/29/2022]
Abstract
AIMS In this study, we report how different cell disruption methods, PCR primers and in silico analyses can seriously bias results from microbial population studies, with consequences for the credibility and reproducibility of the findings. Our results emphasize the pitfalls of commonly used experimental methods that can seriously weaken the interpretation of results. METHODS AND RESULTS Four different cell lysis methods, three commonly used primer pairs and various computer-based analyses were applied to investigate the microbial diversity of a fermentation sample composed of chicken dung. The fault-prone, but still frequently used, amplified rRNA gene restriction analysis was chosen to identify common weaknesses. In contrast to other studies, we focused on the complete analytical process, from cell disruption to in silico analysis, and identified potential error rates. This identified a wide disagreement of results between applied experimental approaches leading to very different community structures depending on the chosen approach. CONCLUSIONS The interpretation of microbial diversity data remains a challenge. In order to accurately investigate the taxonomic diversity and structure of prokaryotic communities, we suggest a multi-level approach combining DNA-based and DNA-independent techniques. SIGNIFICANCE AND IMPACT OF THE STUDY The identified weaknesses of commonly used methods to study microbial diversity can be overcome by a multi-level approach, which produces more reliable data about the fate and behaviour of microbial communities of engineered habitats such as biogas plants, so that the best performance can be ensured.
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Affiliation(s)
- N Krakat
- Department of Bioprocess-Engineering, Leibniz Institute for Agricultural Engineering and Bio-Economy Potsdam, Potsdam, Germany
| | - R Anjum
- Department of Bioprocess-Engineering, Leibniz Institute for Agricultural Engineering and Bio-Economy Potsdam, Potsdam, Germany
| | - B Demirel
- Institute of Environmental Science, Boğaziçi University, Istanbul, Turkey
| | - P Schröder
- Department of Geomikrobiologie, Helmholtz-Zentrum Potsdam, Deutsches Geoforschungszentrum, Telegrafenberg, Potsdam, Germany
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148
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Yun YM, Sung S, Shin HS, Han JI, Kim HW, Kim DH. Producing desulfurized biogas through removal of sulfate in the first-stage of a two-stage anaerobic digestion. Biotechnol Bioeng 2017; 114:970-979. [DOI: 10.1002/bit.26233] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 12/01/2016] [Accepted: 12/04/2016] [Indexed: 11/05/2022]
Affiliation(s)
- Yeo-Myeong Yun
- College of Agriculture, Forestry and Natural Resource Management; University of Hawaii at Hilo; 200 W. Kawili Street Hilo Hawaii 96720
| | - Shihwu Sung
- College of Agriculture, Forestry and Natural Resource Management; University of Hawaii at Hilo; 200 W. Kawili Street Hilo Hawaii 96720
| | - Hang-Sik Shin
- Department of Civil and Environmental Engineering; KAIST; 291 Daehak-ro Yuseong-gu Daejeon 305-701 Republic of Korea
| | - Jong-In Han
- Department of Civil and Environmental Engineering; KAIST; 291 Daehak-ro Yuseong-gu Daejeon 305-701 Republic of Korea
| | - Hyun-Woo Kim
- Department of Environmental Engineering; Chonbuk National University; 567 Baekjedae-ro Deokjin-gu Jeonju Jeonbuk 561-756 Republic of Korea
| | - Dong-Hoon Kim
- Department of Civil Engineering; Inha University; 100 Inha-ro Nam-gu Incheon Republic of Korea
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149
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Thijs S, Sillen W, Weyens N, Vangronsveld J. Phytoremediation: State-of-the-art and a key role for the plant microbiome in future trends and research prospects. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2017; 19:23-38. [PMID: 27484694 DOI: 10.1080/15226514.2016.1216076] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Phytoremediation is increasingly adopted as a more sustainable approach for soil remediation. However, significant advances in efficiency are still necessary to attain higher levels of environmental and economic sustainability. Current interventions do not always give the expected outcomes in field settings due to an incomplete understanding of the multicomponent biological interactions. New advances in -omics are gradually implemented for studying microbial communities of polluted land in situ. This opens new perspectives for the discovery of biodegradative strains and provides us new ways of interfering with microbial communities to enhance bioremediation rates. This review presents retrospectives and future perspectives for plant microbiome studies relevant to phytoremediation, as well as some knowledge gaps in this promising research field. The implementation of phytoremediation in soil clean-up management systems is discussed, and an overview of the promoting factors that determine the growth of the phytoremediation market is given. Continuous growth is expected since elimination of contaminants from the environment is demanded. The evolution of scientific thought from a reductionist view to a more holistic approach will boost phytoremediation as an efficient and reliable phytotechnology. It is anticipated that phytoremediation will prove the most promising for organic contaminant degradation and bioenergy crop production on marginal land.
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Affiliation(s)
- Sofie Thijs
- a Centre for Environmental Sciences, Hasselt University , Diepenbeek , Belgium
| | - Wouter Sillen
- a Centre for Environmental Sciences, Hasselt University , Diepenbeek , Belgium
| | - Nele Weyens
- a Centre for Environmental Sciences, Hasselt University , Diepenbeek , Belgium
| | - Jaco Vangronsveld
- a Centre for Environmental Sciences, Hasselt University , Diepenbeek , Belgium
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150
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Lovley DR. Happy together: microbial communities that hook up to swap electrons. ISME JOURNAL 2016; 11:327-336. [PMID: 27801905 DOI: 10.1038/ismej.2016.136] [Citation(s) in RCA: 179] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 08/29/2016] [Accepted: 09/04/2016] [Indexed: 12/22/2022]
Abstract
The discovery of direct interspecies electron transfer (DIET) and cable bacteria has demonstrated that microbial cells can exchange electrons over long distances (μm-cm) through electrical connections. For example, in the presence of cable bacteria electrons are rapidly transported over centimeter distances, coupling the oxidation of reduced sulfur compounds in anoxic sediments to oxygen reduction in overlying surficial sediments. Bacteria and archaea wired for DIET are found in anaerobic methane-producing and methane-consuming communities. Electrical connections between gut microbes and host cells have also been proposed. Iterative environmental and defined culture studies on methanogenic communities revealed the importance of electrically conductive pili and c-type cytochromes in natural electrical grids, and demonstrated that conductive carbon materials and magnetite can substitute for these biological connectors to facilitate DIET. This understanding has led to strategies to enhance and stabilize anaerobic digestion. Key unknowns warranting further investigation include elucidation of the archaeal electrical connections facilitating DIET-based methane production and consumption; and the mechanisms for long-range electron transfer through cable bacteria. A better understanding of mechanisms for cell-to-cell electron transfer could facilitate the hunt for additional electrically connected microbial communities with omics approaches and could advance spin-off applications such as the development of sustainable bioelectronics materials and bioelectrochemical technologies.
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Affiliation(s)
- Derek R Lovley
- Department of Microbiology, Morrill IV N Science Center, University of Massachusetts, Amherst, MA, USA
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