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Liu B, Sträuber H, Centler F, Harms H, da Rocha UN, Kleinsteuber S. Functional Redundancy Secures Resilience of Chain Elongation Communities upon pH Shifts in Closed Bioreactor Ecosystems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:18350-18361. [PMID: 37097211 PMCID: PMC10666546 DOI: 10.1021/acs.est.2c09573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 04/13/2023] [Accepted: 04/13/2023] [Indexed: 06/19/2023]
Abstract
For anaerobic mixed cultures performing microbial chain elongation, it is unclear how pH alterations affect the abundance of key players, microbial interactions, and community functioning in terms of medium-chain carboxylate yields. We explored pH effects on mixed cultures enriched in continuous anaerobic bioreactors representing closed model ecosystems. Gradual pH increase from 5.5 to 6.5 induced dramatic shifts in community composition, whereas product range and yields returned to previous states after transient fluctuations. To understand community responses to pH perturbations over long-term reactor operation, we applied Aitchison PCA clustering, linear mixed-effects models, and random forest classification on 16S rRNA gene amplicon sequencing and process data. Different pH preferences of two key chain elongation species─one Clostridium IV species related to Ruminococcaceae bacterium CPB6 and one Clostridium sensu stricto species related to Clostridium luticellarii─were determined. Network analysis revealed positive correlations of Clostridium IV with lactic acid bacteria, which switched from Olsenella to Lactobacillus along the pH increase, illustrating the plasticity of the food web in chain elongation communities. Despite long-term cultivation in closed systems over the pH shift experiment, the communities retained functional redundancy in fermentation pathways, reflected by the emergence of rare species and concomitant recovery of chain elongation functions.
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Affiliation(s)
- Bin Liu
- Department
of Environmental Microbiology, Helmholtz
Centre for Environmental Research − UFZ, 04318 Leipzig, Germany
- KU
Leuven, Department of Microbiology,
Immunology and Transplantation, Rega Institute for Medical Research,
Laboratory of Molecular Bacteriology, BE-3000 Leuven, Belgium
| | - Heike Sträuber
- Department
of Environmental Microbiology, Helmholtz
Centre for Environmental Research − UFZ, 04318 Leipzig, Germany
| | - Florian Centler
- Department
of Environmental Microbiology, Helmholtz
Centre for Environmental Research − UFZ, 04318 Leipzig, Germany
- School
of Life Sciences, University of Siegen, 57076 Siegen, Germany
| | - Hauke Harms
- Department
of Environmental Microbiology, Helmholtz
Centre for Environmental Research − UFZ, 04318 Leipzig, Germany
| | - Ulisses Nunes da Rocha
- Department
of Environmental Microbiology, Helmholtz
Centre for Environmental Research − UFZ, 04318 Leipzig, Germany
| | - Sabine Kleinsteuber
- Department
of Environmental Microbiology, Helmholtz
Centre for Environmental Research − UFZ, 04318 Leipzig, Germany
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Application of Magnetite-Nanoparticles and Microbial Fuel Cell on Anaerobic Digestion: Influence of External Resistance. Microorganisms 2023; 11:microorganisms11030643. [PMID: 36985216 PMCID: PMC10055030 DOI: 10.3390/microorganisms11030643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/20/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
In this paper, the application of magnetite-nanoparticles and a microbial fuel cell (MFC) was studied on the anaerobic digestion (AD) of sewage sludge. The experimental set-up included six 1 L biochemical methane potential (BMP) tests with different external resistors: (a) 100 Ω, (b) 300 Ω, (c) 500 Ω, (d) 800 Ω, (e) 1000 Ω, and (f) a control with no external resistor. The BMP tests were carried out using digesters with a working volume of 0.8 L fed with 0.5 L substrate, 0.3 L inoculum, and 0.53 g magnetite-nanoparticles. The results suggested that the ultimate biogas generation reached 692.7 mL/g VSfed in the 500 Ω digester, which was substantially greater than the 102.6 mL/g VSfed of the control. The electrochemical efficiency analysis also demonstrated higher coulombic efficiency (81.2%) and maximum power density (30.17 mW/ m2) for the 500 Ω digester. The digester also revealed a higher maximum voltage generation of 0.431 V, which was approximately 12.7 times the 0.034 V of the lowest-performing MFC (100 Ω digester). In terms of contaminants removed, the best-performing digester was the digester with 500 Ω, which reduced contaminants by more than 89% on COD, TS, VS, TSS and color. In terms of cost-benefit analysis, this digester produced the highest annual energy profit (48.22 ZAR/kWh or 3.45 USD/kWh). This infers the application of magnetite-nanoparticles and MFC on the AD of sewage sludge is very promising for biogas production. The digester with an external resistor of 500 Ω showed a high potential for use in bioelectrochemical biogas generation and contaminant removal for sewage sludge.
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Gao Y, Chen Y, Luo Y, Liu J, Tian P, Nan Z, Zhou Q. The microbiota diversity of Festuca sinensis seeds in Qinghai-Tibet Plateau and their relationship with environments. Front Microbiol 2022; 13:956489. [PMID: 35992719 PMCID: PMC9382023 DOI: 10.3389/fmicb.2022.956489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/01/2022] [Indexed: 11/15/2022] Open
Abstract
A total of 14 Festuca sinensis seed lots were collected from different geographical locations on the Qinghai-Tibet Plateau to study the seed microbiota and determine the abiotic (temperature, precipitation, and elevation) and biotic (Epichloë sinensis infection rate) factors likely to shape the seed microbiome. The 14 seed lots had different bacterial and fungal structures and significantly different diversities (p < 0.05). The α-diversity indices of the bacteria were significantly correlated with precipitation (p < 0.05), whereas those of the fungi were significantly correlated with temperature (p < 0.05). Microbiota analysis showed that Proteobacteria, Cyanobacteria, and Bacteroidetes were the most abundant bacteria at the phylum level in the seeds, and Ascomycota and Basidiomycota were the most abundant fungi. β-diversity analysis suggested large differences in the microbial communities of each sample. Redundancy analysis showed that temperature and precipitation were the main environmental factors that drive variations in the microbial community, at the medium-high elevation (3,000–4,500 m), the impact of temperature and precipitation on microbial community is different, and the other elevations that effect on microbial community were basically identical. Spearman's correlation analysis showed that the relative abundances of the most abundant bacterial phyla were significantly correlated with temperature (p < 0.05), whereas those of the most abundant fungal phyla were significantly correlated with precipitation (p < 0.05). E. sinensis infection rates were significantly correlated with elevation and temperature (p < 0.05). These results suggest that temperature and precipitation are the key factors driving the microbial community, that temperature and elevation also had a great influence on the E. sinensis infection rate, and that environmental factors (temperature and elevation) may further affect the microbial community by regulating the E. sinensis infection rate.
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Affiliation(s)
- Yue Gao
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Youjun Chen
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Yang Luo
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Junying Liu
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Pei Tian
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
- *Correspondence: Pei Tian
| | - Zhibiao Nan
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Qingping Zhou
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
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Gopalakrishnappa C, Gowda K, Prabhakara KH, Kuehn S. An ensemble approach to the structure-function problem in microbial communities. iScience 2022; 25:103761. [PMID: 35141504 PMCID: PMC8810406 DOI: 10.1016/j.isci.2022.103761] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The metabolic activity of microbial communities plays a primary role in the flow of essential nutrients throughout the biosphere. Molecular genetics has revealed the metabolic pathways that model organisms utilize to generate energy and biomass, but we understand little about how the metabolism of diverse, natural communities emerges from the collective action of its constituents. We propose that quantifying and mapping metabolic fluxes to sequencing measurements of genomic, taxonomic, or transcriptional variation across an ensemble of diverse communities, either in the laboratory or in the wild, can reveal low-dimensional descriptions of community structure that can explain or predict their emergent metabolic activity. We survey the types of communities for which this approach might be best suited, review the analytical techniques available for quantifying metabolite fluxes in communities, and discuss what types of data analysis approaches might be lucrative for learning the structure-function mapping in communities from these data.
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Affiliation(s)
| | - Karna Gowda
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
- Center for the Physics of Evolving Systems, University of Chicago, Chicago, IL 60637, USA
| | - Kaumudi H. Prabhakara
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
- Center for the Physics of Evolving Systems, University of Chicago, Chicago, IL 60637, USA
| | - Seppe Kuehn
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
- Center for the Physics of Evolving Systems, University of Chicago, Chicago, IL 60637, USA
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5
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Xiao Y, Zan F, Zhang W, Hao T. Alleviating nutrient imbalance of low carbon-to-nitrogen ratio food waste in anaerobic digestion by controlling the inoculum-to-substrate ratio. BIORESOURCE TECHNOLOGY 2022; 346:126342. [PMID: 34785330 DOI: 10.1016/j.biortech.2021.126342] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
Abstract
Food waste (FW) characterized by a low carbon/nitrogen (C/N) ratio ranging between 6 and 19 was used to investigate the feasibility and mechanism of maneuvering inoculum-to-substrate ratio (ISR) to alleviate the metabolic imbalance caused by imbalanced nutrients in the AD process, through biochemical methane potential tests and methanogenic pathway analysis. The maximum methane yield of 0.4 L/g of volatile solid (VS) was obtained at a C/N ratio of 11 and an ISR of 10:3. Increasing ISR from 1:2 to 10:3 promoted methane production by ∼20% via an enhancement in acetoclastic methanogenesis and the hydrolysis of carbohydrates and proteins. At lower ISR < 1, hydrogenotrophic methanogenic and syntrophic bacteria dominated, and methane production decreased by ∼ 20% due to the energy disadvantages of syntrophic methanogenesis. Efficient digestion of FW with low C/N ratio FW could be achieved by using metabolic pathways to regulate it and increasing ISR from 1:1 to 10:3.
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Affiliation(s)
- Yihang Xiao
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau, China
| | - Feixiang Zan
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Weilan Zhang
- Department of Environmental and Sustainable Engineering, University at Albany, SUNY, Albany, NY 12222, USA
| | - Tianwei Hao
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau, China.
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6
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García-Depraect O, Castro-Muñoz R, Muñoz R, Rene ER, León-Becerril E, Valdez-Vazquez I, Kumar G, Reyes-Alvarado LC, Martínez-Mendoza LJ, Carrillo-Reyes J, Buitrón G. A review on the factors influencing biohydrogen production from lactate: The key to unlocking enhanced dark fermentative processes. BIORESOURCE TECHNOLOGY 2021; 324:124595. [PMID: 33453519 DOI: 10.1016/j.biortech.2020.124595] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/16/2020] [Accepted: 12/18/2020] [Indexed: 05/15/2023]
Abstract
Dark fermentation (DF) is one of the most promising biological methods to produce bio-hydrogen and other value added bio-products from carbohydrate-rich wastes and wastewater. However, process instability and low hydrogen production yields and rates have been highlighted as the major bottlenecks preventing further development. Numerous studies have associated such concerns with the inhibitory activity of lactate-producing bacteria (LAB) against hydrogen producers. However, an increasing number of studies have also shown lactate-based metabolic pathways as the prevailing platform for hydrogen production. This opens a vast potential to develop new strategies to deal with the "Achilles heel" of DF - LAB overgrowth - while untapping high-performance DF. This review discusses the key factors influencing the lactate-driven hydrogen production, paying particular attention to substrate composition, the operating conditions, as well as the microbiota involved in the process and its potential functionality and related biochemical routes. The current limitations and future perspectives in the field are also presented.
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Affiliation(s)
- Octavio García-Depraect
- Institute of Sustainable Processes, University of Valladolid, Dr. Mergelina, s/n, 47011 Valladolid, Spain.
| | - Roberto Castro-Muñoz
- Tecnologico de Monterrey, Campus Toluca, Avenida Eduardo Monroy Cárdenas 2000 San Antonio Buenavista, 50110 Toluca de Lerdo, Mexico; Gdansk University of Technology, Faculty of Chemistry, Department of Process Engineering and Chemical Technology, 11/12 Narutowicza St., 80-233 Gdansk, Poland
| | - Raúl Muñoz
- Institute of Sustainable Processes, University of Valladolid, Dr. Mergelina, s/n, 47011 Valladolid, Spain
| | - Eldon R Rene
- Department of Water Supply, Sanitation and Environmental Engineering, IHE Delft Institute for Water Education, P. O. Box 3015, 2601 DA Delft, the Netherlands
| | - Elizabeth León-Becerril
- Department of Environmental Technology, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C., Av. Normalistas 800, Colinas de la Normal, 44270 Guadalajara, Jalisco, Mexico
| | - Idania Valdez-Vazquez
- Unidad Académica Juriquilla, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Blvd. Juriquilla 3001, 76230 Querétaro, Mexico
| | - Gopalakrishnan Kumar
- Institute of Chemistry, Bioscience and Environmental Engineering, Faculty of Science and Technology, University of Stavanger, Box 8600 Forus, Stavanger 4036, Norway
| | - Luis C Reyes-Alvarado
- Unidad de Energía Renovable, Centro de Investigación Científica de Yucatán, A.C., Parque Científico de Yucatán, A.C., Carretera Sierra Papacal - Chuburná Puerto, km 5., 97302 Mérida, Yucatán, Mexico
| | - Leonardo J Martínez-Mendoza
- Department of Environmental Technology, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C., Av. Normalistas 800, Colinas de la Normal, 44270 Guadalajara, Jalisco, Mexico
| | - Julián Carrillo-Reyes
- Unidad Académica Juriquilla, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Blvd. Juriquilla 3001, 76230 Querétaro, Mexico
| | - Germán Buitrón
- Unidad Académica Juriquilla, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Blvd. Juriquilla 3001, 76230 Querétaro, Mexico
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7
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Dauptain K, Trably E, Santa-Catalina G, Bernet N, Carrere H. Role of indigenous bacteria in dark fermentation of organic substrates. BIORESOURCE TECHNOLOGY 2020; 313:123665. [PMID: 32574750 DOI: 10.1016/j.biortech.2020.123665] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/08/2020] [Accepted: 06/09/2020] [Indexed: 06/11/2023]
Abstract
Hydrogen production by dark fermentation of complex organic substrates, such as biowaste, can naturally take place with indigenous bacteria or by adding an external microbial inoculum issued from various natural environments. This study aims to determine whether indigenous bacteria associated with thermal pretreatment could impact dark fermentation performances. Biochemical hydrogen potential tests were carried out on seven organic substrates. Results showed a strong influence of the indigenous bacteria which are as effective as thermally pretreated exogenous bacteria to produce H2 and metabolites. High abundance in Clostridiales and/or Enterobacteriales was associated with high H2 yield. This study shows that no inoculum nor pretreatment are required to achieve satisfactory dark fermentation performances from organic waste.
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Affiliation(s)
- K Dauptain
- INRAE, Université de Montpellier, LBE, 102 avenue des Étangs, 11100 Narbonne, France
| | - E Trably
- INRAE, Université de Montpellier, LBE, 102 avenue des Étangs, 11100 Narbonne, France.
| | - G Santa-Catalina
- INRAE, Université de Montpellier, LBE, 102 avenue des Étangs, 11100 Narbonne, France
| | - N Bernet
- INRAE, Université de Montpellier, LBE, 102 avenue des Étangs, 11100 Narbonne, France
| | - H Carrere
- INRAE, Université de Montpellier, LBE, 102 avenue des Étangs, 11100 Narbonne, France
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Shaw JLA, Ernakovich JG, Judy JD, Farrell M, Whatmuff M, Kirby J. Long-term effects of copper exposure to agricultural soil function and microbial community structure at a controlled and experimental field site. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 263:114411. [PMID: 32247199 DOI: 10.1016/j.envpol.2020.114411] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 02/25/2020] [Accepted: 03/17/2020] [Indexed: 05/27/2023]
Abstract
The long-term effect of heavy metals on soil microbial communities and their function is relatively unknown and little work has been done in field settings. To address this gap, we revisited a field-based experiment, 12 years after the application of copper (Cu) to agricultural soils, with treatment concentrations ranging from 0 to 3310 mg Cu kg-1 soil. We measured the long-term effects of Cu exposure to soils using multiple functionality assessments and environmental DNA-based community analyses. The assessment results revealed that soils that received moderate to high Cu doses had still not recovered functionality 12-years post exposure. However, plots that received doses of 200 mg kg-1 Cu or less appeared to have a functionality index not dissimilar to control plots. Environmental DNA analyses of the microbial communities revealed a high level of beta diversity in low Cu treatment plots, whereas communities within high Cu treatment plots had similar community structures to one another (low beta diversity), indicating that specific Cu-tolerant or dormant taxa are selected for in high-Cu environments. Interestingly, high Cu plots had higher within-sample taxa counts (alpha diversity) compared with controls and low Cu plots. We hypothesise that taxa in high Cu plots activated dormancy mechanisms, such that their genetic signal remained present, whilst the functionality of the soil was reduced. Many species identified in high Cu plots are known to have associated dormancy mechanisms and survive in high stress environments. Understanding how these mechanisms collectively contribute to contaminant outcomes is of great importance for the goals of predicting and managing microbial communities and their function. As we found that Cu concentrations above 200 mg kg-1 can cause significant functionality loss and a selective pressure on microbial communities, it is recommended that Cu concentrations above 200 mg kg-1are avoided in agricultural soils.
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Affiliation(s)
- J L A Shaw
- Commonwealth Scientific and Industrial Research Organisation, Land and Water, Waite Road, Urrbrae, 5064, Australia.
| | - J G Ernakovich
- Commonwealth Scientific and Industrial Research Organisation, Agriculture & Food, Waite Road, Urrbrae, 5064, Australia; Department of Natural Resources and the Environment, University of New Hampshire, College Road, Durham, NH, 03824, USA
| | - J D Judy
- Commonwealth Scientific and Industrial Research Organisation, Land and Water, Waite Road, Urrbrae, 5064, Australia; University of Florida, Soil and Water Sciences Department, 1692 McCarty Dr, Gainesville, FL, 32603, USA
| | - M Farrell
- Commonwealth Scientific and Industrial Research Organisation, Agriculture & Food, Waite Road, Urrbrae, 5064, Australia
| | - M Whatmuff
- Agriculture NSW, NSW Department of Primary Industries, Private Mail Bag, 4008 Narellan, NSW, 2567, Australia
| | - J Kirby
- Commonwealth Scientific and Industrial Research Organisation, Land and Water, Waite Road, Urrbrae, 5064, Australia
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9
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Dynamic shifts within volatile fatty acid-degrading microbial communities indicate process imbalance in anaerobic digesters. Appl Microbiol Biotechnol 2020; 104:4563-4575. [PMID: 32219463 DOI: 10.1007/s00253-020-10552-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 03/04/2020] [Accepted: 03/15/2020] [Indexed: 10/24/2022]
Abstract
Buildup of volatile fatty acids (VFAs) in anaerobic digesters (ADs) often results in acidification and process failure. Understanding the dynamics of microbial communities involved in VFA degradation under stable and overload conditions may help optimize anaerobic digestion processes. In this study, five triplicate mesophilic completely mixed AD sets were operated at different organic loading rates (OLRs; 1-6 g chemical oxygen demand [COD] LR-1day-1), and changes in the composition and abundance of VFA-degrading microbial communities were monitored using amplicon sequencing and taxon-specific quantitative PCRs, respectively. AD sets operated at OLRs of 1-4 g COD LR-1day-1 were functionally stable throughout the operational period (120 days) whereas process instability (characterized by VFA buildup, pH decline, and decreased methane production rate) occurred in digesters operated at ≥ 5 g COD LR-1day-1. Though microbial taxa involved in propionate (Syntrophobacter and Pelotomaculum) and butyrate (Syntrophomonas) degradation were detected across all ADs, their abundance decreased with increasing OLR. The overload conditions also inhibited the proliferation of the acetoclastic methanogen, Methanosaeta, and caused a microbial community shift to acetate oxidizers (Tepidanaerobacter acetatoxydans) and hydrogenotrophic methanogens (Methanoculleus). This study's results highlight the importance of operating ADs with conditions that promote the maintenance of microbial communities involved in VFA degradation.
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10
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Jha PN, Gomaa AB, Yanni YG, El-Saadany AEY, Stedtfeld TM, Stedtfeld RD, Gantner S, Chai B, Cole J, Hashsham SA, Dazzo FB. Alterations in the Endophyte-Enriched Root-Associated Microbiome of Rice Receiving Growth-Promoting Treatments of Urea Fertilizer and Rhizobium Biofertilizer. MICROBIAL ECOLOGY 2020; 79:367-382. [PMID: 31346687 DOI: 10.1007/s00248-019-01406-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 06/20/2019] [Indexed: 06/10/2023]
Abstract
We examined the bacterial endophyte-enriched root-associated microbiome within rice (Oryza sativa) 55 days after growth in soil with and without urea fertilizer and/or biofertilization with a growth-promotive bacterial strain (Rhizobium leguminosarum bv. trifolii E11). After treatment to deplete rhizosphere/rhizoplane communities, washed roots were macerated and their endophyte-enriched communities were analyzed by 16S ribosomal DNA 454 amplicon pyrosequencing. This analysis clustered 99,990 valid sequence reads into 1105 operational taxonomic units (OTUs) with 97% sequence identity, 133 of which represented a consolidated core assemblage representing 12.04% of the fully detected OTU richness. Taxonomic affiliations indicated Proteobacteria as the most abundant phylum (especially α- and γ-Proteobacteria classes), followed by Firmicutes, Bacteroidetes, Verrucomicrobia, Actinobacteria, and several other phyla. Dominant genera included Rheinheimera, unclassified Rhodospirillaceae, Pseudomonas, Asticcacaulis, Sphingomonas, and Rhizobium. Several OTUs had close taxonomic affiliation to genera of diazotrophic rhizobacteria, including Rhizobium, unclassified Rhizobiales, Azospirillum, Azoarcus, unclassified Rhizobiaceae, Bradyrhizobium, Azonexus, Mesorhizobium, Devosia, Azovibrio, Azospira, Azomonas, and Azotobacter. The endophyte-enriched microbiome was restructured within roots receiving growth-promoting treatments. Compared to the untreated control, endophyte-enriched communities receiving urea and/or biofertilizer treatments were significantly reduced in OTU richness and relative read abundances. Several unique OTUs were enriched in each of the treatment communities. These alterations in structure of root-associated communities suggest dynamic interactions in the host plant microbiome, some of which may influence the well-documented positive synergistic impact of rhizobial biofertilizer inoculation plus low doses of urea-N fertilizer on growth promotion of rice, considered as one of the world's most important food crops.
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Affiliation(s)
- Prabhat N Jha
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Rajasthan, 333031, India
| | - Abu-Bakr Gomaa
- Department of Civil & Environmental Engineering, Michigan State University, East Lansing, MI, 48824, USA
- Department of Biochemistry, Faculty of Science, King Abdul-Aziz University, Jeddah, Saudi Arabia
- Department of Agricultural Microbiology, National Research Centre, Cairo, Egypt
| | - Youssef G Yanni
- Department of Microbiology, Sakha Agricultural Research Station, Kafr El-Sheikh, 33717, Egypt
| | | | - Tiffany M Stedtfeld
- Department of Civil & Environmental Engineering, Michigan State University, East Lansing, MI, 48824, USA
- Swift Biosciences, Inc., Ann Arbor, MI, USA
| | - Robert D Stedtfeld
- Department of Civil & Environmental Engineering, Michigan State University, East Lansing, MI, 48824, USA
- Swift Biosciences, Inc., Ann Arbor, MI, USA
| | - Stephan Gantner
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
- Department of Medicine, Economics and Health, University of Applied Sciences, Cologne, Germany
| | - Benli Chai
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
- Swift Biosciences, Inc., Ann Arbor, MI, USA
| | - James Cole
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Syed A Hashsham
- Department of Civil & Environmental Engineering, Michigan State University, East Lansing, MI, 48824, USA
| | - Frank B Dazzo
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA.
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA.
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11
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Moreira-Grez B, Muñoz-Rojas M, Kariman K, Storer P, O’Donnell AG, Kumaresan D, Whiteley AS. Reconditioning Degraded Mine Site Soils With Exogenous Soil Microbes: Plant Fitness and Soil Microbiome Outcomes. Front Microbiol 2019; 10:1617. [PMID: 31354694 PMCID: PMC6636552 DOI: 10.3389/fmicb.2019.01617] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 06/28/2019] [Indexed: 02/01/2023] Open
Abstract
Mining of mineral resources substantially alters both the above and below-ground soil ecosystem, which then requires rehabilitation back to a pre-mining state. For belowground rehabilitation, recovery of the soil microbiome to a state which can support key biogeochemical cycles, and effective plant colonization is usually required. One solution proposed has been to translate microbial inocula from agricultural systems to mine rehabilitation scenarios, as a means of reconditioning the soil microbiome for planting. Here, we experimentally determine both the aboveground plant fitness outcomes and belowground soil microbiome effects of a commercially available soil microbial inocula (SMI). We analyzed treatment effects at four levels of complexity; no SMI addition control, Nitrogen addition alone, SMI addition and SMI plus Nitrogen addition over a 12-week period. Our culture independent analyses indicated that SMIs had a differential response over the 12-week incubation period, where only a small number of the consortium members persisted in the semi-arid ecosystem, and generated variable plant fitness responses, likely due to plant-microbiome physiological mismatching and low survival rates of many of the SMI constituents. We suggest that new developments in custom-made SMIs to increase rehabilitation success in mine site restoration are required, primarily based upon the need for SMIs to be ecologically adapted to both the prevailing edaphic conditions and a wide range of plant species likely to be encountered.
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Affiliation(s)
- Benjamin Moreira-Grez
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
| | - Miriam Muñoz-Rojas
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
- Kings Park Science, Department of Biodiversity, Conservation and Attractions, Perth, WA, Australia
| | - Khalil Kariman
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
| | - Paul Storer
- Troforte Innovations Pty Ltd., Perth, WA, Australia
| | | | - Deepak Kumaresan
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
- School of Biological Sciences, Queen’s University of Belfast, Belfast, United Kingdom
| | - Andrew S. Whiteley
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
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12
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The role of microbial electrolysis cell in urban wastewater treatment: integration options, challenges, and prospects. Curr Opin Biotechnol 2019; 57:101-110. [DOI: 10.1016/j.copbio.2019.03.007] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 12/07/2018] [Accepted: 03/05/2019] [Indexed: 01/08/2023]
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13
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Zhang Z, Deng Y, Feng K, Cai W, Li S, Yin H, Xu M, Ning D, Qu Y. Deterministic Assembly and Diversity Gradient Altered the Biofilm Community Performances of Bioreactors. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:1315-1324. [PMID: 30615833 DOI: 10.1021/acs.est.8b06044] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Community assembly process (determinism vs stochasticity) determines the composition and diversity of a microbial community, and then shapes its functions. Understanding this complex process and its relationship to the community functions becomes a very important task for the applications of microbial biotechnology. In this study, we applied microbial electrolysis cells (MECs) with moderate species numbers and easily tractable functions as a model ecosystem, and constructed a series of biofilm communities with gradient biodiversity to examine the roles of community assembly in determining microbial community structure and functions. After stable biofilms formed, the best MEC reactor performances (e.g., gas productivity, total energy efficiency) were achieved in the group in which biofilms had the second highest α-diversity, and biofilms with even lower diversity showed declining performance. Null model analyses indicated that both deterministic and stochastic assembly played roles in the formation of biofilm communities. When deterministic assembly dominates this formation, the higher diversity of the biofilm community would generally show better reactor performance. However, when the stochasticity dominates the assembly process, the bioreactor performance would decline. This study provides novel evidence that the assembly mechanism could be one of the key processes to shift the functions, and proposes an important guidance for selecting the most efficient microorganisms for environmental biotechnologies.
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Affiliation(s)
- Zhaojing Zhang
- Institute for Marine Science and Technology , Shandong University , Qingdao 266237 , P. R. China
- State Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology , Dalian University of Technology , Dalian 116024 , P. R. China
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing 100085 , P. R. China
| | - Ye Deng
- Institute for Marine Science and Technology , Shandong University , Qingdao 266237 , P. R. China
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing 100085 , P. R. China
- College of Resources and Environment , University of Chinese Academy of Sciences , Beijing 100190 , P. R. China
| | - Kai Feng
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing 100085 , P. R. China
| | - Weiwei Cai
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing 100085 , P. R. China
- School of Civil Engineering , Beijing Jiaotong University , Beijing 100044 , P. R. China
| | - Shuzhen Li
- State Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology , Dalian University of Technology , Dalian 116024 , P. R. China
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing 100085 , P. R. China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering , Central South University , Changsha 410083 , P. R. China
| | - Meiying Xu
- State Key Laboratory of Applied Microbiology Southern China , Guangdong Institute of Microbiology , Guangzhou 510070 , P. R. China
| | - Daliang Ning
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Science , University of Oklahoma , Norman , Oklahoma 73019 , United States
| | - Yuanyuan Qu
- State Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology , Dalian University of Technology , Dalian 116024 , P. R. China
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14
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Spirito CM, Marzilli AM, Angenent LT. Higher Substrate Ratios of Ethanol to Acetate Steered Chain Elongation toward n-Caprylate in a Bioreactor with Product Extraction. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:13438-13447. [PMID: 30335369 DOI: 10.1021/acs.est.8b03856] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Syngas fermentation to ethanol and acetate has recently been coupled to microbial chain elongation to produce medium-chain carboxylates, including n-caproate and n-caprylate. These medium-chain carboxylates are relatively hydrophobic, and thus easier to extract from solution than miscible ethanol. Here, we examined the effect of 11 different ethanol-to-acetate substrate ratios (ranging from 1.8 to 275 g COD g COD-1 [1.2 to 183 mol mol-1]) on directing chain elongation toward n-caprylate in a 0.7-L upflow anaerobic filter with product extraction. During an eight-month operating period, we monitored the performance and characterized the microbiome composition of this chain-elongating bioreactor. We also developed a thermodynamic model to predict the favorability of n-caprylate production at different substrate ratios. As predicted by our model, higher ethanol-to-acetate substrate ratios fed to our bioreactor led to higher specificities for n-caprylate production. We observed that feeding primarily ethanol to the bioreactor (i.e., ethanol-to-acetate substrate ratio of 275 g COD g COD-1) resulted in the highest specificity for n-caprylate, but the n-caprylate production rate decreased at this high ratio, resulting in lower conversion efficiencies. Thus, care should be taken not to overload the system with primarily ethanol as the substrate and to lower the organic loading rate.
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Affiliation(s)
- Catherine M Spirito
- Department of Biological and Environmental Engineering , Cornell University , Ithaca , New York 14853 , United States
| | - Alexander M Marzilli
- Department of Biological and Environmental Engineering , Cornell University , Ithaca , New York 14853 , United States
| | - Largus T Angenent
- Department of Biological and Environmental Engineering , Cornell University , Ithaca , New York 14853 , United States
- Center for Applied Geosciences , University of Tübingen , 72074 Tübingen , Germany
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15
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Ferguson RMW, Coulon F, Villa R. Understanding microbial ecology can help improve biogas production in AD. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 642:754-763. [PMID: 29920462 DOI: 10.1016/j.scitotenv.2018.06.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 06/01/2018] [Accepted: 06/01/2018] [Indexed: 06/08/2023]
Abstract
454-Pyrosequencing and lipid fingerprinting were used to link anaerobic digestion (AD) process parameters (pH, alkalinity, volatile fatty acids (VFAs), biogas production and methane content) with the reactor microbial community structure and composition. AD microbial communities underwent stress conditions after changes in organic loading rate and digestion substrates. 454-Pyrosequencing analysis showed that, irrespectively of the substrate digested, methane content and pH were always significantly, and positively, correlated with community evenness. In AD, microbial communities with more even distributions of diversity are able to use parallel metabolic pathways and have greater functional stability; hence, they are capable of adapting and responding to disturbances. In all reactors, a decrease in methane content to <30% was always correlated with a 50% increase of Firmicutes sequences (particularly in operational taxonomic units (OTUs) related to Ruminococcaceae and Veillonellaceae). Whereas digesters producing higher methane content (above 60%), contained a high number of sequences related to Synergistetes and unidentified bacterial OTUs. Finally, lipid fingerprinting demonstrated that, under stress, the decrease in archaeal biomass was higher than the bacterial one, and that archaeal Phospholipid etherlipids (PLEL) levels were correlated to reactor performances. These results demonstrate that, across a number of parameters such as lipids, alpha and beta diversity, and OTUs, knowledge of the microbial community structure can be used to predict, monitor, or optimise AD performance.
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Affiliation(s)
- Robert M W Ferguson
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Frédéric Coulon
- School of Water, Energy and Environment, Cranfield University, Cranfield, MK43 0AL, UK
| | - Raffaella Villa
- School of Water, Energy and Environment, Cranfield University, Cranfield, MK43 0AL, UK.
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16
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Matyugina E, Belkova N, Borzenko S, Lukyanov P, Kabilov M, Baturina O, Kley AMV, Nalian A, Ptitsyn A. Structure and diversity dynamics of microbial communities at day and night: investigation of meromictic Lake Doroninskoe, Transbaikalia, Russia. JOURNAL OF OCEANOLOGY AND LIMNOLOGY 2018; 36:1978-1992. [DOI: 10.1007/s00343-018-7332-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 03/27/2018] [Indexed: 07/26/2024]
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17
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Murovec B, Makuc D, Kolbl Repinc S, Prevoršek Z, Zavec D, Šket R, Pečnik K, Plavec J, Stres B. 1H NMR metabolomics of microbial metabolites in the four MW agricultural biogas plant reactors: A case study of inhibition mirroring the acute rumen acidosis symptoms. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2018; 222:428-435. [PMID: 29894946 DOI: 10.1016/j.jenvman.2018.05.068] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Revised: 05/16/2018] [Accepted: 05/21/2018] [Indexed: 06/08/2023]
Abstract
In this study, nuclear magnetic resonance (1H NMR) spectroscopic profiling was used to provide a more comprehensive view of microbial metabolites associated with poor reactor performance in a full-scale 4 MW mesophilic agricultural biogas plant under fully operational and also under inhibited conditions. Multivariate analyses were used to assess the significance of differences between reactors whereas artificial neural networks (ANN) were used to identify the key metabolites responsible for inhibition and their network of interaction. Based on the results of nm-MDS ordination the subsamples of each reactor were similar, but not identical, despite homogenization of the full-scale reactors before sampling. Hence, a certain extent of variability due to the size of the system under analysis was transferred into metabolome analysis. Multivariate analysis showed that fully active reactors were clustered separately from those containing inhibited reactor metabolites and were significantly different. Furthermore, the three distinct inhibited states were significantly different from each other. The inhibited metabolomes were enriched in acetate, caprylate, trimethylamine, thymine, pyruvate, alanine, xanthine and succinate. The differences in the metabolic fingerprint between inactive and fully active reactors observed in this study resembled closely the metabolites differentiating the (sub) acute rumen acidosis inflicted and healthy rumen metabolomes, creating thus favorable conditions for the growth and activity of pathogenic bacteria. The consistency of our data with those reported before for rumen ecosystems shows that 1H NMR based metabolomics is a reliable approach for the evaluation of metabolic events at full-scale biogas reactors.
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Affiliation(s)
- Boštjan Murovec
- Laboratory for Artificial Sight and Automation, Faculty of Electrical Sciences, University of Ljubljana, Ljubljana, Slovenia
| | - Damjan Makuc
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
| | - Sabina Kolbl Repinc
- Faculty of Civil and Geodetic Engineering, Hajdrihova 28, SI-1000, Ljubljana, Slovenia
| | - Zala Prevoršek
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Domen Zavec
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Robert Šket
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Klemen Pečnik
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
| | - Blaž Stres
- Faculty of Civil and Geodetic Engineering, Hajdrihova 28, SI-1000, Ljubljana, Slovenia; Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia; Center for Clinical Neurophysiology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.
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18
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Repinc SK, Šket R, Zavec D, Mikuš KV, Fermoso FG, Stres B. Full-scale agricultural biogas plant metal content and process parameters in relation to bacterial and archaeal microbial communities over 2.5 year span. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2018; 213:566-574. [PMID: 29477353 DOI: 10.1016/j.jenvman.2018.02.058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 02/02/2018] [Accepted: 02/14/2018] [Indexed: 06/08/2023]
Abstract
A start-up of 4 MW agricultural biogas plant in Vučja vas, Slovenia, was monitored from 2011 to 2014. The start-up was carried out in 3 weeks with the intake of biomass from three operating full-scale 1-2 MW donor agricultural biogas plants. The samples were taken from donor digesters and from two serial digesters during the start-up over the course of 2.5 years. Bacterial and Archaeal microbial communities progressively diverged from the composition of donor digesters during the start-up phase. The rate of change of Bacterial community decreased exponentially over the first 2.5 years as dynamics within the first 70 days was comparable to that of the next 1.5 years, whereas approximately constant rate was observed for Archaea. Despite rearrangements, the microbial communities remained functionally stable and produced biogas throughout the whole 2.5 years of observation. All systems parameters measured were ordered according to their Kernel density (Gaussian function) ranging from the most dispersed (substrate categories used as cosubstrates, quantities of each cosubstrate, substate dry and volatile matter, process parameters) towards progressively least dispersed (trace metal and ion profiles, aromatic-polyphenolic compounds, biogas plant functional output (energy)). No deficiency was detected in trace metal content as the distribution of metals and elements fluctuated within the suggested limits for biogas over 2.5 year observation. In contrast to the recorded process variables, Bacterial and Archaeal microbial communities exhibited directed changes oriented in time. Variation partitioning showed that a large fraction of variability in the Bacterial and Archaeal microbial communities (55% and 61%, respectively) remained unexplained despite numerous measured variables (n = 44) and stable biogas production. Our results show that the observed reorganization of microbial communities was not directly associated with impact on the full-scale biogas reactor performance. Novel parameters need to be determined to elucidate the variables directly associated with the reorganization of microbial communities and those relevant for sustained function such as the more in-depth interaction between TSOC, trace metal profiles, aromatic-polyphenolic compounds and ionic strength (e.g. electrical conductivity).
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Affiliation(s)
- Sabina Kolbl Repinc
- Institute of Sanitary Engineering, Faculty of Civil and Geodetic Engineering, Jamova 2, Ljubljana, Slovenia
| | - Robert Šket
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, Ljubljana, Slovenia
| | - Domen Zavec
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, Ljubljana, Slovenia
| | - Katarina Vogel Mikuš
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, Ljubljana, Slovenia
| | | | - Blaž Stres
- Institute of Sanitary Engineering, Faculty of Civil and Geodetic Engineering, Jamova 2, Ljubljana, Slovenia; Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, Ljubljana, Slovenia; University of Ljubljana, Faculty of Medicine, Ljubljana, Vrazov trg 2, Ljubljana, Slovenia.
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19
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Noblecourt A, Christophe G, Larroche C, Fontanille P. Hydrogen production by dark fermentation from pre-fermented depackaging food wastes. BIORESOURCE TECHNOLOGY 2018; 247:864-870. [PMID: 30060424 DOI: 10.1016/j.biortech.2017.09.199] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/26/2017] [Accepted: 09/28/2017] [Indexed: 06/08/2023]
Abstract
In this study, a specific fraction of food waste, i.e. depackaging waste, was studied as substrate for hydrogen production by dark fermentation. During storage and transport of this liquid mixture, inhibitory compounds like acids or alcohol might be produced by endogenous flora. A factorial fractional design based on the composition of the substrate was used to determine the best condition to convert this substrate into hydrogen. First results indicated that the consortium used might convert high quantity of lactate into hydrogen. A batch culture confirmed that lactate was used as the main carbon source and a global yield of 0.4molH2·mollactate-1 was obtained. This study demonstrated the ability of the consortium tested to convert different carbon sources (carbohydrates or lactate) with good efficiency. These data represented an important parameter in the prospect of using an industrial substrate whose composition is liable to vary according to the conditions of storage and transport.
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Affiliation(s)
- Alexandre Noblecourt
- Université Clermont Auvergne, Institut Pascal, TSA 60026, F-63178 Aubière cedex, France; CNRS, UMR 6602, IP, F-63178 Aubière cedex, France; Université Clermont Auvergne, LABEX IMobS3, 63178 Aubière cedex, France
| | - Gwendoline Christophe
- Université Clermont Auvergne, Institut Pascal, TSA 60026, F-63178 Aubière cedex, France; CNRS, UMR 6602, IP, F-63178 Aubière cedex, France; Université Clermont Auvergne, LABEX IMobS3, 63178 Aubière cedex, France
| | - Christian Larroche
- Université Clermont Auvergne, Institut Pascal, TSA 60026, F-63178 Aubière cedex, France; CNRS, UMR 6602, IP, F-63178 Aubière cedex, France; Université Clermont Auvergne, LABEX IMobS3, 63178 Aubière cedex, France
| | - Pierre Fontanille
- Université Clermont Auvergne, Institut Pascal, TSA 60026, F-63178 Aubière cedex, France; CNRS, UMR 6602, IP, F-63178 Aubière cedex, France; Université Clermont Auvergne, LABEX IMobS3, 63178 Aubière cedex, France.
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20
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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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21
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Hari AR, Venkidusamy K, Katuri KP, Bagchi S, Saikaly PE. Temporal Microbial Community Dynamics in Microbial Electrolysis Cells - Influence of Acetate and Propionate Concentration. Front Microbiol 2017; 8:1371. [PMID: 28775719 PMCID: PMC5517442 DOI: 10.3389/fmicb.2017.01371] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 07/05/2017] [Indexed: 11/13/2022] Open
Abstract
Microbial electrolysis cells (MECs) are widely considered as a next generation wastewater treatment system. However, fundamental insight on the temporal dynamics of microbial communities associated with MEC performance under different organic types with varied loading concentrations is still unknown, nevertheless this knowledge is essential for optimizing this technology for real-scale applications. Here, the temporal dynamics of anodic microbial communities associated with MEC performance was examined at low (0.5 g COD/L) and high (4 g COD/L) concentrations of acetate or propionate, which are important intermediates of fermentation of municipal wastewaters and sludge. The results showed that acetate-fed reactors exhibited higher performance in terms of maximum current density (I: 4.25 ± 0.23 A/m2), coulombic efficiency (CE: 95 ± 8%), and substrate degradation rate (98.8 ± 1.2%) than propionate-fed reactors (I: 2.7 ± 0.28 A/m2; CE: 68 ± 9.5%; substrate degradation rate: 84 ± 13%) irrespective of the concentrations tested. Despite of the repeated sampling of the anodic biofilm over time, the high-concentration reactors demonstrated lower and stable performance in terms of current density (I: 1.1 ± 0.14 to 4.2 ± 0.21 A/m2), coulombic efficiency (CE: 44 ± 4.1 to 103 ± 7.2%) and substrate degradation rate (64.9 ± 6.3 to 99.7 ± 0.5%), while the low-concentration reactors produced higher and dynamic performance (I: 1.1 ± 0.12 to 4.6 ± 0.1 A/m2; CE: 52 ± 2.5 to 105 ± 2.7%; substrate degradation rate: 87.2 ± 0.2 to 99.9 ± 0.06%) with the different substrates tested. Correlating reactor's performance with temporal dynamics of microbial communities showed that relatively similar anodic microbial community composition but with varying relative abundances was observed in all the reactors despite differences in the substrate and concentrations tested. Particularly, Geobacter was the predominant bacteria on the anode biofilm of all MECs over time suggesting its possible role in maintaining functional stability of MECs fed with low and high concentrations of acetate and propionate. Taken together, these results provide new insights on the microbial community dynamics and its correlation to performance in MECs fed with different concentrations of acetate and propionate, which are important volatile fatty acids in wastewater.
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Affiliation(s)
- Ananda Rao Hari
- Biological and Environmental Sciences and Engineering Division, Water Desalination and Reuse Research Center, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
| | - Krishnaveni Venkidusamy
- Centre for Environmental Risk Assessment and Remediation, University of South Australia, Mawson LakesSA, Australia
| | - Krishna P Katuri
- Biological and Environmental Sciences and Engineering Division, Water Desalination and Reuse Research Center, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
| | - Samik Bagchi
- Department of Civil, Environmental, and Architectural Engineering, University of Kansas, LawrenceKS, United States
| | - Pascal E Saikaly
- Biological and Environmental Sciences and Engineering Division, Water Desalination and Reuse Research Center, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
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22
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Louca S, Doebeli M. Taxonomic variability and functional stability in microbial communities infected by phages. Environ Microbiol 2017; 19:3863-3878. [PMID: 28371143 DOI: 10.1111/1462-2920.13743] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 03/16/2017] [Accepted: 03/24/2017] [Indexed: 11/28/2022]
Abstract
Microbial communities can display large variation in taxonomic composition, yet this variation can coincide with stable metabolic functional structure and performance. The mechanisms driving the taxonomic variation within functional groups remain largely unknown. Biotic interactions, such as predation by phages, have been suggested as potential cause of taxonomic turnover, but the conditions for this scenario have not been rigorously examined. Further, it is unknown how predation by phages affects community function, and how these effects are modulated by functional redundancy in the communities. Here, we address these questions using a model for a methanogenic microbial community that includes several interacting metabolic functional groups. Each functional group comprises multiple competing clades, and each clade is attacked by a specialist lytic phage. Our model predicts that phages induce intense taxonomic turnover, resembling the variability observed in previous experiments. The functional structure and performance of the community are also disturbed by phage predation, but they become more stable as the functional redundancy in the community increases. The extent of this stabilization depends on the particular functions considered. Our model suggests mechanisms by which functional redundancy stabilizes community function and supports the interpretation that biotic interactions promote taxonomic turnover within microbial functional groups.
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Affiliation(s)
- Stilianos Louca
- Biodiversity Research Centre, University of British Columbia, Canada.,Department of Zoology, University of British Columbia, Canada
| | - Michael Doebeli
- Biodiversity Research Centre, University of British Columbia, Canada.,Department of Zoology, University of British Columbia, Canada.,Department of Mathematics, University of British Columbia, Canada
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23
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Wells GF, Shi Y, Laureni M, Rosenthal A, Szivák I, Weissbrodt DG, Joss A, Buergmann H, Johnson DR, Morgenroth E. Comparing the Resistance, Resilience, and Stability of Replicate Moving Bed Biofilm and Suspended Growth Combined Nitritation-Anammox Reactors. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:5108-5117. [PMID: 28374996 DOI: 10.1021/acs.est.6b05878] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Combined partial nitritation-anammox (PN/A) systems are increasingly being employed for sustainable removal of nitrogen from wastewater, but process instabilities present ongoing challenges for practitioners. The goal of this study was to elucidate differences in process stability between PN/A process variations employing two distinct aggregate types: biofilm [in moving bed biofilm reactors (MBBRs)] and suspended growth biomass. Triplicate reactors for each process variation were studied under baseline conditions and in response to a series of transient perturbations. MBBRs displayed elevated NH4+ removal rates relative to those of suspended growth counterparts over six months of unperturbed baseline operation but also exhibited significantly greater variability in performance. Transient perturbations led to strikingly divergent yet reproducible behavior in biofilm versus suspended growth systems. A temperature perturbation prompted a sharp reduction in NH4+ removal rates with no accumulation of NO2- and rapid recovery in MBBRs, compared to a similar reduction in NH4+ removal rates but a high level of accumulation of NO2- in suspended growth reactors. Pulse additions of a nitrification inhibitor (allylthiourea) prompted only moderate declines in performance in suspended growth reactors compared to sharp decreases in NH4+ removal rates in MBBRs. Quantitative fluorescence in situ hybridization demonstrated a significant enrichment of anammox in MBBRs compared to suspended growth reactors, and conversely a proportionally higher AOB abundance in suspended growth reactors. Overall, MBBRs displayed significantly increased susceptibility to transient perturbations employed in this study compared to that of suspended growth counterparts (stability parameter), including significantly longer recovery times (resilience). No significant difference in the maximal impact of perturbations (resistance) was apparent. Taken together, our results suggest that aggregate architecture (biofilm vs suspended growth) in PN/A processes exerts an unexpectedly strong influence on process stability.
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Affiliation(s)
- G F Wells
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , 8600 Dübendorf, Switzerland
- Department of Civil and Environmental Engineering, Northwestern University , Evanston, Illinois 60208, United States
| | - Y Shi
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , 8600 Dübendorf, Switzerland
- Department of Environmental Science and Engineering, Shandong University , Jinan, China
| | - M Laureni
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , 8600 Dübendorf, Switzerland
- Institute of Environmental Engineering, ETH Zürich , 8093 Zürich, Switzerland
| | - A Rosenthal
- Department of Civil and Environmental Engineering, Northwestern University , Evanston, Illinois 60208, United States
| | - I Szivák
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , 8600 Dübendorf, Switzerland
| | - D G Weissbrodt
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , 8600 Dübendorf, Switzerland
- Institute of Environmental Engineering, ETH Zürich , 8093 Zürich, Switzerland
| | - A Joss
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , 8600 Dübendorf, Switzerland
| | - H Buergmann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , 8600 Dübendorf, Switzerland
| | - D R Johnson
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , 8600 Dübendorf, Switzerland
- Department of Environmental Systems Science, ETH Zürich , 8093 Zürich, Switzerland
| | - E Morgenroth
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , 8600 Dübendorf, Switzerland
- Institute of Environmental Engineering, ETH Zürich , 8093 Zürich, Switzerland
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Venkiteshwaran K, Milferstedt K, Hamelin J, Fujimoto M, Johnson M, Zitomer DH. Correlating methane production to microbiota in anaerobic digesters fed synthetic wastewater. WATER RESEARCH 2017; 110:161-169. [PMID: 28006706 DOI: 10.1016/j.watres.2016.12.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 12/08/2016] [Accepted: 12/09/2016] [Indexed: 06/06/2023]
Abstract
A quantitative structure activity relationship (QSAR) between relative abundance values and digester methane production rate was developed. For this, 50 triplicate anaerobic digester sets (150 total digesters) were each seeded with different methanogenic biomass samples obtained from full-scale, engineered methanogenic systems. Although all digesters were operated identically for at least 5 solids retention times (SRTs), their quasi steady-state function varied significantly, with average daily methane production rates ranging from 0.09 ± 0.004 to 1 ± 0.05 L-CH4/LR-day (LR = Liter of reactor volume) (average ± standard deviation). Digester microbial community structure was analyzed using more than 4.1 million partial 16S rRNA gene sequences of Archaea and Bacteria. At the genus level, 1300 operational taxonomic units (OTUs) were observed across all digesters, whereas each digester contained 158 ± 27 OTUs. Digester function did not correlate with typical biomass descriptors such as volatile suspended solids (VSS) concentration, microbial richness, diversity or evenness indices. However, methane production rate did correlate notably with relative abundances of one Archaeal and nine Bacterial OTUs. These relative abundances were used as descriptors to develop a multiple linear regression (MLR) QSAR equation to predict methane production rates solely based on microbial community data. The model explained over 66% of the variance in the experimental data set based on 149 anaerobic digesters with a standard error of 0.12 L-CH4/LR-day. This study provides a framework to relate engineered process function and microbial community composition which can be further expanded to include different feed stocks and digester operating conditions in order to develop a more robust QSAR model.
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Affiliation(s)
- K Venkiteshwaran
- Department of Civil, Construction and Environmental Engineering, Marquette University, P.O. Box 1881, Milwaukee, WI, 53233, USA.
| | - K Milferstedt
- LBE, INRA, 102 Avenue des Etangs, Narbonne, F-11100, France
| | - J Hamelin
- LBE, INRA, 102 Avenue des Etangs, Narbonne, F-11100, France
| | - M Fujimoto
- Department of Civil, Construction and Environmental Engineering, Marquette University, P.O. Box 1881, Milwaukee, WI, 53233, USA
| | - M Johnson
- Department of Electrical and Computer Engineering, University of Kentucky, Lexington, KY 40506-0046, USA
| | - D H Zitomer
- Department of Civil, Construction and Environmental Engineering, Marquette University, P.O. Box 1881, Milwaukee, WI, 53233, USA
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25
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Cabrol L, Marone A, Tapia-Venegas E, Steyer JP, Ruiz-Filippi G, Trably E. Microbial ecology of fermentative hydrogen producing bioprocesses: useful insights for driving the ecosystem function. FEMS Microbiol Rev 2017; 41:158-181. [DOI: 10.1093/femsre/fuw043] [Citation(s) in RCA: 154] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/05/2016] [Indexed: 11/13/2022] Open
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26
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Cerrillo M, Viñas M, Bonmatí A. Removal of volatile fatty acids and ammonia recovery from unstable anaerobic digesters with a microbial electrolysis cell. BIORESOURCE TECHNOLOGY 2016; 219:348-356. [PMID: 27501031 DOI: 10.1016/j.biortech.2016.07.103] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 07/22/2016] [Accepted: 07/24/2016] [Indexed: 06/06/2023]
Abstract
Continuous assays with a microbial electrolysis cell (MEC) fed with digested pig slurry were performed to evaluate its stability and robustness to malfunction periods of an anaerobic digestion (AD) reactor and its feasibility as a strategy to recover ammonia. When performing punctual pulses of volatile fatty acids (VFA) in the anode compartment of the MEC, simulating a malfunction of the AD process, an increase in the current density was produced (up to 14 times, reaching values of 3500mAm(-2)) as a result of the added chemical oxygen demand (COD), especially when acetate was used. Furthermore, ammonium diffusion from the anode to the cathode compartment was enhanced and the removal efficiency achieved up to 60% during daily basis VFA pulses. An AD-MEC combined system has proven to be a robust and stable configuration to obtain a high quality effluent, with a lower organic and ammonium content.
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Affiliation(s)
- Míriam Cerrillo
- IRTA, GIRO Joint Research Unit IRTA-UPC, Torre Marimon, E-08140, Caldes de Montbui, Barcelona, Spain
| | - Marc Viñas
- IRTA, GIRO Joint Research Unit IRTA-UPC, Torre Marimon, E-08140, Caldes de Montbui, Barcelona, Spain
| | - August Bonmatí
- IRTA, GIRO Joint Research Unit IRTA-UPC, Torre Marimon, E-08140, Caldes de Montbui, Barcelona, Spain.
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Diversity is the question, not the answer. ISME JOURNAL 2016; 11:1-6. [PMID: 27636395 PMCID: PMC5421358 DOI: 10.1038/ismej.2016.118] [Citation(s) in RCA: 242] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 07/07/2016] [Accepted: 08/02/2016] [Indexed: 01/22/2023]
Abstract
Local diversity (within-sample or alpha diversity) is often implicated as a cause of success or failure of a microbial community. However, the relationships between diversity and emergent properties of a community, such as its stability, productivity or invasibility, are much more nuanced. I argue that diversity without context provides limited insights into the mechanisms underpinning community patterns. I provide examples from traditional and microbial ecology to discuss common complications and assumptions about within-sample diversity that may prevent us from digging deeper into the more specific mechanisms underpinning community outcomes. I suggest that measurement of diversity should serve as a starting point for further inquiry of ecological mechanisms rather than an 'answer' to community outcomes.
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28
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29
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Zhou X, Fornara D, Ikenaga M, Akagi I, Zhang R, Jia Z. The Resilience of Microbial Community under Drying and Rewetting Cycles of Three Forest Soils. Front Microbiol 2016; 7:1101. [PMID: 27486444 PMCID: PMC4949271 DOI: 10.3389/fmicb.2016.01101] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 07/01/2016] [Indexed: 02/04/2023] Open
Abstract
Forest soil ecosystems are associated with large pools and fluxes of carbon (C) and nitrogen (N), which could be strongly affected by variation in rainfall events under current climate change. Understanding how dry and wet cycle events might influence the metabolic state of indigenous soil microbes is crucial for predicting forest soil responses to environmental change. We used 454 pyrosequencing and quantitative PCR to address how present (DNA-based) and potentially active (RNA-based) soil bacterial communities might response to the changes in water availability across three different forest types located in two continents (Africa and Asia) under controlled drying and rewetting cycles. Sequencing of rRNA gene and transcript indicated that Proteobacteria, Actinobacteria, and Acidobacteria were the most responsive phyla to changes in water availability. We defined the ratio of rRNA transcript to rRNA gene abundance as a key indicator of potential microbial activity and we found that this ratio was increased following soil dry-down process whereas it decreased after soil rewetting. Following rewetting Crenarchaeota-like 16S rRNA gene transcript increased in some forest soils and this was linked to increases in soil nitrate levels suggesting greater nitrification rates under higher soil water availability. Changes in the relative abundance of (1) different microbial phyla and classes, and (2) 16S and amoA genes were found to be site- and taxa-specific and might have been driven by different life-strategies. Overall, we found that, after rewetting, the structure of the present and potentially active bacterial community structure as well as the abundance of bacterial (16S), archaeal (16S) and ammonia oxidizers (amoA), all returned to pre-dry-down levels. This suggests that microbial taxa have the ability to recover from desiccation, a critical response, which will contribute to maintaining microbial biodiversity in harsh ecosystems under environmental perturbations, such as significant changes in water availability.
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Affiliation(s)
- Xue Zhou
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of SciencesNanjing, China; University of Chinese Academy of SciencesBeijing, China
| | - Dario Fornara
- Agri-Food and Biosciences Institute Belfast, Ireland
| | - Makoto Ikenaga
- Research Field in Agriculture, Agriculture Fisheries and Veterinary Medicine Area, Kagoshima University Kagoshima, Japan
| | - Isao Akagi
- Research Field in Agriculture, Agriculture Fisheries and Veterinary Medicine Area, Kagoshima University Kagoshima, Japan
| | - Ruifu Zhang
- National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agriculture University Nanjing, China
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences Nanjing, China
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30
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Geng H, Sale KL, Tran-Gyamfi MB, Lane TW, Yu ET. Longitudinal Analysis of Microbiota in Microalga Nannochloropsis salina Cultures. MICROBIAL ECOLOGY 2016; 72:14-24. [PMID: 26956183 DOI: 10.1007/s00248-016-0746-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 02/22/2016] [Indexed: 06/05/2023]
Abstract
Large-scale open microalgae cultivation has tremendous potential to make a significant contribution to replacing petroleum-based fuels with biofuels. Open algal cultures are unavoidably inhabited with a diversity of microbes that live on, influence, and shape the fate of these ecosystems. However, there is little understanding of the resilience and stability of the microbial communities in engineered semicontinuous algal systems. To evaluate the dynamics and resilience of the microbial communities in microalgae biofuel cultures, we conducted a longitudinal study on open systems to compare the temporal profiles of the microbiota from two multigenerational algal cohorts, which include one seeded with the microbiota from an in-house culture and the other exogenously seeded with a natural-occurring consortia of bacterial species harvested from the Pacific Ocean. From these month-long, semicontinuous open microalga Nannochloropsis salina cultures, we sequenced a time-series of 46 samples, yielding 8804 operational taxonomic units derived from 9,160,076 high-quality partial 16S rRNA sequences. We provide quantitative evidence that clearly illustrates the development of microbial community is associated with microbiota ancestry. In addition, N. salina growth phases were linked with distinct changes in microbial phylotypes. Alteromonadeles dominated the community in the N. salina exponential phase whereas Alphaproteobacteria and Flavobacteriia were more prevalent in the stationary phase. We also demonstrate that the N. salina-associated microbial community in open cultures is diverse, resilient, and dynamic in response to environmental perturbations. This knowledge has general implications for developing and testing design principles of cultivated algal systems.
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Affiliation(s)
- Haifeng Geng
- Department of Systems Biology, Sandia National Laboratories, 7011 East Ave, Livermore, CA, 94550, USA
| | - Kenneth L Sale
- Department of Biomass Science and Conversion Technology, Sandia National Laboratories, 7011 East Ave, Livermore, CA, 94550, USA
| | - Mary Bao Tran-Gyamfi
- Department of Biomass Science and Conversion Technology, Sandia National Laboratories, 7011 East Ave, Livermore, CA, 94550, USA
| | - Todd W Lane
- Department of Systems Biology, Sandia National Laboratories, 7011 East Ave, Livermore, CA, 94550, USA.
| | - Eizadora T Yu
- Department of Systems Biology, Sandia National Laboratories, 7011 East Ave, Livermore, CA, 94550, USA
- Institute of Chemistry, National Science Complex, University of the Philippines, Diliman Quezon City, 1101, Philippines
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31
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Lin Q, He G, Rui J, Fang X, Tao Y, Li J, Li X. Microorganism-regulated mechanisms of temperature effects on the performance of anaerobic digestion. Microb Cell Fact 2016; 15:96. [PMID: 27260194 PMCID: PMC4893225 DOI: 10.1186/s12934-016-0491-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 05/23/2016] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Temperature is an important factor determining the performance and stability of the anaerobic digestion process. However, the microorganism-regulated mechanisms of temperature effects on the performance of anaerobic digestion systems remain further elusive. To address this issue, we investigated the changes in composition, diversity and activities of microbial communities under temperature gradient from 25 to 55 °C using 16S rRNA gene amplicon sequencing approach based on genomic DNA (refer to as "16S rDNA") and total RNA (refer to as "16S rRNA"). RESULTS Microbial community structure and activities changed dramatically along the temperature gradient, which corresponded to the variations in digestion performance (e.g., daily CH4 production, total biogas production and volatile fatty acids concentration). The ratios of 16S rRNA to 16S rDNA of microbial taxa, as an indicator of the potentially relative activities in situ, and whole activities of microbial community assessed by the similarity between microbial community based on 16S rDNA and rRNA, varied strongly along the temperature gradient, reflecting different metabolic activities. The daily CH4 production increased with temperature from 25 to 50 °C and declined at 55 °C. Among all the examined microbial properties, the whole activities of microbial community and alpha-diversity indices of both microbial communities and potentially relative activities showed highest correlations to the performance. CONCLUSIONS The whole activities of microbial community and alpha-diversity indices of both microbial communities and potentially relative activities were sensitive indicators for the performance of anaerobic digestion systems under temperature gradient, while beta-diversity could predict functional differences. Microorganism-regulated mechanisms of temperature effects on anaerobic digestion performance were likely realized through increasing alpha-diversity of both microbial communities and potentially relative activities to supply more functional pathways and activities for metabolic network, and increasing the whole activities of microbial community, especially methanogenesis, to improve the strength and efficiency in anaerobic digestion process.
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Affiliation(s)
- Qiang Lin
- Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Guihua He
- Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Junpeng Rui
- Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xiaoyu Fang
- Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yong Tao
- Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Jiabao Li
- Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
| | - Xiangzhen Li
- Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
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32
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Linkages of Firmicutes and Bacteroidetes populations to methanogenic process performance. ACTA ACUST UNITED AC 2016; 43:771-81. [DOI: 10.1007/s10295-016-1760-8] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 03/15/2016] [Indexed: 01/24/2023]
Abstract
Abstract
To identify potential linkages between specific bacterial populations and process performance in anaerobic digestion, the dynamics of bacterial community structure was monitored with high-throughput sequencing in triplicate anaerobic digesters treating animal waste. Firmicutes and Bacteroidetes were found as the two most abundant populations, however, with contrasting population dynamics in response to organic overloading. Firmicutes dominated the bacterial community during stable process performance at low organic loading rate, representing over 50 % of the bacterial abundance. In contrast, the onset of organic overloading raised the relative abundance of Bacteroidetes from 20 ± 2.6 to 44 ± 3.1 %. In addition to the significant negative correlation between the relative abundance of Firmicutes and Bacteroidetes, populations of Firmicutes and Bacteroidetes were found to be linked to process parameters including organic loading rate, volatile fatty acids concentration, and methane production. Therefore, the population abundance ratio of Firmicutes to Bacteroidetes (F/B ratio) was suggested as a potential indicator for process performance. The interactions between Firmicutes and Bacteroidetes populations could be exploited to develop strategies for the prevention of performance perturbation in anaerobic digestion processes.
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33
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Cai M, Wilkins D, Chen J, Ng SK, Lu H, Jia Y, Lee PKH. Metagenomic Reconstruction of Key Anaerobic Digestion Pathways in Municipal Sludge and Industrial Wastewater Biogas-Producing Systems. Front Microbiol 2016; 7:778. [PMID: 27252693 PMCID: PMC4879347 DOI: 10.3389/fmicb.2016.00778] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/09/2016] [Indexed: 01/06/2023] Open
Abstract
Anaerobic digestion (AD) is a microbial process widely used to treat organic wastes. While the microbes involved in digestion of municipal sludge are increasingly well characterized, the taxonomic and functional compositions of AD digesters treating industrial wastewater have been understudied. This study examined metagenomes from a biogas-producing digester treating municipal sludge in Shek Wu Hui (SWH), Hong Kong and an industrial wastewater digester in Guangzhou (GZ), China, and compared their taxonomic composition and reconstructed biochemical pathways. Genes encoding carbohydrate metabolism and protein metabolism functions were overrepresented in GZ, while genes encoding functions related to fatty acids, lipids and isoprenoids were overrepresented in SWH, reflecting the plants' feedstocks. Mapping of genera to functions in each community indicated that both digesters had a high level of functional redundancy, and a more even distribution of genera in GZ suggested that it was more functionally stable. While fermentation in both samples was dominated by Clostridia, SWH had an overrepresentation of Proteobacteria, including syntrophic acetogens, reflecting its more complex substrate. Considering the growing importance of biogas as an alternative fuel source, a detailed mechanistic understanding of AD is important and this report will be a basis for further study of industrial wastewater AD.
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Affiliation(s)
- Mingwei Cai
- School of Energy and Environment, City University of Hong Kong Hong Kong, China
| | - David Wilkins
- School of Energy and Environment, City University of Hong Kong Hong Kong, China
| | - Jiapeng Chen
- School of Energy and Environment, City University of Hong Kong Hong Kong, China
| | - Siu-Kin Ng
- School of Energy and Environment, City University of Hong Kong Hong Kong, China
| | - Hongyuan Lu
- School of Energy and Environment, City University of Hong Kong Hong Kong, China
| | - Yangyang Jia
- School of Energy and Environment, City University of Hong Kong Hong Kong, China
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong Hong Kong, China
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34
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Venkiteshwaran K, Bocher B, Maki J, Zitomer D. Relating Anaerobic Digestion Microbial Community and Process Function. Microbiol Insights 2016; 8:37-44. [PMID: 27127410 PMCID: PMC4841157 DOI: 10.4137/mbi.s33593] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 01/19/2016] [Accepted: 01/25/2016] [Indexed: 01/01/2023] Open
Abstract
Anaerobic digestion (AD) involves a consortium of microorganisms that convert substrates into biogas containing methane for renewable energy. The technology has suffered from the perception of being periodically unstable due to limited understanding of the relationship between microbial community structure and function. The emphasis of this review is to describe microbial communities in digesters and quantitative and qualitative relationships between community structure and digester function. Progress has been made in the past few decades to identify key microorganisms influencing AD. Yet, more work is required to realize robust, quantitative relationships between microbial community structure and functions such as methane production rate and resilience after perturbations. Other promising areas of research for improved AD may include methods to increase/control (1) hydrolysis rate, (2) direct interspecies electron transfer to methanogens, (3) community structure-function relationships of methanogens, (4) methanogenesis via acetate oxidation, and (5) bioaugmentation to study community-activity relationships or improve engineered bioprocesses.
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Affiliation(s)
- Kaushik Venkiteshwaran
- Department of Civil, Construction and Environmental Engineering, Marquette University, Milwaukee, WI, USA
| | | | - James Maki
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
| | - Daniel Zitomer
- Department of Civil, Construction and Environmental Engineering, Marquette University, Milwaukee, WI, USA
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35
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Hari AR, Katuri KP, Gorron E, Logan BE, Saikaly PE. Multiple paths of electron flow to current in microbial electrolysis cells fed with low and high concentrations of propionate. Appl Microbiol Biotechnol 2016; 100:5999-6011. [PMID: 26936773 DOI: 10.1007/s00253-016-7402-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 02/14/2016] [Accepted: 02/16/2016] [Indexed: 11/25/2022]
Abstract
Microbial electrolysis cells (MECs) provide a viable approach for bioenergy generation from fermentable substrates such as propionate. However, the paths of electron flow during propionate oxidation in the anode of MECs are unknown. Here, the paths of electron flow involved in propionate oxidation in the anode of two-chambered MECs were examined at low (4.5 mM) and high (36 mM) propionate concentrations. Electron mass balances and microbial community analysis revealed that multiple paths of electron flow (via acetate/H2 or acetate/formate) to current could occur simultaneously during propionate oxidation regardless of the concentration tested. Current (57-96 %) was the largest electron sink and methane (0-2.3 %) production was relatively unimportant at both concentrations based on electron balances. At a low propionate concentration, reactors supplemented with 2-bromoethanesulfonate had slightly higher coulombic efficiencies than reactors lacking this methanogenesis inhibitor. However, an opposite trend was observed at high propionate concentration, where reactors supplemented with 2-bromoethanesulfonate had a lower coulombic efficiency and there was a greater percentage of electron loss (23.5 %) to undefined sinks compared to reactors without 2-bromoethanesulfonate (11.2 %). Propionate removal efficiencies were 98 % (low propionate concentration) and 78 % (high propionate concentration). Analysis of 16S rRNA gene pyrosequencing revealed the dominance of sequences most similar to Geobacter sulfurreducens PCA and G. sulfurreducens subsp. ethanolicus. Collectively, these results provide new insights on the paths of electron flow during propionate oxidation in the anode of MECs fed with low and high propionate concentrations.
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Affiliation(s)
- Ananda Rao Hari
- Biological and Environmental Sciences and Engineering Division, Water Desalination and Reuse Research Center, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Krishna P Katuri
- Biological and Environmental Sciences and Engineering Division, Water Desalination and Reuse Research Center, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Eduardo Gorron
- Biological and Environmental Sciences and Engineering Division, Water Desalination and Reuse Research Center, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Bruce E Logan
- Department of Civil and Environmental Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Pascal E Saikaly
- Biological and Environmental Sciences and Engineering Division, Water Desalination and Reuse Research Center, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia.
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36
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Marsolek MD, Rittmann BE. Effect of substrate characteristics on microbial community structure, function, resistance, and resilience; application to coupled photocatalytic-biological treatment. WATER RESEARCH 2016; 90:1-8. [PMID: 26722990 DOI: 10.1016/j.watres.2015.12.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 11/30/2015] [Accepted: 12/01/2015] [Indexed: 06/05/2023]
Abstract
Advanced oxidation (AO) coupled with biodegradation is an emerging treatment technology for wastewaters containing biologically recalcitrant and inhibitory organics, including those containing chlorinated aromatic compounds. The composition of the AO effluent organics can vary significantly with reaction conditions, and this composition can affect the performance of subsequent biodegradation. Three synthetic effluents were used to mimic varying degrees of AO of 2,4,5-trichlorophenol: 4-chlorocatechol to mimic light transformation, 2-chloromuconic acid to mimic moderate transformation, and acetate to mimic extensive transformation. The substrates were fed to identical chemostats and analyzed at steady state for removal of chemical oxygen demand (COD) and dissolved organic carbon (DOC), biomass concentration, and bacterial diversity. The chemostat fed acetate performed best at steady state. The 2-chloromuconic acid chemostat was next in terms of steady-state performance, and the 4-chlorocatechol reactor performed worst, correlating with degree of AO transformation. A spike of 100 μM 2,4,5-trichlorophenol was then applied to each chemostat. The chemostat fed 4-chlorocatechol exhibited the best resistance to the perturbation in terms of maintaining consistent community structure and biomass concentration, whereas the performance of the acetate-fed chemostat was severely impaired in these categories, although it quickly regained capacity to remove organics near pre-perturbation levels demonstrating good resilience. The opposing trends for steady-state versus perturbed performance highlight tradeoffs inherent in coupled chemical-biological systems.
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Affiliation(s)
- Michael D Marsolek
- Department of Civil and Environmental Engineering, Seattle University, Seattle, WA 98122, USA.
| | - Bruce E Rittmann
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University, Tempe, AZ 85287-5701, USA
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Tao Y, Hu X, Zhu X, Jin H, Xu Z, Tang Q, Li X. Production of Butyrate from Lactate by a Newly Isolated Clostridium sp. BPY5. Appl Biochem Biotechnol 2016; 179:361-74. [DOI: 10.1007/s12010-016-1999-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 01/24/2016] [Indexed: 10/22/2022]
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Aziz FAA, Suzuki K, Ohtaki A, Sagegami K, Hirai H, Seno J, Mizuno N, Inuzuka Y, Saito Y, Tashiro Y, Hiraishi A, Futamata H. Interspecies interactions are an integral determinant of microbial community dynamics. Front Microbiol 2015; 6:1148. [PMID: 26539177 PMCID: PMC4611161 DOI: 10.3389/fmicb.2015.01148] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 10/05/2015] [Indexed: 11/26/2022] Open
Abstract
This study investigated the factors that determine the dynamics of bacterial communities in a complex system using multidisciplinary methods. Since natural and engineered microbial ecosystems are too complex to study, six types of synthetic microbial ecosystems (SMEs) were constructed under chemostat conditions with phenol as the sole carbon and energy source. Two to four phenol-degrading, phylogenetically and physiologically different bacterial strains were used in each SME. Phylogeny was based on the nucleotide sequence of 16S rRNA genes, while physiologic traits were based on kinetic and growth parameters on phenol. Two indices, J parameter and “interspecies interaction,” were compared to predict which strain would become dominant in an SME. The J parameter was calculated from kinetic and growth parameters. On the other hand, “interspecies interaction,” a new index proposed in this study, was evaluated by measuring the specific growth activity, which was determined on the basis of relative growth of a strain with or without the supernatant prepared from other bacterial cultures. Population densities of strains used in SMEs were enumerated by real-time quantitative PCR (qPCR) targeting the gene encoding the large subunit of phenol hydroxylase and were compared to predictions made from J parameter and interspecies interaction calculations. In 4 of 6 SEMs tested the final dominant strain shown by real-time qPCR analyses coincided with the strain predicted by both the J parameter and the interspecies interaction. However, in SMEII-2 and SMEII-3 the final dominant Variovorax strains coincided with prediction of the interspecies interaction but not the J parameter. These results demonstrate that the effects of interspecies interactions within microbial communities contribute to determining the dynamics of the microbial ecosystem.
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Affiliation(s)
- Fatma A A Aziz
- Laboratory of Food Crops, Institute of Tropical Agriculture, Universiti Putra Malaysia Serdang, Malaysia ; Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University Hamamatsu, Japan
| | - Kenshi Suzuki
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University Hamamatsu, Japan
| | - Akihiro Ohtaki
- Department of Environmental and Life Sciences, Toyohashi University of Technology Toyohashi, Japan
| | - Keita Sagegami
- Department of Environmental and Life Sciences, Toyohashi University of Technology Toyohashi, Japan
| | - Hidetaka Hirai
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University Hamamatsu, Japan
| | - Jun Seno
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University Hamamatsu, Japan
| | - Naoko Mizuno
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University Hamamatsu, Japan
| | - Yuma Inuzuka
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University Hamamatsu, Japan
| | - Yasuhisa Saito
- Department of Mathematics, Shimane University Matsue, Japan
| | - Yosuke Tashiro
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University Hamamatsu, Japan
| | - Akira Hiraishi
- Department of Environmental and Life Sciences, Toyohashi University of Technology Toyohashi, Japan
| | - Hiroyuki Futamata
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University Hamamatsu, Japan
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Abstract
UNLABELLED Two full-scale slow sand filters (SSFs) were sampled periodically from April until November 2011 to study the spatial and temporal structures of the bacterial communities found in the filters. To monitor global changes in the microbial communities, DNA from sand samples taken at different depths and locations within the SSFs and at different filters ages was used for Illumina 16S rRNA gene sequencing. Additionally, 15 water quality parameters were monitored to assess filter performance, with functionally relevant microbial members being identified by using multivariate statistics. The bacterial diversity in the SSFs was found to be much larger than previously documented, with community composition being shaped by the characteristics of the SSFs (filter age and depth) and sampling characteristics (month, side, and distance from the influent and effluent pipes). We found that several key genera (Acidovorax, Halomonas, Sphingobium, and Sphingomonas) were associated with filter performance. In addition, at the whole-community level, a strong positive correlation was found between species evenness and filter performance. This study is the first to comprehensively characterize the microbial community of SSFs and link specific microbes to water quality parameters. In doing so, we reveal key patterns in microbial community structure that relate to overall community function. IMPORTANCE The supply of sustainable, energy-efficient, and safe drinking water to an increasing world population is a huge challenge faced by the water industry. SSFs have been used for hundreds of years to provide a safe and reliable source of potable drinking water, with minimal energy requirements. However, a lack of knowledge pertaining to the treatment mechanisms, particularly the biological processes, underpinning SSF operation has meant that SSFs are still operated as "black boxes." Understanding these dynamics alongside performance-induced effects associated with operational differences will promote optimized SSF design, maintenance, and operation, creating more efficient and environmentally sustainable filters. Through a spatial-temporal survey of full-scale SSFs at various points of operation, we present the most detailed characterization to date of the functional microbial communities found in SSFs, linking various taxa and community metrics to optimal water quality production.
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Niu Q, Takemura Y, Kubota K, Li YY. Comparing mesophilic and thermophilic anaerobic digestion of chicken manure: Microbial community dynamics and process resilience. WASTE MANAGEMENT (NEW YORK, N.Y.) 2015; 43:114-22. [PMID: 26054964 DOI: 10.1016/j.wasman.2015.05.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 05/10/2015] [Accepted: 05/12/2015] [Indexed: 05/19/2023]
Abstract
While methane fermentation is considered as the most successful bioenergy treatment for chicken manure, the relationship between operational performance and the dynamic transition of archaeal and bacterial communities remains poorly understood. Two continuous stirred-tank reactors were investigated under thermophilic and mesophilic conditions feeding with 10%TS. The tolerance of thermophilic reactor on total ammonia nitrogen (TAN) was found to be 8000mg/L with free ammonia (FA) 2000mg/L compared to 16,000mg/L (FA1500mg/L) of mesophilic reactor. Biomethane production was 0.29 L/gVSin in the steady stage and decreased following TAN increase. After serious inhibition, the mesophilic reactor was recovered successfully by dilution and washing stratagem compared to the unrecoverable of thermophilic reactor. The relationship between the microbial community structure, the bioreactor performance and inhibitors such as TAN, FA, and volatile fatty acid was evaluated by canonical correspondence analysis. The performance of methanogenic activity and substrate removal efficiency were changed significantly correlating with the community evenness and phylogenetic structure. The resilient archaeal community was found even after serious inhibition in both reactors. Obvious dynamics of bacterial communities were observed in acidogenic and hydrolytic functional bacteria following TAN variation in the different stages.
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Affiliation(s)
- Qigui Niu
- Department of Civil and Environmental Engineering, Graduate School of Engineering Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Yasuyuki Takemura
- Department of Civil and Environmental Engineering, Graduate School of Engineering Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Kengo Kubota
- Department of Civil and Environmental Engineering, Graduate School of Engineering Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Yu-You Li
- Department of Civil and Environmental Engineering, Graduate School of Engineering Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan; Key Lab of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, PR China.
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Mathai PP, Zitomer DH, Maki JS. Quantitative detection of syntrophic fatty acid-degrading bacterial communities in methanogenic environments. Microbiology (Reading) 2015; 161:1189-97. [DOI: 10.1099/mic.0.000085] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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42
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Dynamics of the microbial community during continuous methane fermentation in continuously stirred tank reactors. J Biosci Bioeng 2015; 119:375-83. [DOI: 10.1016/j.jbiosc.2014.09.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 09/03/2014] [Accepted: 09/16/2014] [Indexed: 11/20/2022]
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43
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Use of CMEIAS Image Analysis Software to Accurately Compute Attributes of Cell Size, Morphology, Spatial Aggregation and Color Segmentation that Signify in Situ Ecophysiological Adaptations in Microbial Biofilm Communities. COMPUTATION 2015. [DOI: 10.3390/computation3010072] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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44
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Hori T, Haruta S, Sasaki D, Hanajima D, Ueno Y, Ogata A, Ishii M, Igarashi Y. Reorganization of the bacterial and archaeal populations associated with organic loading conditions in a thermophilic anaerobic digester. J Biosci Bioeng 2015; 119:337-44. [DOI: 10.1016/j.jbiosc.2014.09.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Revised: 07/28/2014] [Accepted: 09/02/2014] [Indexed: 10/24/2022]
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45
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Bocher BTW, Cherukuri K, Maki JS, Johnson M, Zitomer DH. Relating methanogen community structure and anaerobic digester function. WATER RESEARCH 2015; 70:425-435. [PMID: 25562581 DOI: 10.1016/j.watres.2014.12.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 11/13/2014] [Accepted: 12/08/2014] [Indexed: 06/04/2023]
Abstract
Much remains unknown about the relationships between microbial community structure and anaerobic digester function. However, knowledge of links between community structure and function, such as specific methanogenic activity (SMA) and COD removal rate, are valuable to improve anaerobic bioprocesses. In this work, quantitative structure-activity relationships (QSARs) were developed using multiple linear regression (MLR) to predict SMA using methanogen community structure descriptors for 49 cultures. Community descriptors were DGGE demeaned standardized band intensities for amplicons of a methanogen functional gene (mcrA). First, predictive accuracy of MLR QSARs was assessed using cross validation with training (n = 30) and test sets (n = 19) for glucose and propionate SMA data. MLR equations correlating band intensities and SMA demonstrated good predictability for glucose (q(2) = 0.54) and propionate (q(2) = 0.53). Subsequently, data from all 49 cultures were used to develop QSARs to predict SMA values. Higher intensities of two bands were correlated with higher SMA values; high abundance of methanogens associated with these two bands should be encouraged to attain high SMA values. QSARs are helpful tools to identify key microorganisms or to study and improve many bioprocesses. Development of new, more robust QSARs is encouraged for anaerobic digestion or other bioprocesses, including nitrification, nitritation, denitrification, anaerobic ammonium oxidation, and enhanced biological phosphorus removal.
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Affiliation(s)
- B T W Bocher
- BP Americas Inc., Petrochemicals Technology: Water Treatment, 150 Warrenville Rd., Naperville, IL, United States
| | - K Cherukuri
- Marquette University, Department of Biological Sciences, P.O. Box 1881, Milwaukee, WI 53201-1881, United states
| | - J S Maki
- Marquette University, Department of Biological Sciences, P.O. Box 1881, Milwaukee, WI 53201-1881, United states
| | - M Johnson
- Marquette University, Department of Electrical and Computer Engineering, P.O. Box 1881, Milwaukee, WI 53201-1881, United States
| | - D H Zitomer
- Marquette University, Department of Civil, Construction and Environmental Engineering, P.O. Box 1881, Milwaukee, WI 53201-1881, United States.
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Massalha N, Brenner A, Sheindorf C, Sabbah I. The effect of anaerobic biomass drying and exposure to air on their recovery and evolution. WATER RESEARCH 2014; 63:42-51. [PMID: 24981742 DOI: 10.1016/j.watres.2014.05.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 05/01/2014] [Accepted: 05/12/2014] [Indexed: 06/03/2023]
Abstract
The main goal of this study was to test the effect of various drying methods of granular anaerobic biomass on biomass survival, potential and rate of methane re-production, and structure. This may facilitate the development of drying methods to preserve excess anaerobic biomass in dry form for re-inoculation of existing digesters after process failure or wash out or for the start-up of new digesters. To that end, anaerobic granular biomass was collected from an up-flow anaerobic sludge blanket (UASB) reactor. The biomass was dried using two alternative methods: oven with air circulation at 50 °C for 24 h (DAO), and vacuum rotary evaporator at anaerobic conditions (DAN). For comparison, the control was a biomass with no drying (WET). Biomass samples were tested for specific methanogenic activity using synthetic wastewater. The microbial communities were also tested for viability using the LIVE/DEAD kit, and total biomass was initially quantified by qPCR targeting 16S rRNA genes. In addition, the mcrA functional gene was used s a target for the detection of the most abundant methanogens. Basic bacterial morphology classification was done by VIT(®) gene probe technology using a fluorescence microscope. Dried DAN and DAO biomasses required approximately four operational runs to recover their initial methanogenic activity compared to WET biomass. LIVE/DEAD results showed clear increases in the proportions of the viable biomass of the total bacterial communities over time, especially for the DAN and DAO samples. A comparison of the qPCR results of both DAN and DAO to the WET biomass showed that the methanogenic mcrA gene fraction of the total biomass population of 16S rRNA gene concentrations decreased moderately by about 17.2% in the samples of DAO and by approximately 6.7% in the samples of DAN over all runs after Run1.
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Affiliation(s)
- Nedal Massalha
- Unit of Environmental Engineering, Faculty of Engineering Sciences, Ben-Gurion University of the Negev (BGU), Beer-Sheva, Israel; The Galilee Society Institute of Applied Research, Shefa-Amr, Israel
| | - Asher Brenner
- Unit of Environmental Engineering, Faculty of Engineering Sciences, Ben-Gurion University of the Negev (BGU), Beer-Sheva, Israel
| | - Chaim Sheindorf
- Chemical Engineering Department, Shenkar Engineering College, Ramat Gan, Israel
| | - Isam Sabbah
- The Galilee Society Institute of Applied Research, Shefa-Amr, Israel; Prof. Ephraim Katzir Department of Biotechnology Engineering, Braude College, Karmeil, Israel.
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Folland I, Trione D, Dazzo F. Accuracy of biovolume formulas for CMEIAS computer-assisted microscopy and body size analysis of morphologically diverse microbial populations and communities. MICROBIAL ECOLOGY 2014; 68:596-610. [PMID: 24763979 DOI: 10.1007/s00248-014-0410-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 03/06/2014] [Indexed: 06/03/2023]
Abstract
Cell biovolume is a commonly used metric of microbial abundance analyzed by computer-assisted microscopy, but the accuracies of most biovolume formulas have not been validated by ground truth data. We examined the accuracy of 17 biovolume formulas by comparing the computed volumes of 3D models representing 11 microbial morphotypes (cocci, spirals, curved rods, U-shaped rods, regular straight rods, unbranched filaments, ellipsoids, clubs, prosthecates, rudimentary branched rods, and branched filaments) to the volume displacement of the same objects as ground truth. As anticipated, formula accuracy was significantly influenced by the morphotype examined. A few formulas performed very accurately (> 95 %), especially those that adapted to the cell's shape, whereas others were consistently inaccurate or only accurate for one or two morphotypes. As an example of application, indices of morphological diversity in a freshwater biofilm assemblage were shown to be significantly different when microbial abundance among morphotype classes was measured as biovolume body mass rather than cell counts. Spatial analysis of biovolume body mass can also provide insights on the in situ ecophysiological attributes among individuals in microbial populations and communities, including their spatially autocorrelated allometric scaling interrelationships between body size, metabolic activity, resource apportionment and use, food web dynamics, and various cell-cell interactions affecting their growth and colonization behavior within spatially structured biofilm landscapes. This improved computing technology of biovolume algorithms with proven accuracy identifies which formula(s) should be used to compute microbial biovolumes in 2D images of morphologically diverse communities acquired by conventional phase-contrast light microscopy at single-cell resolution.
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Affiliation(s)
- Ingrid Folland
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
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48
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Ferguson RMW, Villa R, Coulon F. Bioengineering options and strategies for the optimization of anaerobic digestion processes. ACTA ACUST UNITED AC 2014. [DOI: 10.1080/09593330.2014.907362] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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49
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Microbial community dynamics and stability during an ammonia-induced shift to syntrophic acetate oxidation. Appl Environ Microbiol 2014; 80:3375-83. [PMID: 24657858 DOI: 10.1128/aem.00166-14] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Anaerobic digesters rely on the diversity and distribution of parallel metabolic pathways mediated by complex syntrophic microbial communities to maintain robust and optimal performance. Using mesophilic swine waste digesters, we experimented with increased ammonia loading to induce a shift from aceticlastic methanogenesis to an alternative acetate-consuming pathway of syntrophic acetate oxidation. In comparison with control digesters, we observed shifts in bacterial 16S rRNA gene content and in functional gene repertoires over the course of the digesters' 3-year operating period. During the first year, under identical startup conditions, all bioreactors mirrored each other closely in terms of bacterial phylotype content, phylogenetic structure, and evenness. When we perturbed the digesters by increasing the ammonia concentration or temperature, the distribution of bacterial phylotypes became more uneven, followed by a return to more even communities once syntrophic acetate oxidation had allowed the experimental bioreactors to regain stable operation. The emergence of syntrophic acetate oxidation coincided with a partial shift from aceticlastic to hydrogenotrophic methanogens. Our 16S rRNA gene analysis also revealed that acetate-fed enrichment experiments resulted in communities that did not represent the bioreactor community. Analysis of shotgun sequencing of community DNA suggests that syntrophic acetate oxidation was carried out by a heterogeneous community rather than by a specific keystone population with representatives of enriched cultures with this metabolic capacity.
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50
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Johnson DR, Lee TK, Park J, Fenner K, Helbling DE. The functional and taxonomic richness of wastewater treatment plant microbial communities are associated with each other and with ambient nitrogen and carbon availability. Environ Microbiol 2014; 17:4851-60. [PMID: 24552172 DOI: 10.1111/1462-2920.12429] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 12/30/2013] [Accepted: 02/11/2014] [Indexed: 02/01/2023]
Abstract
The number of functional traits of a wastewater treatment plant (WWTP) microbial community (i.e. functional richness) is thought to be an important determinant of its overall functional performance, but the ecological factors that determine functional richness remain unclear. The number of taxa within a community (i.e. taxonomic richness) is one ecological factor that might be important. Communities that contain more taxa are more likely to have more functional traits, and a positive association is therefore expected between functional and taxonomic richness. Empirical tests for this positive association among WWTP communities, however, are lacking. We address this knowledge gap by measuring the functional and taxonomic richness of 10 independent WWTP communities. We demonstrate that functional and taxonomic richness are positively associated with each other. We further demonstrate that functional and taxonomic richness are negatively associated with the effluent NH4 -N and BOD5 concentrations. This led us to hypothesize that correlated variation in functional and taxonomic richness is likely related to variation in ambient nitrogen and carbon availability. We finally demonstrate that this hypothesis is consistent with the functional and taxonomic attributes of the WWTP communities. Together, our results improve our basic understanding of the ecology and functioning of WWTP communities.
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Affiliation(s)
- David R Johnson
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland.,Department of Environmental Microbiology, Eawag, Dübendorf, Switzerland
| | - Tae Kwon Lee
- School of Civil and Environmental Engineering, Yonsei University, Seoul, Korea
| | - Joonhong Park
- School of Civil and Environmental Engineering, Yonsei University, Seoul, Korea
| | - Kathrin Fenner
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland.,Department of Environmental Chemistry, Eawag, Dübendorf, Switzerland
| | - Damian E Helbling
- Department of Environmental Microbiology, Eawag, Dübendorf, Switzerland.,School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, USA
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