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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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2
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Alarcón-Vivero M, Moena NRT, Gonzalez F, Jopia-Contreras P, Aspé E, Briones HU, Fernandez KS. Anaerobic biofilm enriched with an ammonia tolerant methanogenic consortium to improve wastewater treatment in the fishing industry. Biotechnol Lett 2022; 44:239-251. [PMID: 35037233 DOI: 10.1007/s10529-021-03213-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 11/29/2021] [Indexed: 11/29/2022]
Abstract
The digestion efficiency of liquid industrial wastes increases when using bioreactors colonized by microbial biofilms. High concentrations of proteins derived from the fish processing industry lead to the production of ammonia, which inhibits methane production. Two bioreactors were constructed to compare methanogenic activity: one enriched with mMPA (methylaminotrofic methane production archaea) consortia (control bioreactor), and the second with NH3 tolerant consortia (treatment bioreactor). Ammonia tolerant activity was assessed by applying an ammonia shock (755 mg NH3/L). Methane production, consumption of total organic carbon (TOC) and the taxonomic composition of bacteria and archaea was evaluated using 16S rDNA in the acclimatization, ammonia shock, and recovery phases.The ammonia shock significantly affected both methane production and the consumption of TOC in the control reactor (p < 0.05) and taxonomical composition of the microbial consortia (OTU). These values remained constant in the treatment reactor. The analysis of biofilm composition showed a predominance of Methanosarcinaceae (Methanomethylovorans sp., and probably two different species of Methanosarcina sp.) in bioreactors. These results demonstrate that using acclimated biofilms enriched with ammonia tolerant methanogens control the inhibitory effect of ammonia on methanogenesis.
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Affiliation(s)
- Manuel Alarcón-Vivero
- Instituto de Acuicultura, Universidad Austral de Chile (UACh), Sede Puerto Montt, Puerto Montt, Chile
| | - Nathaly Ruiz-Tagle Moena
- Lab. Biopelículas y Microbiología Ambiental, Centro de Biotecnología, Universidad de Concepción, Concepción, Chile
| | - Fidelina Gonzalez
- Departamento de Biología Celular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | | | - Estrella Aspé
- Departamento de Ingeniería Química, Facultad de Ingeniería, Universidad de Concepción, Concepción, Chile
| | - Homero Urrutia Briones
- Lab. Biopelículas y Microbiología Ambiental, Centro de Biotecnología, Universidad de Concepción, Concepción, Chile.,Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Katherine Sossa Fernandez
- Lab. Biopelículas y Microbiología Ambiental, Centro de Biotecnología, Universidad de Concepción, Concepción, Chile. .,Facultad de Ciencias Forestales, Universidad de Concepción, Concepción, Chile.
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3
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Closed microbial communities self-organize to persistently cycle carbon. Proc Natl Acad Sci U S A 2021; 118:2013564118. [PMID: 34740965 PMCID: PMC8609437 DOI: 10.1073/pnas.2013564118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2021] [Indexed: 12/16/2022] Open
Abstract
Life on Earth depends on ecologically driven nutrient cycles to regenerate resources. Understanding how nutrient cycles emerge from a complex web of ecological processes is a central challenge in ecology. However, we lack model ecosystems that can be replicated, manipulated, and quantified in the laboratory, making it challenging to determine how changes in composition and the environment impact cycling. Enabled by a new high-precision method to quantify carbon cycling, we show that materially closed microbial ecosystems (CES) provided with only light self-organize to robustly cycle carbon. Studying replicate CES that support a carbon cycle reveals variable community composition but a conserved set of metabolic capabilities. Our study helps establish CES as model biospheres for studying how ecosystems persistently cycle nutrients. Cycles of nutrients (N, P, etc.) and resources (C) are a defining emergent feature of ecosystems. Cycling plays a critical role in determining ecosystem structure at all scales, from microbial communities to the entire biosphere. Stable cycles are essential for ecosystem persistence because they allow resources and nutrients to be regenerated. Therefore, a central problem in ecology is understanding how ecosystems are organized to sustain robust cycles. Addressing this problem quantitatively has proved challenging because of the difficulties associated with manipulating ecosystem structure while measuring cycling. We address this problem using closed microbial ecosystems (CES), hermetically sealed microbial consortia provided with only light. We develop a technique for quantifying carbon cycling in hermetically sealed microbial communities and show that CES composed of an alga and diverse bacterial consortia self-organize to robustly cycle carbon for months. Comparing replicates of diverse CES, we find that carbon cycling does not depend strongly on the taxonomy of the bacteria present. Moreover, despite strong taxonomic differences, self-organized CES exhibit a conserved set of metabolic capabilities. Therefore, an emergent carbon cycle enforces metabolic but not taxonomic constraints on ecosystem organization. Our study helps establish closed microbial communities as model ecosystems to study emergent function and persistence in replicate systems while controlling community composition and the environment.
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4
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Mohd Din ARJ, Suzuki K, Honjo M, Amano K, Nishimura T, Moriuchi R, Dohra H, Ishizawa H, Kimura M, Tashiro Y, Futamata H. Imbalance in Carbon and Nitrogen Metabolism in Comamonas testosteroni R2 Is Caused by Negative Feedback and Rescued by L-arginine. Microbes Environ 2021; 36. [PMID: 34645730 PMCID: PMC8674442 DOI: 10.1264/jsme2.me21050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The collapse of Comamonas testosteroni R2 under chemostat conditions and the aerobic growth of strain R2 under batch conditions with phenol as the sole carbon source were investigated using physiological and transcriptomic techniques. Phenol-/catechol-degrading activities under chemostat conditions gradually decreased, suggesting that metabolites produced from strain R2 accumulated in the culture, which caused negative feedback. The competitive inhibition of phenol hydroxylase and catechol dioxygenase was observed in a crude extract of the supernatant collected from the collapsed culture. Transcriptomic analyses showed that genes related to nitrogen transport were up-regulated; the ammonium transporter amtB was up-regulated approximately 190-fold in the collapsed status, suggesting an increase in the concentration of ammonium in cells. The transcriptional levels of most of the genes related to gluconeogenesis, glycolysis, the pentose phosphate pathway, and the TCA and urea cycles decreased by ~0.7-fold in the stable status, whereas the activities of glutamate synthase and glutamine synthetase increased by ~2-fold. These results suggest that ammonium was assimilated into glutamate and glutamine via 2-oxoglutarate under the limited supply of carbon skeletons, whereas the synthesis of other amino acids and nucleotides was repressed by 0.6-fold. Furthermore, negative feedback appeared to cause an imbalance between carbon and nitrogen metabolism, resulting in collapse. The effects of amino acids on negative feedback were investigated. L-arginine allowed strain R2 to grow normally, even under growth-inhibiting conditions, suggesting that the imbalance was corrected by the stimulation of the urea cycle, resulting in the rescue of strain R2.
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Affiliation(s)
- Abd Rahman Jabir Mohd Din
- Graduate School of Science and Technology, Shizuoka University.,Innovation Centre in Agritechnology for Advanced Bioprocess, UTM Pagoh Research Center
| | - Kenshi Suzuki
- Microbial Ecotechnology (Social Cooperation Laboratory), Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Masahiro Honjo
- Graduate School of Science and Technology, Shizuoka University
| | - Koki Amano
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University
| | - Tomoka Nishimura
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University
| | - Ryota Moriuchi
- Research Institution of Green Science and Technology, Shizuoka University
| | - Hideo Dohra
- Research Institution of Green Science and Technology, Shizuoka University
| | - Hidehiro Ishizawa
- Research Institution of Green Science and Technology, Shizuoka University
| | - Motohiko Kimura
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University
| | - Yosuke Tashiro
- Graduate School of Science and Technology, Shizuoka University.,Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University
| | - Hiroyuki Futamata
- Graduate School of Science and Technology, Shizuoka University.,Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University.,Research Institution of Green Science and Technology, Shizuoka University
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5
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Tandon K, Wan MT, Yang CC, Yang SH, Baatar B, Chiu CY, Tsai JW, Liu WC, Ng CS, Tang SL. Aquatic microbial community is partially functionally redundant: Insights from an in situ reciprocal transplant experiment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 786:147433. [PMID: 33971597 DOI: 10.1016/j.scitotenv.2021.147433] [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: 03/03/2021] [Revised: 04/06/2021] [Accepted: 04/25/2021] [Indexed: 06/12/2023]
Abstract
Microbial communities are considered to be functionally redundant, but few studies have tested this hypothesis empirically. In this study, we performed an in situ reciprocal transplant experiment on the surface and bottom waters of two lakes (Tsuei-Feng (T) and Yuan-Yang (Y)) with disparate trophic states and tracked changes in their microbial community composition and functions for 6 weeks using high-throughput sequencing and functional approaches. T lake's surface (Ts) and bottom (Tb) water active bacterial community (16S rRNA gene-transcript) was dominated by Actinobacteria, Bacteroidia, and Cyanobacteria, whereas Y lake's surface (Ys) and bottom (Yb) water had Gammaproteobacteria, Alphaproteobacteria, and Bacteroidia as the dominant classes. The community composition was resistant to changes in environmental conditions following the reciprocal transplant, but their functions tended to become similar to the incubating lakes' functional profiles. A significant linear positive relationship was observed between the microbial community and functional attributes (surface: R2 = 0.5065, p < 0.0001; bottom: R2 = 0.4592, p < 0.0001), though with varying scales of similarity (1-Bray Curtis distance), suggesting partial functional redundancy. Also, the entropy-based L-divergence measure identified high divergence in community composition (surface: 1.21 ± 0.54; bottom: 1.17 ± 0.51), and relatively low divergence in functional attributes (surface: 0.04 ± 0.01; bottom: 0.04 ± 0.01) in the two lakes' surface and bottom waters, providing further support for the presence of partial functional redundancy. This study enriches our understanding of community functional relationships and establishes the presence of partial functional redundancy in freshwater ecosystems.
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Affiliation(s)
- Kshitij Tandon
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan; Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan; Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Min-Tao Wan
- EcoHealth Microbiology Laboratory, WanYu Co., Ltd., Chiayi 600, Taiwan
| | - Chia-Chin Yang
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Shan-Hua Yang
- Institute of Fisheries Science, National Taiwan University, Taipei 10617, Taiwan
| | | | - Chih-Yu Chiu
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Jeng-Wei Tsai
- China Medical University, Department of Biological Science and Technology, Taichung 404, Taiwan
| | - Wen-Cheng Liu
- Department of Civil and Disaster Prevention Engineering, National United University, Miao-Li, Taiwan
| | - Chen Siang Ng
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan; Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan.
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6
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Jing X, Su S, Zhang C, Zhu J, Hou Y, Li Z, Yang X, Zhou X, He X, Munganga BP, Tang Y, Xu P. Dynamic changes in microbial community structure in farming pond water and their effect on the intestinal microbial community profile in juvenile common carp (Cyprinus carpio L.). Genomics 2021; 113:2547-2560. [PMID: 34029696 DOI: 10.1016/j.ygeno.2021.05.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 05/03/2021] [Accepted: 05/19/2021] [Indexed: 11/29/2022]
Abstract
Water quality parameter dynamics, gut, sediment and water bacteria communities were studied to understand the environmental influence on the gut microbial community of a new strain of Huanghe common carp. A total of 3,384,078 raw tags and 5105 OTUs were obtained for the gut, water and sediment bacteria. The water quality had a stronger influence on the water bacteria community than gut and sediment bacteria communities. The ambient water quality parameters also significantly influenced the water and sediment bacteria communities. Comparing the gut, sediment, and water microbial communities, a relationship was found among them. However, gut bacteria were more closely related to sediment bacterial communities than to water bacteria communities. The results showed that the top three bacterial taxa were identical in gut and sediment samples in the early days of rearing. Interestingly, bacterial communities in the carp gut, water, and sediment had different adaptabilities to variations in environmental factors.
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Affiliation(s)
- Xiaojun Jing
- College of Fisheries, Huazhong Agricultural University, Wuhan, PR China; Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, PR China
| | - Shengyan Su
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, PR China; Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, PR China
| | - Chengfeng Zhang
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, PR China
| | - Jian Zhu
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, PR China
| | - Yiran Hou
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, PR China
| | - Zhixun Li
- Henan Academy of Fishery Sciences, Zhengzhou 2450044, PR China
| | - Xingli Yang
- Henan Academy of Fishery Sciences, Zhengzhou 2450044, PR China
| | - Xiaolin Zhou
- Henan Academy of Fishery Sciences, Zhengzhou 2450044, PR China
| | - Xugang He
- College of Fisheries, Huazhong Agricultural University, Wuhan, PR China.
| | | | - Yongkai Tang
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, PR China; Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, PR China
| | - Pao Xu
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, PR China; Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, PR China.
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7
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Pacheco AR, Osborne ML, Segrè D. Non-additive microbial community responses to environmental complexity. Nat Commun 2021; 12:2365. [PMID: 33888697 PMCID: PMC8062479 DOI: 10.1038/s41467-021-22426-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 03/15/2021] [Indexed: 02/07/2023] Open
Abstract
Environmental composition is a major, though poorly understood, determinant of microbiome dynamics. Here we ask whether general principles govern how microbial community growth yield and diversity scale with an increasing number of environmental molecules. By assembling hundreds of synthetic consortia in vitro, we find that growth yield can remain constant or increase in a non-additive manner with environmental complexity. Conversely, taxonomic diversity is often much lower than expected. To better understand these deviations, we formulate metrics for epistatic interactions between environments and use them to compare our results to communities simulated with experimentally-parametrized consumer resource models. We find that key metabolic and ecological factors, including species similarity, degree of specialization, and metabolic interactions, modulate the observed non-additivity and govern the response of communities to combinations of resource pools. Our results demonstrate that environmental complexity alone is not sufficient for maintaining community diversity, and provide practical guidance for designing and controlling microbial ecosystems.
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Affiliation(s)
- Alan R Pacheco
- Graduate Program in Bioinformatics, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
| | - Melisa L Osborne
- Graduate Program in Bioinformatics, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
| | - Daniel Segrè
- Graduate Program in Bioinformatics, Boston University, Boston, MA, USA.
- Biological Design Center, Boston University, Boston, MA, USA.
- Department of Biology, Boston University, Boston, MA, USA.
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.
- Department of Physics, Boston University, Boston, MA, USA.
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8
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Diego D, Hannisdal B, Dahle H. On how the power supply shapes microbial survival. Math Biosci 2021; 338:108615. [PMID: 33857526 DOI: 10.1016/j.mbs.2021.108615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 03/29/2021] [Accepted: 04/04/2021] [Indexed: 10/21/2022]
Abstract
Understanding how environmental factors affect microbial survival is an important open problem in microbial ecology. Patterns of microbial community structure have been characterized across a wide range of different environmental settings, but the mechanisms generating these patterns remain poorly understood. Here, we use mathematical modelling to investigate fundamental connections between chemical power supply to a system and patterns of microbial survival. We reveal a complex set of interdependences between power supply and distributions of survival probability across microbial habitats, in a case without interspecific resource competition. We also find that different properties determining power supply, such as substrate fluxes and Gibbs energies of reactions, affect microbial survival in fundamentally different ways. Moreover, we show how simple connections between power supply and growth can give rise to complex patterns of microbial survival across physicochemical gradients, such as pH gradients. Our findings show the importance of taking energy fluxes into account in order to reveal fundamental connections between microbial survival and environmental conditions, and to obtain a better understanding of microbial population dynamics in natural environments.
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Affiliation(s)
- David Diego
- Department of Earth Science, University of Bergen, Allégaten, NO-5007 Bergen, Norway; K.G. Jebsen Centre for Deep Sea Research, Allégaten, NO-5007 Bergen, Norway.
| | - Bjarte Hannisdal
- Department of Earth Science, University of Bergen, Allégaten, NO-5007 Bergen, Norway; K.G. Jebsen Centre for Deep Sea Research, Allégaten, NO-5007 Bergen, Norway
| | - Håkon Dahle
- K.G. Jebsen Centre for Deep Sea Research, Allégaten, NO-5007 Bergen, Norway; Department of Biological Sciences, University of Bergen, Thormøhlens gate 53A, NO-5006 Bergen, Norway; Computational Biology Unit, Department of Informatics, University of Bergen, N-5020 Bergen, Norway
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9
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Sörenson E, Capo E, Farnelid H, Lindehoff E, Legrand C. Temperature Stress Induces Shift From Co-Existence to Competition for Organic Carbon in Microalgae-Bacterial Photobioreactor Community - Enabling Continuous Production of Microalgal Biomass. Front Microbiol 2021; 12:607601. [PMID: 33643237 PMCID: PMC7905023 DOI: 10.3389/fmicb.2021.607601] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 01/12/2021] [Indexed: 12/17/2022] Open
Abstract
To better predict the consequences of environmental change on aquatic microbial ecosystems it is important to understand what enables community resilience. The mechanisms by which a microbial community maintain its overall function, for example, the cycling of carbon, when exposed to a stressor, can be explored by considering three concepts: biotic interactions, functional adaptations, and community structure. Interactions between species are traditionally considered as, e.g., mutualistic, parasitic, or neutral but are here broadly defined as either coexistence or competition, while functions relate to their metabolism (e.g., autotrophy or heterotrophy) and roles in ecosystem functioning (e.g., oxygen production, organic matter degradation). The term structure here align with species richness and diversity, where a more diverse community is though to exhibit a broader functional capacity than a less diverse community. These concepts have here been combined with ecological theories commonly used in resilience studies, i.e., adaptive cycles, panarchy, and cross-scale resilience, that describe how the status and behavior at one trophic level impact that of surrounding levels. This allows us to explore the resilience of a marine microbial community, cultivated in an outdoor photobioreactor, when exposed to a naturally occurring seasonal stress. The culture was monitored for 6weeks during which it was exposed to two different temperature regimes (21 ± 2 and 11 ± 1°C). Samples were taken for metatranscriptomic analysis, in order to assess the regulation of carbon uptake and utilization, and for amplicon (18S and 16S rRNA gene) sequencing, to characterize the community structure of both autotrophs (dominated by the green microalgae Mychonastes) and heterotrophs (associated bacterioplankton). Differential gene expression analyses suggested that community function at warm temperatures was based on concomitant utilization of inorganic and organic carbon assigned to autotrophs and heterotrophs, while at colder temperatures, the uptake of organic carbon was performed primarily by autotrophs. Upon the shift from high to low temperature, community interactions shifted from coexistence to competition for organic carbon. Network analysis indicated that the community structure showed opposite trends for autotrophs and heterotrophs in having either high or low diversity. Despite an abrupt change of temperature, the microbial community as a whole responded in a way that maintained the overall level of diversity and function within and across autotrophic and heterotrophic levels. This is in line with cross-scale resilience theory describing how ecosystems may balance functional overlaps within and functional redundancy between levels in order to be resilient to environmental change (such as temperature).
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Affiliation(s)
- Eva Sörenson
- Department of Biology and Environmental Science, Centre of Ecology and Evolution and Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Eric Capo
- Department of Chemistry, Umeå University, Umeå, Sweden
| | - Hanna Farnelid
- Department of Biology and Environmental Science, Centre of Ecology and Evolution and Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Elin Lindehoff
- Department of Biology and Environmental Science, Centre of Ecology and Evolution and Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Catherine Legrand
- Department of Biology and Environmental Science, Centre of Ecology and Evolution and Microbial Model Systems, Linnaeus University, Kalmar, Sweden
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10
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Zhu M, Li N, Lu Y, Hu Z, Chen S, Zeng RJ. The performance and microbial communities of an anaerobic membrane bioreactor for treating fluctuating 2-chlorophenol wastewater. BIORESOURCE TECHNOLOGY 2020; 317:124001. [PMID: 32805483 DOI: 10.1016/j.biortech.2020.124001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/07/2020] [Accepted: 08/08/2020] [Indexed: 06/11/2023]
Abstract
An anaerobic membrane bioreactor (AnMBR) was used to treat low to high (5-200 mg/L) concentrations of 2-chlorophenol (2-CP) wastewater. The AnMBR achieved high and stable chemical oxygen demand removal and 2-CP removal with an average value of 93.2% and 94.2% under long hydraulic retention times (HRTs, 48-96 h), respectively. 2-CP removal efficiency of 98.6 mg/L/d was achieved with 2-CP concentration of 200 mg/L, which was much higher than that of other anaerobic bioreactors. Furthermore, volatile fatty acids didn't accumulate under high 2-CP loading. Long HRTs significantly reduced the membrane fouling as the fouling rate (0.90 × 109-5.44 × 109 m-1h-1) was low. Spirochaetaceae and Methanosaeta were the dominant microbes responsible for dechlorination, methanogenesis, and shock resistance. All these results demonstrate that this AnMBR operated under long HRTs is good and robust for fluctuating chlorophenols wastewater treatment, which has high potential for treating fluctuating refractory organics wastewater with the low membrane fouling rate.
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Affiliation(s)
- Mingchao Zhu
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Na Li
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.
| | - Yongze Lu
- School of Energy and Environment, Southeast University, Nanjing 210096, China
| | - Zhaoxia Hu
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Shouwen Chen
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Raymond Jianxiong Zeng
- Center of Wastewater Resource Recovery, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
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11
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Adler A, Holliger C. Multistability and Reversibility of Aerobic Granular Sludge Microbial Communities Upon Changes From Simple to Complex Synthetic Wastewater and Back. Front Microbiol 2020; 11:574361. [PMID: 33324361 PMCID: PMC7726351 DOI: 10.3389/fmicb.2020.574361] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 10/12/2020] [Indexed: 01/31/2023] Open
Abstract
Aerobic granular sludge (AGS) is a promising alternative wastewater treatment to the conventional activated sludge system allowing space and energy saving. Basic understanding of AGS has mainly been obtained using simple wastewater containing acetate and propionate as carbon source. Yet, the aspect and performances of AGS grown in such model systems are different from those obtained in reactor treating real wastewater. The impact of fermentable and hydrolyzable compounds on already formed AGS was assessed separately by changing the composition of the influent from simple wastewater containing volatile fatty acids to complex monomeric wastewater containing amino acids and glucose, and then to complex polymeric wastewater containing also starch and peptone. The reversibility of the observed changes was assessed by changing the composition of the wastewater from complex monomeric back to simple. The introduction of fermentable compounds in the influent left the settling properties and nutrient removal performance unchanged, but had a significant impact on the bacterial community. The proportion of Gammaproteobacteria diminished to the benefit of Actinobacteria and the Saccharibateria phylum. On the other hand, the introduction of polymeric compounds altered the settling properties and denitrification efficiency, but induced smaller changes in the bacterial community. The changes induced by the wastewater transition were only partly reversed. Seven distinct stables states of the bacterial community were detected during the 921 days of experiment, four of them observed with the complex monomeric wastewater. The transitions between these states were not only caused by wastewater changes but also by operation failures and other incidences. However, the nutrient removal performance and settling properties of the AGS were globally maintained due to the functional redundancy of its bacterial community.
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Affiliation(s)
- Aline Adler
- Laboratory for Environmental Biotechnology, School for Architecture, Civil and Environmental Engineering, Environmental Engineering Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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12
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Abdul Aziz FA, Suzuki K, Honjo M, Amano K, Mohd Din ARJB, Tashiro Y, Futamata H. Coexisting mechanisms of bacterial community are changeable even under similar stable conditions in a chemostat culture. J Biosci Bioeng 2020; 131:77-83. [PMID: 33268319 DOI: 10.1016/j.jbiosc.2020.09.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 12/24/2022]
Abstract
The coexisting mechanism of a synthetic bacterial community (SBC) was investigated to better understand how to manage microbial communities. The SBC was constructed with three kinds of phenol-utilizing bacteria, Pseudomonas sp. LAB-08, Comamonas testosteroni R2, and Cupriavidus sp. P-10, under chemostat conditions supplied with phenol as a sole carbon and energy source. Population densities of all strains were monitored by real-time quantitative PCR (qPCR) targeting the gene encoding the large subunit of phenol hydroxylase. Although the supply of phenol was stopped to allow perturbation in the SBC, all of the strains coexisted and the degradation of phenol was maintained for more than 800 days. The qPCR analyses showed that strains LAB-08 and R2 became dominant simultaneously, whereas strain P-10 was a minor population. This phenomenon was observed before and after the phenol-supply stoppage. The kinetic parameters for phenol of the SBC changed before and after the phenol-supply stoppage, which suggests a change in functional roles of strains in the SBC. Transcriptional levels of phenol hydroxylase and catechol dioxygenases of three strains were monitored by reverse-transcription qPCR (RT-qPCR). The RT-qPCR analyses revealed that all strains shared phenol and survived independently before the phenol-supply stoppage. After the stoppage, strain P-10 would incur the cost for degradation of phenol and catechol, whereas strains LAB-08 and R2 seemed to be cheaters using metabolites, indicating the development of the metabolic network. These results indicated that it is important for the management and redesign of microbial communities to understand the metabolism of bacterial communities.
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Affiliation(s)
- Fatma Azwani Abdul Aziz
- Laboratory of Food Crops, Institute of Tropical Agriculture, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Kenshi Suzuki
- Graduate School of Science and Technology, Shizuoka University, Hamamatsu 432-8011, Japan
| | - Masahiro Honjo
- Graduate School of Science and Technology, Shizuoka University, Hamamatsu 432-8011, Japan
| | - Koki Amano
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University, Hamamatsu 432-8011, Japan
| | | | - Yosuke Tashiro
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University, Hamamatsu 432-8011, Japan
| | - Hiroyuki Futamata
- Graduate School of Science and Technology, Shizuoka University, Hamamatsu 432-8011, Japan; Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University, Hamamatsu 432-8011, Japan; Research Institution of Green Science and Technology, Shizuoka University, Shizuoka 422-8529, Japan.
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13
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Louca S, Rubin IN, Madilao LL, Bohlmann J, Doebeli M, Wegener Parfrey L. Effects of forced taxonomic transitions on metabolic composition and function in microbial microcosms. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:514-524. [PMID: 32618124 DOI: 10.1111/1758-2229.12866] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 06/29/2020] [Indexed: 06/11/2023]
Abstract
Surveys of microbial systems indicate that in many situations taxonomy and function may constitute largely independent ('decoupled') axes of variation. However, this decoupling is rarely explicitly tested experimentally, partly because it is hard to directly induce taxonomic variation without affecting functional composition. Here we experimentally evaluate this paradigm using microcosms resembling lake sediments and subjected to two different levels of salinity (0 and 19) and otherwise similar environmental conditions. We used DNA sequencing for taxonomic and functional profiling of bacteria and archaea and physicochemical measurements to monitor metabolic function, over 13 months. We found that the taxonomic composition of the saline systems gradually but strongly diverged from the fresh systems. In contrast, the metabolic composition (in terms of proportions of various genes) remained nearly identical across treatments and over time. Oxygen consumption rates and methane concentrations were substantially lower in the saline treatment, however, their similarity either increased (for oxygen) or did not change significantly (for methane) between the first and last sampling time, indicating that the lower metabolic activity in the saline treatments was directly and immediately caused by salinity rather than the gradual taxonomic divergence. Our experiment demonstrates that strong taxonomic shifts need not directly affect metabolic rates.
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Affiliation(s)
- Stilianos Louca
- Department of Biology, University of Oregon, Eugene, OR, USA
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Ilan N Rubin
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | - Lufiani L Madilao
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Wine Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Jörg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Wine Research Centre, University of British Columbia, Vancouver, BC, Canada
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Michael Doebeli
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
- Department of Mathematics, University of British Columbia, Vancouver, BC, Canada
| | - Laura Wegener Parfrey
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
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14
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Wang C, Wang Y, Wang Y, Cheung KK, Ju F, Xia Y, Zhang T. Genome-centric microbiome analysis reveals solid retention time (SRT)-shaped species interactions and niche differentiation in food waste and sludge co-digesters. WATER RESEARCH 2020; 181:115858. [PMID: 32505886 DOI: 10.1016/j.watres.2020.115858] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 04/19/2020] [Accepted: 04/21/2020] [Indexed: 06/11/2023]
Abstract
Co-digestion of food waste with sewage sludge is widely applied for waste stabilization and energy recovery around the world. However, the effect of solid retention time (SRT) on the microbial population dynamics, metabolism and interspecies interaction have not been fully elucidated. Here, the influence of SRTs (5-25 days) on the performance of the co-digestion system was investigated and state-of-the-art genome-centric metagenomic analysis was employed to uncover the dynamics and metabolic network of the key players underlying the well-functioned and poorly-functioned co-digestion microbial communities. The results of the microbial analyses indicated that SRT largely shaped microbial community structure by enriching the syntrophic specialist Syntrophomonas and CO2/H2 ( formate)-using methanogen Methanocorpusculum in the well-functioned co-digester operated at SRT of 25 days, while selecting acid-tolerant populations Lactobacillus at SRT of 5 days. The metagenome assembled genomes (MAGs) of key players, such as Syntrophomonadaceae, Methanocorpusculum, and Mesotoga, were retrieved, additionally, the syntrophic acetate oxidation plus hydrogenotrophic methanogenesis (SAO-HM) were proposed as the dominant pathway for methane production. The metabolic interaction in the co-digestion microbial consortia was profiled by assigning MAGs into functional guilds. Functional redundancy was found in the bacterial groups in hydrolysis step, and the members in these groups reduced the direct competition by niche differentiation.
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Affiliation(s)
- Chunxiao Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Yubo Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Yulin Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | | | - Feng Ju
- Environmental Microbiome and Biotechnology Laboratory (EMBLab), School of Engineering, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, China
| | - Yu Xia
- State Environmental Protection Key Laboratory of Integrated Surface Water- Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.
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15
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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: 5] [Impact Index Per Article: 1.3] [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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16
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Obata O, Salar-Garcia MJ, Greenman J, Kurt H, Chandran K, Ieropoulos I. Development of efficient electroactive biofilm in urine-fed microbial fuel cell cascades for bioelectricity generation. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 258:109992. [PMID: 31929046 PMCID: PMC7001104 DOI: 10.1016/j.jenvman.2019.109992] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 12/03/2019] [Accepted: 12/11/2019] [Indexed: 05/20/2023]
Abstract
The Microbial fuel cell (MFC) technology harnesses the potential of some naturally occurring bacteria for electricity generation. Digested sludge is commonly used as the inoculum to initiate the process. There are, however, health hazards and practical issues associated with the use of digested sludge depending on its origin as well as the location for system deployment. This work reports the development of an efficient electroactive bacterial community within ceramic-based MFCs fed with human urine in the absence of sludge inoculum. The results show the development of a uniform bacterial community with power output levels equal to or higher than those generated from MFCs inoculated with sludge. In this case, the power generation begins within 2 days of the experimental set-up, compared to about 5 days in some sludge-inoculated MFCs, thus significantly reducing the start-up time. The metagenomics analysis of the successfully formed electroactive biofilm (EAB) shows significant shifts between the microbial ecology of the feeding material (fresh urine) and the developed anodic biofilm. A total of 21 bacteria genera were detected in the urine feedstock whilst up to 35 different genera were recorded in the developed biofilm. Members of Pseudomonas (18%) and Anaerolineaceae (17%) dominate the bacterial community of the fresh urine feed while members of Burkholderiaceae (up to 50%) and Tissierella (up to 29%) dominate the anodic EAB. These results highlight a significant shift in the bacterial community of the feedstock towards a selection and adaptation required for the various electrochemical reactions essential for survival through power generation.
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Affiliation(s)
- Oluwatosin Obata
- Bristol BioEnergy Centre, Bristol Robotics Laboratory, University of the West of England, BS16 1QY, UK.
| | - Maria J Salar-Garcia
- Bristol BioEnergy Centre, Bristol Robotics Laboratory, University of the West of England, BS16 1QY, UK
| | - John Greenman
- Bristol BioEnergy Centre, Bristol Robotics Laboratory, University of the West of England, BS16 1QY, UK; Biological, Biomedical and Analytical Sciences, University of the West of England, BS16 1QY, UK
| | - Halil Kurt
- Department of Earth and Environmental Engineering, Columbia University, NY, USA
| | - Kartik Chandran
- Department of Earth and Environmental Engineering, Columbia University, NY, USA
| | - Ioannis Ieropoulos
- Bristol BioEnergy Centre, Bristol Robotics Laboratory, University of the West of England, BS16 1QY, UK.
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17
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Zhang B, Ning D, Yang Y, Van Nostrand JD, Zhou J, Wen X. Biodegradability of wastewater determines microbial assembly mechanisms in full-scale wastewater treatment plants. WATER RESEARCH 2020; 169:115276. [PMID: 31731242 DOI: 10.1016/j.watres.2019.115276] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 10/25/2019] [Accepted: 11/03/2019] [Indexed: 05/13/2023]
Abstract
Wastewater treatment plants (WWTPs) are critical for maintaining sustainable development in modern societies, wherein microbial populations residing in activated sludge (AS) are responsible for the removal of pollutants from wastewater. The biodegradability [biological oxygen demand/chemical oxygen demand (B/C ratio)] of influent, as a measure of the degree of available energy and toxicity to microorganisms in AS, has been hypothesized to drive AS microbial community assembly. However, the validity of this hypothesis has not been tested in full-scale WWTPs. In this study, we assessed the pollutant removal loads, the microbial community diversity, the relative importance of deterministic and stochastic assembly processes, and bio-interactions within the communities by analyzing 195 AS samples comprising nearly 5 000 000 16S rRNA sequences. Our results indicate that the effects of B/C ratio on pollutant removal loads can be perfectly reflected through biological properties, implying that B/C ratio determined WWTPs performance through affecting microbial community. Very low and/or very high B/C ratios result in low microbial diversity, strong stochastic processes, and large, complex networks, leading to low pollutant removal load of treatment. A B/C ratio of around 0.5 was optimal for system stability and efficiency. Based on the results of this study, the authors propose using the B/C ratio as an indispensable index to assess system performance and to provide an indicator of an impending process upset before function deteriorates significantly. This study provides a specific measure that can be used to evaluate strategies for process optimization and operation of WWTPs.
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Affiliation(s)
- Bing Zhang
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, 100084, Beijing, PR China
| | - Daliang Ning
- Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, OK, USA
| | - Yunfeng Yang
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, 100084, Beijing, PR China
| | - Joy D Van Nostrand
- Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, OK, USA
| | - Jizhong Zhou
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, 100084, Beijing, PR China; Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, OK, USA
| | - Xianghua Wen
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, 100084, Beijing, PR China.
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18
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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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19
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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: 21] [Impact Index Per Article: 4.2] [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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20
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Chiellini C, Lombardo K, Mocali S, Miceli E, Fani R. Pseudomonas strains isolated from different environmental niches exhibit different antagonistic ability. ETHOL ECOL EVOL 2019. [DOI: 10.1080/03949370.2019.1621391] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Carolina Chiellini
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino (Firenze), 50019, Italy
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, Pisa, 56124, Italy
| | - Katia Lombardo
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino (Firenze), 50019, Italy
| | - Stefano Mocali
- Centro di Ricerca Agricoltura e Ambiente, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria ― Centro di Ricerca Agricoltura e Ambiente (CREA-AA), Cascine del Riccio (Firenze), 50125, Italy
| | - Elisangela Miceli
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino (Firenze), 50019, Italy
| | - Renato Fani
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino (Firenze), 50019, Italy
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21
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Fujimoto M, Carey DE, Zitomer DH, McNamara PJ. Syntroph diversity and abundance in anaerobic digestion revealed through a comparative core microbiome approach. Appl Microbiol Biotechnol 2019; 103:6353-6367. [PMID: 31161391 DOI: 10.1007/s00253-019-09862-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 04/04/2019] [Accepted: 04/22/2019] [Indexed: 11/27/2022]
Abstract
Anaerobic digestion is an important biotechnology treatment process for conversion of waste to energy. In this study, a comparative core microbiome approach, i.e., determining taxa that are shared in functioning digesters but not shared in non-functioning digesters, was used to determine microbial taxa that could play key roles for effective anaerobic digestion. Anaerobic digester functions were impaired by adding the broad-spectrum antimicrobial triclosan (TCS) or triclocarban (TCC) at different concentrations, and the core microbiomes in both functioning and non-functioning anaerobic digesters were compared. Digesters treated with high (2500 mg/kg) or medium (450 mg/kg) TCS and high (850 mg/kg) TCC concentrations lost their function, i.e., methane production decreased, effluent volatile fatty acid concentrations increased, and pH decreased. Changes in microbial community diversity and compositions were assessed using 16S rRNA gene amplicon sequencing. Microbial richness decreased significantly in non-functioning digesters (p < 0.001). Microbial community compositions in non-functioning digesters significantly differed from those in functioning digesters (p = 0.001, ANOSIM). Microbes identified as potentially key taxa included previously known fatty acid-degrading syntrophs and amino acid-degrading syntrophs. A diverse group of syntrophs detected in this study had low relative abundance in functioning digesters, suggesting the importance of rare microbes in anaerobic digester operation. The comparative microbiome approach used in this study can be applied to other microbial systems where a community-driven biological phenomena can be observed directly.
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Affiliation(s)
- Masanori Fujimoto
- Water Quality Center, Department of Civil, Construction and Environmental Engineering, Marquette University, Milwaukee, WI, USA.,Soil and Water Sciences Department, Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
| | - Daniel E Carey
- Water Quality Center, Department of Civil, Construction and Environmental Engineering, Marquette University, Milwaukee, WI, USA.,Advisian, Charlotte, NC, USA
| | - Daniel H Zitomer
- Water Quality Center, Department of Civil, Construction and Environmental Engineering, Marquette University, Milwaukee, WI, USA
| | - Patrick J McNamara
- Water Quality Center, Department of Civil, Construction and Environmental Engineering, Marquette University, Milwaukee, WI, USA.
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22
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Koo T, Lee J, Hwang S. Development of an interspecies interaction model: An experiment on Clostridium cadaveris and Clostridium sporogenes under anaerobic condition. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 237:247-254. [PMID: 30798043 DOI: 10.1016/j.jenvman.2019.02.084] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 02/15/2019] [Accepted: 02/17/2019] [Indexed: 05/26/2023]
Abstract
The specific primer and probe sets for quantifying Clostridium cadaveris and Clostridium sporogenes using a quantitative real-time PCR were designed. Each primer and probe set detected only the target species very specifically. The two species were cultivated in pure and mixed culture in batch mode with glucose as the only carbon source. The designed QPCR sets were used successfully to estimate the biokinetic parameters of each species in pure culture: i.e., maximum specific growth rate μmax, half saturation concentration Ks, growth yield Y, and decay coefficient Kd. of C. cadaveris and C. sporogenes were 0.311 ± 0.020 and 0.360 ± 0.019 h-1, 4.241 ± 1.653 and 5.171 ± 1.097 g/L, 0.301 ± 0.065 and 0.199 ± 0.037 1011 copies/g, 0.005 ± 0.043 and 0.009 ± 0.025 h-1, respectively. The effect of interspecific interaction of on substrate consumption rate and microbial growth was evaluated using mixed culture; curve fitting and comparison of coefficients detected increase in substrate consumption rate but decrease in microbial growth rate; these results imply interspecific interaction effect. A new model was of the interspecific interaction was developed, with focus on accuracy, realism, simplicity and biological significance. This interspecific interaction model may be extended to more-complex bioprocesses such as biological wastewater treatment systems and anaerobic digestion.
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Affiliation(s)
- Taewoan Koo
- Division of Environmental Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, South Korea
| | - Joonyeob Lee
- Division of Environmental Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, South Korea
| | - Seokhwan Hwang
- Division of Environmental Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, South Korea.
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23
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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: 94] [Impact Index Per Article: 18.8] [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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24
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Li T, Liu J. Factors affecting performance and functional stratification of membrane-aerated biofilms with a counter-diffusion configuration. RSC Adv 2019; 9:29337-29346. [PMID: 35528414 PMCID: PMC9071987 DOI: 10.1039/c9ra03128f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/12/2019] [Indexed: 11/25/2022] Open
Abstract
Membrane-aerated biofilms (MABs) developed with a novel counter-diffusion configuration in oxygen and substrate supply were examined for the effect of biofilm thickness on the functional activity and microbial community structure of the biofilm with the simultaneous degradation of acetonitrile, and nitrification and denitrification. Results demonstrated that different biofilm thicknesses under different surface loading rates (SLRs) caused substantially varied profiles of the microbial activities with distinct functions in the biofilm. Both thick and thin MABs achieved high-rate performance in terms of acetonitrile removal (>99%), but the performance differed in the removal efficiencies of total nitrogen (TN), which was 1.3 times higher in the thick MAB (85%) than in the thin MAB (36.3%). The specific ammonia-oxidizing rate (SAOR) and the specific acetonitrile-degrading rate (SADR) exhibited similar declining and ascending trends in both the thin and thick MABs, respectively. In contrast, the specific denitrifying rate (SDNR) was relatively uniform at a concentration near the detection limit in the thin MAB but exhibited a hump-shaped variation with the highest rate occurring in an intermediate region in the thick MAB. Microbial community analysis revealed a dramatic shift in the dominant bacteria of the community composition with low diversity across the biofilm. This study suggests that the biofilm thickness developed under SLRs, which controls the mass transfer of oxygen and substrates into biofilms, is an important factor affecting the structural and functional stratification of bacterial populations in a single MAB treating organonitrile wastewater. Biofilm thickness is a key factor affecting structural and functional stratification of community in counter-diffusion membrane-aerated biofilms (MABs) with the simultaneous degradation of acetonitrile, and nitrification and denitrification.![]()
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Affiliation(s)
- Tinggang Li
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
- People's Republic of China
| | - Junxin Liu
- Research Center for Eco-Environmental Sciences
- Chinese Academy of Sciences
- Beijing 100085
- People's Republic of China
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25
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De Vrieze J, Ijaz UZ, Saunders AM, Theuerl S. Terminal restriction fragment length polymorphism is an "old school" reliable technique for swift microbial community screening in anaerobic digestion. Sci Rep 2018; 8:16818. [PMID: 30429514 PMCID: PMC6235954 DOI: 10.1038/s41598-018-34921-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 10/04/2018] [Indexed: 11/08/2022] Open
Abstract
The microbial community in anaerobic digestion has been analysed through microbial fingerprinting techniques, such as terminal restriction fragment length polymorphism (TRFLP), for decades. In the last decade, high-throughput 16S rRNA gene amplicon sequencing has replaced these techniques, but the time-consuming and complex nature of high-throughput techniques is a potential bottleneck for full-scale anaerobic digestion application, when monitoring community dynamics. Here, the bacterial and archaeal TRFLP profiles were compared with 16S rRNA gene amplicon profiles (Illumina platform) of 25 full-scale anaerobic digestion plants. The α-diversity analysis revealed a higher richness based on Illumina data, compared with the TRFLP data. This coincided with a clear difference in community organisation, Pareto distribution, and co-occurrence network statistics, i.e., betweenness centrality and normalised degree. The β-diversity analysis showed a similar clustering profile for the Illumina, bacterial TRFLP and archaeal TRFLP data, based on different distance measures and independent of phylogenetic identification, with pH and temperature as the two key operational parameters determining microbial community composition. The combined knowledge of temporal dynamics and projected clustering in the β-diversity profile, based on the TRFLP data, distinctly showed that TRFLP is a reliable technique for swift microbial community dynamics screening in full-scale anaerobic digestion plants.
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Affiliation(s)
- Jo De Vrieze
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000, Gent, Belgium.
| | - Umer Z Ijaz
- Infrastructure and Environment Research Division, School of Engineering, University of Glasgow, Glasgow, UK
| | - Aaron M Saunders
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Sohngardsholmsvej 49, 9000, Aalborg, Denmark
| | - Susanne Theuerl
- Leibniz Institute for Agricultural Engineering and Bioeconomy e.V. (ATB), Department Bioengineering, Max-Eyth-Allee 100, D-14469, Potsdam, Germany
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26
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Lv Z, Leite AF, Harms H, Glaser K, Liebetrau J, Kleinsteuber S, Nikolausz M. Microbial community shifts in biogas reactors upon complete or partial ammonia inhibition. Appl Microbiol Biotechnol 2018; 103:519-533. [DOI: 10.1007/s00253-018-9444-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 09/17/2018] [Accepted: 10/08/2018] [Indexed: 10/28/2022]
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27
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Jeong D, Cho K, Lee CH, Lee S, Bae H. Effects of salinity on nitrification efficiency and bacterial community structure in a nitrifying osmotic membrane bioreactor. Process Biochem 2018. [DOI: 10.1016/j.procbio.2018.08.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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28
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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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29
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Liu C, Wachemo AC, Tong H, Shi S, Zhang L, Yuan H, Li X. Biogas production and microbial community properties during anaerobic digestion of corn stover at different temperatures. BIORESOURCE TECHNOLOGY 2018; 261:93-103. [PMID: 29654999 DOI: 10.1016/j.biortech.2017.12.076] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 12/21/2017] [Accepted: 12/25/2017] [Indexed: 06/08/2023]
Abstract
Temperature has different effects on anaerobic digestion (AD) of various biomasses, which could bring out changes in microbial communities. The relationship between microbial community and methane production at 35 °C (R35), 38 °C (R38), 41 °C (R41), and 44 °C (R44) was analyzed during AD of corn stover (CS). The results showed that the daily biogas and methane production from R44 were 16.6%-42.4% and 16.2%-40.6% higher than yields from R35, R38 and R41, respectively. The abundance of Bacteroidetes in R35, R38 and R41 was relatively close (30.70%-39.36%), which was low in R44 (16.00%). The abundance of Firmicutes in R35 was 32.30%, however, Firmicutes was the most dominant phylum at R44 (66.58%). The abundance of Miscellaneous_Crenarchaeotic_Group and Euryarchaeota were 54.63 ± 6.47% and 44.43 ± 6.73% across all digesters. This research demonstrated that among all temperatures studied, 44 °C could enhance the conversion efficiency of the substrates to methane and be recommended for better conversion of CS in AD process.
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Affiliation(s)
- ChunMei Liu
- Department of Environmental Science and Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing 100029, PR China; Beijing Sound Environmental Engineering Company Ltd., PR China
| | - Akiber Chufo Wachemo
- Department of Environmental Science and Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing 100029, PR China; Department of Water Supply and Environmental Engineering, Arba Minch University, P.O. Box 21, Arba Minch, Ethiopia
| | - Huan Tong
- Department of Environmental Science and Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing 100029, PR China
| | - SiHui Shi
- Department of Environmental Science and Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing 100029, PR China
| | - Liang Zhang
- Department of Environmental Science and Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing 100029, PR China
| | - HaiRong Yuan
- Department of Environmental Science and Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing 100029, PR China
| | - XiuJin Li
- Department of Environmental Science and Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing 100029, PR China.
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30
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Martin Vincent N, Wei Y, Zhang J, Yu D, Tong J. Characterization and Dynamic Shift of Microbial Communities during Start-Up, Overloading and Steady-State in an Anaerobic Membrane Bioreactor. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15071399. [PMID: 29970829 PMCID: PMC6068774 DOI: 10.3390/ijerph15071399] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 06/19/2018] [Accepted: 06/26/2018] [Indexed: 01/10/2023]
Abstract
A lab-scale anaerobic membrane bioreactor (AnMBR) with a side stream tubular membrane was developed to treat synthetic domestic sewage to evaluate its performance and the dynamic shift of bacterial and archaeal communities during the start-up, steady-state, overloading and recovery periods of operation at mesophilic temperatures. During the start-up period, the bacterial and archaeal communities changed drastically, and Proteobacteria and Bacteroidetes predominated. During the steady-state period, the AnMBR exhibited excellent COD removal above 91%, and COD of the effluent was below 50 mg/L. High-throughput sequencing analysis results revealed that bacterial and archaeal communities shifted significantly from the start-up to the steady-state period, and that the Proteobacteria phylum predominated on days 140, 162 and 190, and the archaea community hydrogenotrophic methanogen genus Methanolinea (1.5–6.64%) predominated over the aceticlastic methanogen genus Methanothrix (1.35–3.07%). During the overloading period, significant changes occurred in microbial community on day 210, e.g., the phyla Bacteroidetes (30%), Proteobacteria (23%) and Firmicutes (18%) predominated and the archaeal community was completely suppressed, and Methanobrevibacter (0.7%) was the only methanogen genus that emerged in the overloading period. After a shock loading period, the microbial communities exhibited significant changes within the ranks of methanogens and shifted to dominance of the aceticlastic methanogen pathway. In addition, the TVFAs to alkalinity ratio in this study was suitable as an indicator of monitoring performance in the AnMBR operation.
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Affiliation(s)
- Nsanzumukiza Martin Vincent
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
- Department of Water Pollution Control Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yuansong Wei
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
- Department of Water Pollution Control Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
- Institute of Energy, Jiangxi Academy of Sciences, Nanchang 330096, China.
| | - Junya Zhang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
- Department of Water Pollution Control Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Dawei Yu
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
- Department of Water Pollution Control Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Juan Tong
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
- Department of Water Pollution Control Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
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31
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Hassa J, Maus I, Off S, Pühler A, Scherer P, Klocke M, Schlüter A. Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants. Appl Microbiol Biotechnol 2018; 102:5045-5063. [PMID: 29713790 PMCID: PMC5959977 DOI: 10.1007/s00253-018-8976-7] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 03/27/2018] [Accepted: 03/28/2018] [Indexed: 12/15/2022]
Abstract
The production of biogas by anaerobic digestion (AD) of agricultural residues, organic wastes, animal excrements, municipal sludge, and energy crops has a firm place in sustainable energy production and bio-economy strategies. Focusing on the microbial community involved in biomass conversion offers the opportunity to control and engineer the biogas process with the objective to optimize its efficiency. Taxonomic profiling of biogas producing communities by means of high-throughput 16S rRNA gene amplicon sequencing provided high-resolution insights into bacterial and archaeal structures of AD assemblages and their linkages to fed substrates and process parameters. Commonly, the bacterial phyla Firmicutes and Bacteroidetes appeared to dominate biogas communities in varying abundances depending on the apparent process conditions. Regarding the community of methanogenic Archaea, their diversity was mainly affected by the nature and composition of the substrates, availability of nutrients and ammonium/ammonia contents, but not by the temperature. It also appeared that a high proportion of 16S rRNA sequences can only be classified on higher taxonomic ranks indicating that many community members and their participation in AD within functional networks are still unknown. Although cultivation-based approaches to isolate microorganisms from biogas fermentation samples yielded hundreds of novel species and strains, this approach intrinsically is limited to the cultivable fraction of the community. To obtain genome sequence information of non-cultivable biogas community members, metagenome sequencing including assembly and binning strategies was highly valuable. Corresponding research has led to the compilation of hundreds of metagenome-assembled genomes (MAGs) frequently representing novel taxa whose metabolism and lifestyle could be reconstructed based on nucleotide sequence information. In contrast to metagenome analyses revealing the genetic potential of microbial communities, metatranscriptome sequencing provided insights into the metabolically active community. Taking advantage of genome sequence information, transcriptional activities were evaluated considering the microorganism's genetic background. Metaproteome studies uncovered enzyme profiles expressed by biogas community members. Enzymes involved in cellulose and hemicellulose decomposition and utilization of other complex biopolymers were identified. Future studies on biogas functional microbial networks will increasingly involve integrated multi-omics analyses evaluating metagenome, transcriptome, proteome, and metabolome datasets.
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Affiliation(s)
- Julia Hassa
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstrasse 27, 33615, Bielefeld, Germany
| | - Irena Maus
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstrasse 27, 33615, Bielefeld, Germany
| | - Sandra Off
- Dept. Biotechnologie, Hochschule für angewandte Wissenschaften (HAW) Hamburg Ulmenliet 20, 21033, Hamburg, Germany
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstrasse 27, 33615, Bielefeld, Germany
| | - Paul Scherer
- Dept. Biotechnologie, Hochschule für angewandte Wissenschaften (HAW) Hamburg Ulmenliet 20, 21033, Hamburg, Germany
| | - Michael Klocke
- Dept. Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy, Max-Eyth-Allee 100, 14469, Potsdam, Germany
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstrasse 27, 33615, Bielefeld, Germany.
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32
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Hassa J, Maus I, Off S, Pühler A, Scherer P, Klocke M, Schlüter A. Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants. Appl Microbiol Biotechnol 2018. [PMID: 29713790 DOI: 10.1007/s00253-018-8976-7)] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The production of biogas by anaerobic digestion (AD) of agricultural residues, organic wastes, animal excrements, municipal sludge, and energy crops has a firm place in sustainable energy production and bio-economy strategies. Focusing on the microbial community involved in biomass conversion offers the opportunity to control and engineer the biogas process with the objective to optimize its efficiency. Taxonomic profiling of biogas producing communities by means of high-throughput 16S rRNA gene amplicon sequencing provided high-resolution insights into bacterial and archaeal structures of AD assemblages and their linkages to fed substrates and process parameters. Commonly, the bacterial phyla Firmicutes and Bacteroidetes appeared to dominate biogas communities in varying abundances depending on the apparent process conditions. Regarding the community of methanogenic Archaea, their diversity was mainly affected by the nature and composition of the substrates, availability of nutrients and ammonium/ammonia contents, but not by the temperature. It also appeared that a high proportion of 16S rRNA sequences can only be classified on higher taxonomic ranks indicating that many community members and their participation in AD within functional networks are still unknown. Although cultivation-based approaches to isolate microorganisms from biogas fermentation samples yielded hundreds of novel species and strains, this approach intrinsically is limited to the cultivable fraction of the community. To obtain genome sequence information of non-cultivable biogas community members, metagenome sequencing including assembly and binning strategies was highly valuable. Corresponding research has led to the compilation of hundreds of metagenome-assembled genomes (MAGs) frequently representing novel taxa whose metabolism and lifestyle could be reconstructed based on nucleotide sequence information. In contrast to metagenome analyses revealing the genetic potential of microbial communities, metatranscriptome sequencing provided insights into the metabolically active community. Taking advantage of genome sequence information, transcriptional activities were evaluated considering the microorganism's genetic background. Metaproteome studies uncovered enzyme profiles expressed by biogas community members. Enzymes involved in cellulose and hemicellulose decomposition and utilization of other complex biopolymers were identified. Future studies on biogas functional microbial networks will increasingly involve integrated multi-omics analyses evaluating metagenome, transcriptome, proteome, and metabolome datasets.
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Affiliation(s)
- Julia Hassa
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstrasse 27, 33615, Bielefeld, Germany
| | - Irena Maus
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstrasse 27, 33615, Bielefeld, Germany
| | - Sandra Off
- Dept. Biotechnologie, Hochschule für angewandte Wissenschaften (HAW) Hamburg Ulmenliet 20, 21033, Hamburg, Germany
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstrasse 27, 33615, Bielefeld, Germany
| | - Paul Scherer
- Dept. Biotechnologie, Hochschule für angewandte Wissenschaften (HAW) Hamburg Ulmenliet 20, 21033, Hamburg, Germany
| | - Michael Klocke
- Dept. Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy, Max-Eyth-Allee 100, 14469, Potsdam, Germany
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstrasse 27, 33615, Bielefeld, Germany.
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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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Redundancy in Anaerobic Digestion Microbiomes during Disturbances by the Antibiotic Monensin. Appl Environ Microbiol 2018; 84:AEM.02692-17. [PMID: 29500266 PMCID: PMC5930344 DOI: 10.1128/aem.02692-17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Accepted: 02/22/2018] [Indexed: 01/08/2023] Open
Abstract
The antibiotic monensin is fed to dairy cows to increase milk production efficiency. A fraction of this monensin is excreted into the cow manure. Previous studies have found that cow manure containing monensin can negatively impact the performance of anaerobic digesters, especially upon first introduction. Few studies have examined whether the anaerobic digester microbiome can adapt to monensin during the operating time. Here, we conducted a long-term time series study of four lab-scale anaerobic digesters fed with cow manure. We examined changes in both the microbiome composition and function of the anaerobic digesters when subjected to the dairy antibiotic monensin. In our digesters, monensin was not rapidly degraded under anaerobic conditions. The two anaerobic digesters that were subjected to manure from monensin feed-dosed cows exhibited relatively small changes in microbiome composition and function due to relatively low monensin concentrations. At higher concentrations of monensin, which we dosed directly to control manure (from dairy cows without monensin), we observed major changes in the microbiome composition and function of two anaerobic digesters. A rapid introduction of monensin to one of these anaerobic digesters led to the impairment of methane production. Conversely, more gradual additions of the same concentrations of monensin to the other anaerobic digester led to the adaptation of the anaerobic digester microbiomes to the relatively high monensin concentrations. A member of the candidate OP11 (Microgenomates) phylum arose in this anaerobic digester and appeared to be redundant with certain Bacteroidetes phylum members, which previously were dominating.IMPORTANCE Monensin is a common antibiotic given to dairy cows in the United States and is partly excreted with dairy manure. An improved understanding of how monensin affects the anaerobic digester microbiome composition and function is important to prevent process failure for farm-based anaerobic digesters. This time series study demonstrates how anaerobic digester microbiomes are inert to low monensin concentrations and can adapt to relatively high monensin concentrations by redundancy in an already existing population. Therefore, our work provides further insight into the importance of microbiome redundancy in maintaining the stability of anaerobic digesters.
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König S, Worrich A, Banitz T, Harms H, Kästner M, Miltner A, Wick LY, Frank K, Thullner M, Centler F. Functional Resistance to Recurrent Spatially Heterogeneous Disturbances Is Facilitated by Increased Activity of Surviving Bacteria in a Virtual Ecosystem. Front Microbiol 2018; 9:734. [PMID: 29696013 PMCID: PMC5904252 DOI: 10.3389/fmicb.2018.00734] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 03/28/2018] [Indexed: 11/13/2022] Open
Abstract
Bacterial degradation of organic compounds is an important ecosystem function with relevance to, e.g., the cycling of elements or the degradation of organic contaminants. It remains an open question, however, to which extent ecosystems are able to maintain such biodegradation function under recurrent disturbances (functional resistance) and how this is related to the bacterial biomass abundance. In this paper, we use a numerical simulation approach to systematically analyze the dynamic response of a microbial population to recurrent disturbances of different spatial distribution. The spatially explicit model considers microbial degradation, growth, dispersal, and spatial networks that facilitate bacterial dispersal mimicking effects of mycelial networks in nature. We find: (i) There is a certain capacity for high resistance of biodegradation performance to recurrent disturbances. (ii) If this resistance capacity is exceeded, spatial zones of different biodegradation performance develop, ranging from no or reduced to even increased performance. (iii) Bacterial biomass and biodegradation dynamics respond inversely to the spatial fragmentation of disturbances: overall biodegradation performance improves with increasing fragmentation, but bacterial biomass declines. (iv) Bacterial dispersal networks can enhance functional resistance against recurrent disturbances, mainly by reactivating zones in the core of disturbed areas, even though this leads to an overall reduction of bacterial biomass.
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Affiliation(s)
- Sara König
- Department of Ecological Modelling, The UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
- Department of Environmental Microbiology, The UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
- Institute of Environmental Systems Research, University of Osnabrück, Osnabrück, Germany
| | - Anja Worrich
- Department of Environmental Microbiology, The UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
- Department of Environmental Biotechnology, The UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Thomas Banitz
- Department of Ecological Modelling, The UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Hauke Harms
- Department of Environmental Microbiology, The UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Matthias Kästner
- Department of Environmental Biotechnology, The UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Anja Miltner
- Department of Environmental Biotechnology, The UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Lukas Y. Wick
- Department of Environmental Microbiology, The UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Karin Frank
- Department of Ecological Modelling, The UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
- Institute of Environmental Systems Research, University of Osnabrück, Osnabrück, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Martin Thullner
- Department of Environmental Microbiology, The UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Florian Centler
- Department of Environmental Microbiology, The UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
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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: 9] [Impact Index Per Article: 1.5] [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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37
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Hornick KM, Buschmann AH. Insights into the diversity and metabolic function of bacterial communities in sediments from Chilean salmon aquaculture sites. ANN MICROBIOL 2017. [DOI: 10.1007/s13213-017-1317-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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38
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The microbiome as engineering tool: Manufacturing and trading between microorganisms. N Biotechnol 2017; 39:206-214. [DOI: 10.1016/j.nbt.2017.07.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 04/21/2017] [Accepted: 07/01/2017] [Indexed: 11/24/2022]
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39
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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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40
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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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41
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Samad T, Billings N, Birjiniuk A, Crouzier T, Doyle PS, Ribbeck K. Swimming bacteria promote dispersal of non-motile staphylococcal species. ISME JOURNAL 2017; 11:1933-1937. [PMID: 28398350 DOI: 10.1038/ismej.2017.23] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 12/24/2016] [Accepted: 01/22/2017] [Indexed: 11/09/2022]
Abstract
Swimming motility is considered a beneficial trait among bacterial species as it enables movement across fluid environments and augments invasion of tissues within the host. However, non-swimming bacteria also flourish in fluid habitats, but how they effectively spread and colonize distant ecological niches remains unclear. We show that non-motile staphylococci can gain motility by hitchhiking on swimming bacteria, leading to extended and directed motion with increased velocity. This phoretic interaction was observed between Staphylococcus aureus and Pseudomonas aeruginosa, Staphylococcus epidermidis and P. aeruginosa, as well as S. aureus and Escherichia coli, suggesting hitchhiking as a general translocation mechanism for non-motile staphylococcal species. By leveraging the motility of swimming bacteria, it was observed that staphylococci can colonize new niches that are less available in the absence of swimming carriers. This work highlights the importance of considering interactions between species within polymicrobial communities, in which bacteria can utilize each other as resources.
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Affiliation(s)
- Tahoura Samad
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nicole Billings
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alona Birjiniuk
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Thomas Crouzier
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Patrick S Doyle
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Katharina Ribbeck
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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42
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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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Zhang Q, Yuan Y, Luo W, Zeng L, Wu Z, Zhang W. Characterization of Prokaryotic Community Diversity in New and Aged Pit Muds from Chinese Luzhou-flavor Liquor Distillery. FOOD SCIENCE AND TECHNOLOGY RESEARCH 2017. [DOI: 10.3136/fstr.23.213] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Qianying Zhang
- College of Light Industry, Textile and Food Engineering, Sichuan University
| | - Yuju Yuan
- College of Light Industry, Textile and Food Engineering, Sichuan University
| | - Wen Luo
- College of Light Industry, Textile and Food Engineering, Sichuan University
| | - Liyun Zeng
- College of Light Industry, Textile and Food Engineering, Sichuan University
| | - Zhengyun Wu
- College of Light Industry, Textile and Food Engineering, Sichuan University
| | - Wenxue Zhang
- College of Light Industry, Textile and Food Engineering, Sichuan University
- School of Liquor-Making Engineering, Sichuan University Jinjiang College
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Bacterial community structure and function shift along a successional series of tidal flats in the Yellow River Delta. Sci Rep 2016; 6:36550. [PMID: 27824160 PMCID: PMC5099912 DOI: 10.1038/srep36550] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 10/18/2016] [Indexed: 11/19/2022] Open
Abstract
Coastal ecosystems play significant ecological and economic roles but are threatened and facing decline. Microbes drive various biogeochemical processes in coastal ecosystems. Tidal flats are critical components of coastal ecosystems; however, the structure and function of microbial communities in tidal flats are poorly understood. Here we investigated the seasonal variations of bacterial communities along a tidal flat series (subtidal, intertidal and supratidal flats) and the factors affecting the variations. Bacterial community composition and diversity were analyzed over four seasons by 16S rRNA genes using the Ion Torrent PGM platform. Bacterial community composition differed significantly along the tidal flat series. Bacterial phylogenetic diversity increased while phylogenetic turnover decreased from subtidal to supratidal flats. Moreover, the bacterial community structure differed seasonally. Canonical correspondence analysis identified salinity as a major environmental factor structuring the microbial community in the sediment along the successional series. Meanwhile, temperature and nitrite concentration were major drivers of seasonal microbial changes. Despite major compositional shifts, nitrogen, methane and energy metabolisms predicted by PICRUSt were inhibited in the winter. Taken together, this study indicates that bacterial community structure changed along the successional tidal flat series and provides new insights on the characteristics of bacterial communities in coastal ecosystems.
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45
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De Vrieze J, Raport L, Roume H, Vilchez-Vargas R, Jáuregui R, Pieper DH, Boon N. The full-scale anaerobic digestion microbiome is represented by specific marker populations. WATER RESEARCH 2016; 104:101-110. [PMID: 27522020 DOI: 10.1016/j.watres.2016.08.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 08/01/2016] [Accepted: 08/04/2016] [Indexed: 05/20/2023]
Abstract
Anaerobic digestion is a well-established microbial-based technology for the treatment of organic waste streams and subsequent biogas recovery. A robust and versatile microbial community to ensure overall stability of the process is essential. Four full-scale anaerobic digestion plants were followed for one year to link operational characteristics with microbial community composition and structure. Similarities between digesters, community dynamics and co-occurrence between bacteria and archaea within each digester were analysed. Free ammonia concentration (>200 mg N L-1) and conductivity (>30 mS cm-1) hindered acetoclastic methanogenesis by Methanosaetaceae. Thus, methanogenesis was pushed to the hydrogenotrophic pathway carried out by Methanobacteriales and Methanomicrobiales. Firmicutes dominated the overall bacterial community in each of the digesters (>50%), however, principal coordinate analysis of Bray-Curtis indices showed that each of the four digesters hosted a unique microbial community. The uniqueness of this community was related to two phylotypes belonging to the Syntrophomonas genus (Phy32 and Phy34) and to one unclassified bacterium (Phy2), which could both be considered marker populations in the community. A clear differentiation in co-occurrence of methanogens with several bacteria was observed between the different digesters. Our results demonstrated that full-scale anaerobic digestion plants show constant dynamics and co-occurrence patterns in function of time, but are unique in terms of composition, related to the presence of marker populations.
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Affiliation(s)
- Jo De Vrieze
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000, Gent, Belgium
| | - Linde Raport
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000, Gent, Belgium; Innolab, Derbystraat 223, 9051, Sint-Denijs-Westrem, Belgium
| | - Hugo Roume
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000, Gent, Belgium
| | - Ramiro Vilchez-Vargas
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000, Gent, Belgium
| | - Ruy Jáuregui
- Microbial Interactions and Processes Research Group, Department of Medical Microbiology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Dietmar H Pieper
- Microbial Interactions and Processes Research Group, Department of Medical Microbiology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000, Gent, Belgium.
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Harb M, Wei CH, Wang N, Amy G, Hong PY. Organic micropollutants in aerobic and anaerobic membrane bioreactors: Changes in microbial communities and gene expression. BIORESOURCE TECHNOLOGY 2016; 218:882-891. [PMID: 27441825 DOI: 10.1016/j.biortech.2016.07.036] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 07/06/2016] [Accepted: 07/09/2016] [Indexed: 06/06/2023]
Abstract
Organic micro-pollutants (OMPs) are contaminants of emerging concern in wastewater treatment due to the risk of their proliferation into the environment, but their impact on the biological treatment process is not well understood. The purpose of this study is to examine the effects of the presence of OMPs on the core microbial populations of wastewater treatment. Two nanofiltration-coupled membrane bioreactors (aerobic and anaerobic) were subjected to the same operating conditions while treating synthetic municipal wastewater spiked with OMPs. Microbial community dynamics, gene expression levels, and antibiotic resistance genes were analyzed using molecular-based approaches. Results showed that presence of OMPs in the wastewater feed had a clear effect on keystone bacterial populations in both the aerobic and anaerobic sludge while also significantly impacting biodegradation-associated gene expression levels. Finally, multiple antibiotic-type OMPs were found to have higher removal rates in the anaerobic MBR, while associated antibiotic resistance genes were lower.
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Affiliation(s)
- Moustapha Harb
- King Abdullah University of Science and Technology (KAUST), Water Desalination and Reuse Center (WDRC), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal 23955-6900, Saudi Arabia
| | - Chun-Hai Wei
- King Abdullah University of Science and Technology (KAUST), Water Desalination and Reuse Center (WDRC), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal 23955-6900, Saudi Arabia
| | - Nan Wang
- King Abdullah University of Science and Technology (KAUST), Water Desalination and Reuse Center (WDRC), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal 23955-6900, Saudi Arabia
| | - Gary Amy
- King Abdullah University of Science and Technology (KAUST), Water Desalination and Reuse Center (WDRC), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal 23955-6900, Saudi Arabia
| | - Pei-Ying Hong
- King Abdullah University of Science and Technology (KAUST), Water Desalination and Reuse Center (WDRC), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal 23955-6900, Saudi Arabia.
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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: 236] [Impact Index Per Article: 29.5] [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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Fernandez-Gonzalez N, Huber JA, Vallino JJ. Microbial Communities Are Well Adapted to Disturbances in Energy Input. mSystems 2016; 1:e00117-16. [PMID: 27822558 PMCID: PMC5080406 DOI: 10.1128/msystems.00117-16] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 08/16/2016] [Indexed: 11/20/2022] Open
Abstract
Although microbial systems are well suited for studying concepts in ecological theory, little is known about how microbial communities respond to long-term periodic perturbations beyond diel oscillations. Taking advantage of an ongoing microcosm experiment, we studied how methanotrophic microbial communities adapted to disturbances in energy input over a 20-day cycle period. Sequencing of bacterial 16S rRNA genes together with quantification of microbial abundance and ecosystem function were used to explore the long-term dynamics (510 days) of methanotrophic communities under continuous versus cyclic chemical energy supply. We observed that microbial communities appeared inherently well adapted to disturbances in energy input and that changes in community structure in both treatments were more dependent on internal dynamics than on external forcing. The results also showed that the rare biosphere was critical to seeding the internal community dynamics, perhaps due to cross-feeding or other strategies. We conclude that in our experimental system, internal feedbacks were more important than external drivers in shaping the community dynamics over time, suggesting that ecosystems can maintain their function despite inherently unstable community dynamics. IMPORTANCE Within the broader ecological context, biological communities are often viewed as stable and as only experiencing succession or replacement when subject to external perturbations, such as changes in food availability or the introduction of exotic species. Our findings indicate that microbial communities can exhibit strong internal dynamics that may be more important in shaping community succession than external drivers. Dynamic "unstable" communities may be important for ecosystem functional stability, with rare organisms playing an important role in community restructuring. Understanding the mechanisms responsible for internal community dynamics will certainly be required for understanding and manipulating microbiomes in both host-associated and natural ecosystems.
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Affiliation(s)
| | - Julie A. Huber
- The Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Joseph J. Vallino
- Ecosystems Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
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Ferguson RMW, Coulon F, Villa R. Organic loading rate: A promising microbial management tool in anaerobic digestion. WATER RESEARCH 2016; 100:348-356. [PMID: 27214347 DOI: 10.1016/j.watres.2016.05.009] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 04/25/2016] [Accepted: 05/02/2016] [Indexed: 06/05/2023]
Abstract
This study investigated the effect of changes in organic loading rate (OLR) and feedstock on the volatile fatty acids (VFAs) production and their potential use as a bioengineering management tool to improve stability of anaerobic digesters. Digesters were exposed to one or two changes in OLR using the same or different co-substrates (Fat Oil and Grease waste (FOG) and/or glycerol). Although all the OLR fluctuations produced a decrease in biogas and methane production, the digesters exposed twice to glycerol showed faster recovery towards stable conditions after the second OLR change. This was correlated with the composition of the VFAs produced and their mode of production, from parallel to sequential, resulting in a more efficient recovery from inhibition of methanogenesis. The change in acids processing after the first OLR increase induced a shift in the microbial community responsible of the process optimisation when the digesters were exposed to a subsequent OLR increase with the same feedstock. When the digesters were exposed to an OLR change with a different feedstock (FOG), the recovery took 7d longer than with the same one (glycerol). However, the microbial community showed functional resilience and was able to perform similarly to pre-exposure conditions. Thus, changes in operational conditions can be used to influence microbial community structure for anaerobic digestion (AD) optimisation. Finally, shorter recovery times and increased resilience of digesters were linked to higher numbers of Clostridia incertae sedis XV, suggesting that this group may be a good candidate for AD bioaugmentation to speed up recovery after process instability or OLR increase.
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Affiliation(s)
- Robert M W Ferguson
- Cranfield University, School of Water, Energy and Environment, Cranfield, MK43 0AL, UK
| | - Frédéric Coulon
- Cranfield University, School of Water, Energy and Environment, Cranfield, MK43 0AL, UK
| | - Raffaella Villa
- Cranfield University, School of Water, Energy and Environment, Cranfield, MK43 0AL, UK.
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