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Pierro R, Moussa A, Mori N, Marcone C, Quaglino F, Romanazzi G. Bois noir management in vineyard: a review on effective and promising control strategies. FRONTIERS IN PLANT SCIENCE 2024; 15:1364241. [PMID: 38601314 PMCID: PMC11004249 DOI: 10.3389/fpls.2024.1364241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 03/07/2024] [Indexed: 04/12/2024]
Abstract
Among grapevine yellows, Bois noir (BN), associated with 'Candidatus Phytoplasma solani', represents the biggest threat in the main wine-growing areas worldwide, causing significant losses in berry quality and yields. BN epidemiology involves multiple plant hosts and several insect vectors, making considerably complex the development of effective management strategies. Since application of insecticides on the grapevine canopy is not effective to manage vectors, BN management includes an integrated approach based on treatments to the canopy to make the plant more resistant to the pathogen and/or inhibit the vector feeding, and actions on reservoir plants to reduce possibilities that the vector reaches the grapevine and transmit the phytoplasma. Innovative sustainable strategies developed in the last twenty years to improve the BN management are reviewed and discussed.
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Affiliation(s)
- Roberto Pierro
- Department of Pharmacy, University of Salerno, Fisciano, Salerno, Italy
| | - Abdelhameed Moussa
- Pests and Plant Protection Department, Agricultural & Biological Research Institute, National Research Centre, Cairo, Egypt
| | - Nicola Mori
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Carmine Marcone
- Department of Pharmacy, University of Salerno, Fisciano, Salerno, Italy
| | - Fabio Quaglino
- Department of Agricultural and Environmental Sciences – Production, Landscape, Agroenergy, University of Milan, Milan, Italy
| | - Gianfranco Romanazzi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
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2
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Barone M, D'Amico F, Fabbrini M, Rampelli S, Brigidi P, Turroni S. Over-feeding the gut microbiome: A scoping review on health implications and therapeutic perspectives. World J Gastroenterol 2021; 27:7041-7064. [PMID: 34887627 PMCID: PMC8613651 DOI: 10.3748/wjg.v27.i41.7041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/02/2021] [Accepted: 10/14/2021] [Indexed: 02/06/2023] Open
Abstract
The human gut microbiome has gained increasing attention over the past two decades. Several findings have shown that this complex and dynamic microbial ecosystem can contribute to the maintenance of host health or, when subject to imbalances, to the pathogenesis of various enteric and non-enteric diseases. This scoping review summarizes the current knowledge on how the gut microbiota and microbially-derived compounds affect host metabolism, especially in the context of obesity and related disorders. Examples of microbiome-based targeted intervention strategies that aim to restore and maintain an eubiotic layout are then discussed. Adjuvant therapeutic interventions to alleviate obesity and associated comorbidities are traditionally based on diet modulation and the supplementation of prebiotics, probiotics and synbiotics. However, these approaches have shown only moderate ability to induce sustained changes in the gut microbial ecosystem, making the development of innovative and tailored microbiome-based intervention strategies of utmost importance in clinical practice. In this regard, the administration of next-generation probiotics and engineered microbiomes has shown promising results, together with more radical intervention strategies based on the replacement of the dysbiotic ecosystem by means of fecal microbiota transplantation from healthy donors or with the introduction of synthetic communities specifically designed to achieve the desired therapeutic outcome. Finally, we provide a perspective for future translational investigations through the implementation of bioinformatics approaches, including machine and deep learning, to predict health risks and therapeutic outcomes.
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Affiliation(s)
- Monica Barone
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, Bologna 40138, Italy
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Federica D'Amico
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, Bologna 40138, Italy
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Marco Fabbrini
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, Bologna 40138, Italy
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Simone Rampelli
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Patrizia Brigidi
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, Bologna 40138, Italy
| | - Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
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3
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Bruno A, Sandionigi A, Magnani D, Bernasconi M, Pannuzzo B, Consolandi C, Camboni T, Labra M, Casiraghi M. Different Effects of Mineral Versus Vegetal Granular Activated Carbon Filters on the Microbial Community Composition of a Drinking Water Treatment Plant. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.615513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Drinking water quality and safety is strictly regulated and constantly monitored, but little is known about the microorganisms inhabiting drinking water treatment plants (DWTPs). This lack of knowledge prevents optimization of designs and operational controls. Here we investigated the drinking water microbial community harbored by a groundwater-derived DWTP, involving mineral and vegetal granular activated carbon filters (GACs). We used 16S rRNA gene sequencing to analyze water microbiome variations through the potabilization process, considering (i) different GAC materials and (ii) time from GAC regeneration. Our results revealed the predominance of Cand. Patescibacteria, uncultivable bacteria with limited metabolic capacities and small genomes, from source to downstream water. Microbial communities clustered per sampling date, with the noteworthy exception of groundwater samples. If the groundwater microbiome showed no significant variations over time, the community structure of water downstream GACs (both mineral and vegetal) seemed to be affected by time from GAC regeneration. Looking at a finer scale, different GAC material affected microbiome assembly over time with significant variation in the relative abundances of specific taxa. The significance of our research is in identifying the environmental microorganisms intrinsic of deep groundwater and the community shift after the perturbations induced by potabilization processes. Which microorganisms colonize different GACs and become abundant after GACs regeneration and over time is a first step toward advanced control of microbial communities, improving drinking water safety and management of operational costs.
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Qin W, Hammes F. Substrate Pre-loading Influences Initial Colonization of GAC Biofilter Biofilms. Front Microbiol 2021; 11:596156. [PMID: 33510720 PMCID: PMC7835318 DOI: 10.3389/fmicb.2020.596156] [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] [Received: 08/19/2020] [Accepted: 12/11/2020] [Indexed: 12/05/2022] Open
Abstract
Microbial community composition and stability affect pollutant removal for biological/granular activated carbon (BAC/GAC) processes. Here, we pre-loaded the organic carbon substrates sucrose, lactose, and Lysogeny Broth (LB) medium onto new GAC prior to use and then tested whether this substrate pre-loading promoted development of biofilms with high coverage that remained stable for prolonged operational periods. Temporal dynamics of the biomass and microbial community on the GAC were monitored via flow cytometry (FCM) and sequencing, respectively, in both batch and continuous-flow experiments. In comparison with the non-loaded GAC (control), the initial biofilm biomass on substrate-loaded GAC was 3–114 times higher, but the initial richness was considerably lower (only accounting for 13–28% of the control). The initial community compositions were significantly different between batch and continuous-flow column experiments, even when loaded with the same substrates. In the continuous-flow column experiments, both biomass and microbial community composition became remarkably similar to the control filters after 64 days of operation. From these findings, we conclude that substrate-loaded GAC could enhance initial colonization, affecting both biomass and microbial community composition. However, the biomass and composition did not remain stable during long-term operation due to continuous dispersal and competition from influent bacteria.
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Affiliation(s)
- Wen Qin
- School of Civil and Transportation Engineering, Guangdong University of Technology, Guangzhou, China.,Department of Environmental Microbiology, Eawag-Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Frederik Hammes
- Department of Environmental Microbiology, Eawag-Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
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5
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Liu J, Ding Y, Ji Y, Gao G, Wang Y. Effect of Maize Straw Biochar on Bacterial Communities in Agricultural Soil. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2020; 104:333-338. [PMID: 32006054 DOI: 10.1007/s00128-020-02793-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 01/18/2020] [Indexed: 06/10/2023]
Abstract
Biochar has become a popular soil amendment. However, its effect on soil microbial community is still unclear. In the present study, maize straw biochar was pyrolysed at 300°C, 450°C and 600°C, respectively, and then was added to agricultural soil at the ratio of 0.5%, 1% and 2%. Bacterial dynamics was analyzed in the pot experiments using denaturing gradient gel electrophoresis. The results indicated that the pyrolysis temperature has great impact on the elemental composition, pH and porous structures of biochar. Moreover, pyrolysis temperature was primary factor to drive the variation of bacterial community structure in biochar amended soil. In addition, the results suggested that biochar amendments on agricultural soil would decrease the bacterial diversity, and selectively promote growth of functional bacteria to become the dominant community, which could increase the bacterial community organization and improve the stability of bacteria to counteract effects of perturbation.
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Affiliation(s)
- Jie Liu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin, 300071, China
- State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, Lanzhou University, Lanzhou, 730000, China
| | - Yanli Ding
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin, 300071, China
| | - Yurui Ji
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin, 300071, China
- New Energy Department, Tianjin Sino-German University of Applied Sciences, Tianjin, 300350, China
| | - Guanghai Gao
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin, 300071, China
| | - Yingying Wang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin, 300071, China.
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6
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Effect of a Profound Feedstock Change on the Structure and Performance of Biogas Microbiomes. Microorganisms 2020; 8:microorganisms8020169. [PMID: 31991721 PMCID: PMC7074709 DOI: 10.3390/microorganisms8020169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/20/2020] [Accepted: 01/21/2020] [Indexed: 11/17/2022] Open
Abstract
In this study the response of biogas-producing microbiomes to a profound feedstock change was investigated. The microbiomes were adapted to the digestion of either 100% sugar beet, maize silage, or of the silages with elevated amounts of total ammonium nitrogen (TAN) by adding ammonium carbonate or animal manure. The feedstock exchange resulted in a short-range decrease or increase in the biogas yields according to the level of chemical feedstock complexity. Fifteen taxa were found in all reactors and can be considered as generalists. Thirteen taxa were detected in the reactors operated with low TAN and six in the reactors with high TAN concentration. Taxa assigned to the phylum Bacteroidetes and to the order Spirochaetales increased with the exchange to sugar beet silage, indicating an affinity to easily degradable compounds. The recorded TAN-sensitive taxa (phylum Cloacimonetes) showed no specific affinity to maize or sugar beet silage. The archaeal community remained unchanged. The reported findings showed a smooth adaptation of the microbial communities, without a profound negative impact on the overall biogas production indicating that the two feedstocks, sugar beet and maize silage, potentially do not contain chemical compounds that are difficult to handle during anaerobic digestion.
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Smirnova DV, Zalomova LV, Zagainova AV, Makarov VV, Mezhevikina LM, Fesenko EE, Yudin SM. Cryopreservation of the human gut microbiota: Current state and perspectives. Int J Med Microbiol 2019; 309:259-269. [PMID: 31204202 DOI: 10.1016/j.ijmm.2019.06.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 05/21/2019] [Accepted: 06/02/2019] [Indexed: 02/06/2023] Open
Abstract
The human intestinal microbiota is a complex ecosystem that consists of thousands of bacterial species that are responsible for human health and disease. The intestinal microbiota is a natural resource for production of therapeutic and preventive medicals, such as probiotics and fecal transplants. Modern lifestyles have resulted in the extinction of evolutionally selected microbial populations upon exposure to environmental factors. Therefore, it is very important to preserve the human gut microbiota to have the opportunity for timely restoration with minimal safety risks. Cryopreservation techniques that are suitable for the preservation of viable, mixed microbial communities and a biobanking approach are currently under development in different countries. However, the number of studies in this area is very limited. The variety of morphological and physiological characteristics of microbes in the microbiota, the different cryopreservation goals, and the criteria for the evaluation of cryopreservation effectiveness are the main challenges in the creation of a universal and standardized cryopreservation protocol. In this review, we summarized the current progress of the main cryopreservation techniques for gut microbiota communities and the methods for the assessment of the effectiveness of these techniques in the context of practical application.
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Affiliation(s)
- Daria V Smirnova
- Center for Strategic Planning and Management of Medical and Biological Health Risks, Moscow, 119121, Russian Federation.
| | - Ljubov V Zalomova
- Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation
| | - Angelika V Zagainova
- Center for Strategic Planning and Management of Medical and Biological Health Risks, Moscow, 119121, Russian Federation
| | - Valentin V Makarov
- Center for Strategic Planning and Management of Medical and Biological Health Risks, Moscow, 119121, Russian Federation
| | - Ludmila M Mezhevikina
- Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation
| | - Eugeny E Fesenko
- Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation
| | - Sergey M Yudin
- Center for Strategic Planning and Management of Medical and Biological Health Risks, Moscow, 119121, Russian Federation
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8
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Braz GHR, Fernandez-Gonzalez N, Lema JM, Carballa M. Organic overloading affects the microbial interactions during anaerobic digestion in sewage sludge reactors. CHEMOSPHERE 2019; 222:323-332. [PMID: 30708166 DOI: 10.1016/j.chemosphere.2019.01.124] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 11/21/2018] [Accepted: 01/19/2019] [Indexed: 06/09/2023]
Abstract
There is still a lack of information about microbial interactions of anaerobic digestion microbiome during process disturbance which limits our ability to predict the mechanisms that drive community dynamics on these events. This paper aims to determine how an organic overloading affects these interactions and to characterize in detail the microbiome structure and diversity in sewage sludge anaerobic reactors during an acidosis event. Two identical sewage sludge anaerobic reactors were subjected to an organic loading shock by adding glycerol waste. As consequence, volatile fatty acids accumulated after only 24 h (up to 2.5 g/L) while Bacteroidales and Methanomicrobiales became displaced by Firmicutes and Methanosaeta sp, showing that reactor acidosis can occur without an immediate decline of this methanogen. Network analysis revealed 9 clusters of co-occurring microorganisms with different behaviors during overloading. At first, Veillonellaceae family, the main glycerol degrading, associated with Candidatus Cloacimonetes, volatile fatty acids fermenters, increased their relative abundance in detriment of the syntrophic bacteria; although as conditions become more acidic, these groups were displaced by other fermenters like Porphyromonadaceae and Chitinophagaceae. Eventually, the methanogenesis failed 72 h after organic overloading, when pH reached values lower than 6. Overall, our results showed a succession of functionally redundant microorganisms, most likely because of niche specialization during organic overloading. The detailed temporal analysis elucidated the processes governing the dynamics anaerobic digestion microbiome, a knowledge required to develop anaerobic digestion management strategies based on its microbiome during process disturbances.
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Affiliation(s)
- Guilherme H R Braz
- Department of Chemical Engineering, Institute of Technology, Universidade de Santiago de Compostela, Constantino Candeira s/n, 15782 Santiago de Compostela, Galicia, Spain.
| | - Nuria Fernandez-Gonzalez
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineerings, Venue Dr. Mergelina, C/ Dr. Mergelina, s/n, Valladolid 47011, Spain; Department of Chemical Engineering, Institute of Technology, Universidade de Santiago de Compostela, Constantino Candeira s/n, 15782 Santiago de Compostela, Galicia, Spain.
| | - Juan M Lema
- Department of Chemical Engineering, Institute of Technology, Universidade de Santiago de Compostela, Constantino Candeira s/n, 15782 Santiago de Compostela, Galicia, Spain.
| | - Marta Carballa
- Department of Chemical Engineering, Institute of Technology, Universidade de Santiago de Compostela, Constantino Candeira s/n, 15782 Santiago de Compostela, Galicia, Spain.
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A novel method: using an adenosine triphosphate (ATP) luminescence-based assay to rapidly assess the biological stability of drinking water. Appl Microbiol Biotechnol 2019; 103:4269-4277. [PMID: 30972459 DOI: 10.1007/s00253-019-09774-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 03/15/2019] [Accepted: 03/15/2019] [Indexed: 10/27/2022]
Abstract
The rapid and credible evaluations of the microbial stability of a drinking water distribution system (DWDS) are of great significance for ensuring the safety of drinking water and predicting microbial pollution. Conventional biostability assessment methods mainly focus on bacterial regrowth or evaluation of the level of nutrients that support bacterial regrowth. However, such methods are time-consuming and have many limitations. An adenosine triphosphate (ATP) assay can rapidly measure all active microorganisms and is known to be a useful method to assess the microbial activity of drinking water. The measurement of ATP has been used for more than a decade in the field of drinking water research. This article reviews the application of an ATP luminescence-based method to assess the biostability of drinking water and discusses the feasibility of ATP measurement as a parameter for quickly evaluating this criterion. ATP measurement will help researchers and water managers better monitor the biological stability of drinking water from the source to the consumer's tap. This review covers the: (1) principle and application of the ATP measurement in drinking water quality assessment; (2) comparison of the merits and demerits of several methods for evaluating the biostability of drinking water; (3) discussions on using ATP measurement in evaluating biostability; and (4) improvements in the use of ATP measurement in evaluating biostability. At the end of this review, recommendations were given for better application of the ATP measurement as a parameter for monitoring the microbial quality of drinking water.
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10
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Dynamics of Hydrology and Anaerobic Hydrocarbon Degrader Communities in A Tar-Oil Contaminated Aquifer. Microorganisms 2019; 7:microorganisms7020046. [PMID: 30744114 PMCID: PMC6406676 DOI: 10.3390/microorganisms7020046] [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: 12/21/2018] [Revised: 01/30/2019] [Accepted: 02/06/2019] [Indexed: 11/17/2022] Open
Abstract
Aquifers are typically perceived as rather stable habitats, characterized by low biogeochemical and microbial community dynamics. Upon contamination, aquifers shift to a perturbed ecological status, in which specialized populations of contaminant degraders establish and mediate aquifer restoration. However, the ecological controls of such degrader populations, and possible feedbacks between hydraulic and microbial habitat components, remain poorly understood. Here, we provide evidence of such couplings, via 4 years of annual sampling of groundwater and sediments across a high-resolution depth-transect of a hydrocarbon plume. Specialized anaerobic degrader populations are known to be established at the reactive fringes of the plume. Here, we show that fluctuations of the groundwater table were paralleled by pronounced dynamics of biogeochemical processes, pollutant degradation, and plume microbiota. Importantly, a switching in maximal relative abundance between dominant degrader populations within the Desulfobulbaceae and Desulfosporosinus spp. was observed after hydraulic dynamics. Thus, functional redundancy amongst anaerobic hydrocarbon degraders could have been relevant in sustaining biodegradation processes after hydraulic fluctuations. These findings contribute to an improved ecological perspective of contaminant plumes as a dynamic microbial habitat, with implications for both monitoring and remediation strategies in situ.
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11
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Process Disturbances in Agricultural Biogas Production—Causes, Mechanisms and Effects on the Biogas Microbiome: A Review. ENERGIES 2019. [DOI: 10.3390/en12030365] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Disturbances of the anaerobic digestion process reduce the economic and environmental performance of biogas systems. A better understanding of the highly complex process is of crucial importance in order to avoid disturbances. This review defines process disturbances as significant changes in the functionality within the microbial community leading to unacceptable and severe decreases in biogas production and requiring an active counteraction to be overcome. The main types of process disturbances in agricultural biogas production are classified as unfavorable process temperatures, fluctuations in the availability of macro- and micronutrients (feedstock variability), overload of the microbial degradation potential, process-related accumulation of inhibiting metabolites such as hydrogen (H2), ammonium/ammonia (NH4+/NH3) or hydrogen sulphide (H2S) and inhibition by other organic and inorganic toxicants. Causes, mechanisms and effects on the biogas microbiome are discussed. The need for a knowledge-based microbiome management to ensure a stable and efficient production of biogas with low susceptibility to disturbances is derived and an outlook on potential future process monitoring and control by means of microbial indicators is provided.
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12
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Braz GHR, Fernandez-Gonzalez N, Lema JM, Carballa M. The time response of anaerobic digestion microbiome during an organic loading rate shock. Appl Microbiol Biotechnol 2018; 102:10285-10297. [PMID: 30276715 DOI: 10.1007/s00253-018-9383-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 08/04/2018] [Accepted: 09/09/2018] [Indexed: 01/30/2023]
Abstract
Knowledge of connections between operational conditions, process stability, and microbial community dynamics is essential to enhance anaerobic digestion (AD) process efficiency and management. In this study, the detailed temporal effects of a sudden glycerol-based organic overloading on the AD microbial community and process imbalance were investigated in two replicate anaerobic digesters by a time-intensive sampling scheme. The microbial community time response to the overloading event was shorter than the shifts of reactor performance parameters. An increase in bacterial community dynamics and in the abundances of several microbial taxa, mainly within the Firmicutes, Tenericutes, and Chloroflexi phyla and Methanoculleus genera, could be detected prior to any shift on the reactor operational parameters. Reactor acidification already started within the first 24 h of the shock and headed the AD process to total inhibition in 72 h alongside with the largest shifts on microbiome, mostly the increase of Anaerosinus sp. and hydrogenotrophic methanogenic Archaea. In sum, this work proved that AD microbial community reacts very quickly to an organic overloading and some shifts occur prior to alterations on the performance parameters. The latter is very interesting as it can be used to improve AD process management protocols.
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Affiliation(s)
- G H R Braz
- Department of Chemical Engineering, Institute of Technology, Universidade de Santiago de Compostela, Constantino Candeira s/n, 15782, Santiago de Compostela, Galicia, Spain
| | - N Fernandez-Gonzalez
- Department of Chemical Engineering, Institute of Technology, Universidade de Santiago de Compostela, Constantino Candeira s/n, 15782, Santiago de Compostela, Galicia, Spain.
| | - J M Lema
- Department of Chemical Engineering, Institute of Technology, Universidade de Santiago de Compostela, Constantino Candeira s/n, 15782, Santiago de Compostela, Galicia, Spain
| | - M Carballa
- Department of Chemical Engineering, Institute of Technology, Universidade de Santiago de Compostela, Constantino Candeira s/n, 15782, Santiago de Compostela, Galicia, Spain
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13
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De Vrieze J, Pinto AJ, Sloan WT, Ijaz UZ. The active microbial community more accurately reflects the anaerobic digestion process: 16S rRNA (gene) sequencing as a predictive tool. MICROBIOME 2018; 6:63. [PMID: 29609653 PMCID: PMC5879801 DOI: 10.1186/s40168-018-0449-9] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 03/16/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND Amplicon sequencing methods targeting the 16S rRNA gene have been used extensively to investigate microbial community composition and dynamics in anaerobic digestion. These methods successfully characterize amplicons but do not distinguish micro-organisms that are actually responsible for the process. In this research, the archaeal and bacterial community of 48 full-scale anaerobic digestion plants were evaluated on DNA (total community) and RNA (active community) level via 16S rRNA (gene) amplicon sequencing. RESULTS A significantly higher diversity on DNA compared with the RNA level was observed for archaea, but not for bacteria. Beta diversity analysis showed a significant difference in community composition between the DNA and RNA of both bacteria and archaea. This related with 25.5 and 42.3% of total OTUs for bacteria and archaea, respectively, that showed a significant difference in their DNA and RNA profiles. Similar operational parameters affected the bacterial and archaeal community, yet the differentiating effect between DNA and RNA was much stronger for archaea. Co-occurrence networks and functional prediction profiling confirmed the clear differentiation between DNA and RNA profiles. CONCLUSIONS In conclusion, a clear difference in active (RNA) and total (DNA) community profiles was observed, implying the need for a combined approach to estimate community stability in anaerobic digestion.
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Affiliation(s)
- Jo De Vrieze
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
- Infrastructure and Environment Research Division, School of Engineering, University of Glasgow, Rankine Building, Oakfield Avenue, Glasgow, G12 8LT UK
| | - Ameet J. Pinto
- Northeastern University, 360 Huntington Avenue, Boston, MA 02115 USA
| | - William T. Sloan
- Infrastructure and Environment Research Division, School of Engineering, University of Glasgow, Rankine Building, Oakfield Avenue, Glasgow, G12 8LT UK
| | - Umer Zeeshan Ijaz
- Infrastructure and Environment Research Division, School of Engineering, University of Glasgow, Rankine Building, Oakfield Avenue, Glasgow, G12 8LT UK
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Calusinska M, Goux X, Fossépré M, Muller EEL, Wilmes P, Delfosse P. A year of monitoring 20 mesophilic full-scale bioreactors reveals the existence of stable but different core microbiomes in bio-waste and wastewater anaerobic digestion systems. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:196. [PMID: 30038663 PMCID: PMC6052691 DOI: 10.1186/s13068-018-1195-8] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 07/06/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND Anaerobic digestion (AD) is a microbe-driven process of biomass decomposition to CH4 and CO2. In addition to renewable and cost-effective energy production, AD has emerged in the European Union as an environmentally friendly model of bio-waste valorisation and nutrient recycling. Nevertheless, due to the high diversity of uncharacterised microbes, a typical AD microbiome is still considered as "dark matter". RESULTS Using the high-throughput sequencing of small rRNA gene, and a monthly monitoring of the physicochemical parameters for 20 different mesophilic full-scale bioreactors over 1 year, we generated a detailed view of AD microbial ecology towards a better understanding of factors that influence and shape these communities. By studying the broadly distributed OTUs present in over 80% of analysed samples, we identified putatively important core bacteria and archaea to the AD process that accounted for over 70% of the whole microbial community relative abundances. AD reactors localised at the wastewater treatment plants were shown to operate with distinct core microbiomes than the agricultural and bio-waste treating biogas units. We also showed that both the core microbiomes were composed of low (with average community abundance ≤ 1%) and highly abundant microbial populations; the vast majority of which remains yet uncharacterised, e.g. abundant candidate Cloacimonetes. Using non-metric multidimensional scaling, we observed microorganisms grouping into clusters that well reflected the origin of the samples, e.g. wastewater versus agricultural and bio-waste treating biogas units. The calculated diversity patterns differed markedly between the different community clusters, mainly due to the presence of highly diverse and dynamic transient species. Core microbial communities appeared relatively stable over the monitoring period. CONCLUSIONS In this study, we characterised microbial communities in different AD systems that were monitored over a 1-year period. Evidences were shown to support the concept of a core community driving the AD process, whereas the vast majority of dominant microorganisms remain yet to be characterised.
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Affiliation(s)
- Magdalena Calusinska
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, 41 rue du Brill, 4422 Belvaux, Luxembourg
| | - Xavier Goux
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, 41 rue du Brill, 4422 Belvaux, Luxembourg
| | - Marie Fossépré
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, 41 rue du Brill, 4422 Belvaux, Luxembourg
| | - Emilie E. L. Muller
- Eco-Systems Biology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 avenue des Hauts-Fourneaux, 4362 Esch-sur-Alzette, Luxembourg
- Department of Microbiology, Genomics and the Environment, Université de Strasbourg, CNRS, GMGM, UMR 7156, Strasbourg, France
| | - Paul Wilmes
- Eco-Systems Biology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 avenue des Hauts-Fourneaux, 4362 Esch-sur-Alzette, Luxembourg
| | - Philippe Delfosse
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, 41 rue du Brill, 4422 Belvaux, Luxembourg
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15
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McIlroy SJ, Kirkegaard RH, McIlroy B, Nierychlo M, Kristensen JM, Karst SM, Albertsen M, Nielsen PH. MiDAS 2.0: an ecosystem-specific taxonomy and online database for the organisms of wastewater treatment systems expanded for anaerobic digester groups. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2017; 2017:3074787. [PMID: 28365734 PMCID: PMC5467571 DOI: 10.1093/database/bax016] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 02/13/2017] [Indexed: 11/13/2022]
Abstract
Wastewater is increasingly viewed as a resource, with anaerobic digester technology being routinely implemented for biogas production. Characterising the microbial communities involved in wastewater treatment facilities and their anaerobic digesters is considered key to their optimal design and operation. Amplicon sequencing of the 16S rRNA gene allows high-throughput monitoring of these systems. The MiDAS field guide is a public resource providing amplicon sequencing protocols and an ecosystem-specific taxonomic database optimized for use with wastewater treatment facility samples. The curated taxonomy endeavours to provide a genus-level-classification for abundant phylotypes and the online field guide links this identity to published information regarding their ecology, function and distribution. This article describes the expansion of the database resources to cover the organisms of the anaerobic digester systems fed primary sludge and surplus activated sludge. The updated database includes descriptions of the abundant genus-level-taxa in influent wastewater, activated sludge and anaerobic digesters. Abundance information is also included to allow assessment of the role of emigration in the ecology of each phylotype. MiDAS is intended as a collaborative resource for the progression of research into the ecology of wastewater treatment, by providing a public repository for knowledge that is accessible to all interested in these biotechnologically important systems. Database URL http://www.midasfieldguide.org.
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Affiliation(s)
- Simon Jon McIlroy
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg DK-9220, Denmark
| | - Rasmus Hansen Kirkegaard
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg DK-9220, Denmark
| | - Bianca McIlroy
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg DK-9220, Denmark
| | - Marta Nierychlo
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg DK-9220, Denmark
| | - Jannie Munk Kristensen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg DK-9220, Denmark
| | - Søren Michael Karst
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg DK-9220, Denmark
| | - Mads Albertsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg DK-9220, Denmark
| | - Per Halkjær Nielsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg DK-9220, Denmark
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16
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Verstraete W, De Vrieze J. Microbial technology with major potentials for the urgent environmental needs of the next decades. Microb Biotechnol 2017; 10:988-994. [PMID: 28771931 PMCID: PMC5609260 DOI: 10.1111/1751-7915.12779] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 06/20/2017] [Indexed: 01/20/2023] Open
Abstract
Several needs in the context of the water-energy-food nexus will become more prominent in the next decades. It is crucial to delineate these challenges and to find opportunities for innovative microbial technologies in the framework of sustainability and climate change. Here, we focus on four key issues, that is the imbalance in the nitrogen cycle, the diffuse emission of methane, the necessity for carbon capture and the deterioration of freshwater reserves. We suggest a set of microbial technologies to deal with each of these issues, such as (i) the production of microbial protein as food and feed, (ii) the control of methanogenic archaea and better use of methanotrophic consortia, (iii) the avoidance of nitrification and (iv) the upgrading of CO2 to microbial bioproducts. The central message is that instead of using crude methods to exploit microorganisms for degradations, the potentials of the microbiomes should be used to create processes and products that fit the demands of the cyclic market economy.
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Affiliation(s)
- Willy Verstraete
- Center for Microbial Ecology and Technology (CMET)Ghent UniversityCoupure Links 653B‐9000GentBelgium
| | - Jo De Vrieze
- Center for Microbial Ecology and Technology (CMET)Ghent UniversityCoupure Links 653B‐9000GentBelgium
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17
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Nuzzo A, Negroni A, Zanaroli G, Fava F. Identification of two organohalide-respiring Dehalococcoidia associated to different dechlorination activities in PCB-impacted marine sediments. Microb Cell Fact 2017; 16:127. [PMID: 28738864 PMCID: PMC5525228 DOI: 10.1186/s12934-017-0743-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 07/14/2017] [Indexed: 01/02/2023] Open
Abstract
Background Microbial reductive dechlorination of polychlorinated biphenyls (PCBs) plays a major role in detoxifying anoxic contaminated freshwater and marine sediments from PCBs. Known members of the phylum Chloroflexi are typically responsible for this activity in freshwater sediments, whereas less is known about the microorganisms responsible for this activity in marine sediments. PCB-respiring activities were detected in PCB-impacted marine sediments of the Venice Lagoon. The aim of this work was to identify the indigenous organohalide-respiring microorganisms in such environments and assess their dechlorination specificity against spiked Aroclor™ 1254 PCBs under laboratory conditions resembling the in situ biogeochemistry. Results High PCB dechlorination activities (from 150 ± 7 to 380 ± 44 μmol of chlorine removed kg−1 week−1) were detected in three out of six sediments sampled from different locations of the lagoon. An uncultured non-Dehalococcoides phylotype of the class Dehalococcoidia closely related to Dehalobium chlorocoercia DF-1, namely phylotype VLD-1, was detected and enriched up to 109 16S rRNA gene copies per gram of sediment where dechlorination activities were higher and 25-4/24-4 and 25-2/24-2/4-4 chlorobiphenyls (CB) accumulated as the main tri-/dichlorinated products. Conversely, a different phylotype closely related to the SF1/m-1 clade, namely VLD-2, also enriched highly where lower dechlorination activity and the accumulation of 25-3 CB as main tri-chlorinated product occurred, albeit in the simultaneous presence of VLD-1. Both phylotypes showed growth yields higher or comparable to known organohalide respirers and neither phylotypes enriched in sediment cultures not exhibiting dechlorination. Conclusions These findings confirm the presence of different PCB-respiring microorganisms in the indigenous microbial communities of Venice Lagoon sediments and relate two non-Dehalococcoides phylotypes of the class Dehalococcoidia to different PCB dechlorination rates and specificities. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0743-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrea Nuzzo
- Department of Civil, Chemical, Environmental and Materials Engineering, University of Bologna, Via Terracini 28, 40131, Bologna, Italy
| | - Andrea Negroni
- Department of Civil, Chemical, Environmental and Materials Engineering, University of Bologna, Via Terracini 28, 40131, Bologna, Italy
| | - Giulio Zanaroli
- Department of Civil, Chemical, Environmental and Materials Engineering, University of Bologna, Via Terracini 28, 40131, Bologna, Italy.
| | - Fabio Fava
- Department of Civil, Chemical, Environmental and Materials Engineering, University of Bologna, Via Terracini 28, 40131, Bologna, Italy
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18
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Grativol AD, Marchetti AA, Wetler-Tonini RM, Venancio TM, Gatts CE, Thompson FL, Rezende CE. Bacterial interactions and implications for oil biodegradation process in mangrove sediments. MARINE POLLUTION BULLETIN 2017; 118:221-228. [PMID: 28259419 DOI: 10.1016/j.marpolbul.2017.02.052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 02/18/2017] [Accepted: 02/18/2017] [Indexed: 06/06/2023]
Abstract
Mangrove sediment harbors a unique microbiome and is a hospitable environment for a diverse group of bacteria capable of oil biodegradation. Our goal was to understand bacterial community dynamics from mangrove sediments contaminated with heavy-oil and to evaluate patterns potentially associated with oil biodegradation is such environments. We tested the previously proposed hypothesis of a two-phase pattern of petroleum biodegradation, under which key events in the degradation process take place in the first three weeks after contamination. Two sample sites with different oil pollution histories were compared through T-RFLP analyses and using a pragmatic approach based on the Microbial Resource Management Framework. Our data corroborated the already reported two-phase pattern of oil biodegradation, although the original proposed explanation related to the biophysical properties of the soil is questioned, opening the possibility to consider other plausible hypotheses of microbial interactions as the main drivers of this pattern.
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Affiliation(s)
- Adriana Daudt Grativol
- Centro de Biociências e Biotecnologia/Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio de Janeiro, Brazil.
| | - Albany A Marchetti
- Centro de Biociências e Biotecnologia/Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Rita M Wetler-Tonini
- Centro de Biociências e Biotecnologia/Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Thiago M Venancio
- Centro de Biociências e Biotecnologia/Laboratório de Química e Funções de Proteínas e Peptídeos, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Carlos En Gatts
- Centro de Ciências e Tecnologia/Laboratório de Ciências Físicas, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Fabiano L Thompson
- Instituto de Biologia, CCS, Laboratório de Microbiologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Carlos E Rezende
- Centro de Biociências e Biotecnologia/Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio de Janeiro, Brazil
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19
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Nuzzo A, Hosseinkhani B, Boon N, Zanaroli G, Fava F. Impact of bio-palladium nanoparticles (bio-Pd NPs) on the activity and structure of a marine microbial community. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 220:1068-1078. [PMID: 27894722 DOI: 10.1016/j.envpol.2016.11.036] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/31/2016] [Accepted: 11/14/2016] [Indexed: 06/06/2023]
Abstract
Biogenic palladium nanoparticles (bio-Pd NPs) represent a promising catalyst for organohalide remediation in water and sediments. However, the available information regarding their possible impact in case of release into the environment, particularly on the environmental microbiota, is limited. In this study the toxicity of bio-Pd NPs on the model marine bacterium V. fischeri was assessed. The impacts of different concentrations of bio-Pd NPs on the respiratory metabolisms (i.e. organohalide respiration, sulfate reduction and methanogenesis) and the structure of a PCB-dechlorinating microbial community enriched form a marine sediment were also investigated in microcosms mimicking the actual sampling site conditions. Bio-Pd NPs had no toxic effect on V. fischeri. In addition, they had no significant effects on PCB-dehalogenating activity, while showing a partial, dose-dependent inhibitory effect on sulfate reduction as well as on methanogenesis. No toxic effects by bio-Pd NPs could be also observed on the total bacterial community structure, as its biodiversity was increased compared to the not exposed community. In addition, resilience of the microbial community to bio-Pd NPs exposure was observed, being the final community organization (Gini coefficient) of samples exposed to bio-Pd NPs similar to that of the not exposed one. Considering all the factors evaluated, bio-Pd NPs could be deemed as non-toxic to the marine microbiota in the conditions tested. This is the first study in which the impact of bio-Pd NPs is extensively evaluated over a microbial community in relevant environmental conditions, providing important information for the assessment of their environmental safety.
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Affiliation(s)
- Andrea Nuzzo
- Department of Civil, Chemical, Environmental and Materials Engineering, University of Bologna, Via Terracini 28, 40131 Bologna, Italy
| | - Baharak Hosseinkhani
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| | - Giulio Zanaroli
- Department of Civil, Chemical, Environmental and Materials Engineering, University of Bologna, Via Terracini 28, 40131 Bologna, Italy.
| | - Fabio Fava
- Department of Civil, Chemical, Environmental and Materials Engineering, University of Bologna, Via Terracini 28, 40131 Bologna, Italy
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20
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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: 4.6] [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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21
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Lucas R, Groeneveld J, Harms H, Johst K, Frank K, Kleinsteuber S. A critical evaluation of ecological indices for the comparative analysis of microbial communities based on molecular datasets. FEMS Microbiol Ecol 2016; 93:fiw209. [PMID: 27798064 DOI: 10.1093/femsec/fiw209] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2016] [Indexed: 01/15/2023] Open
Abstract
In times of global change and intensified resource exploitation, advanced knowledge of ecophysiological processes in natural and engineered systems driven by complex microbial communities is crucial for both safeguarding environmental processes and optimising rational control of biotechnological processes. To gain such knowledge, high-throughput molecular techniques are routinely employed to investigate microbial community composition and dynamics within a wide range of natural or engineered environments. However, for molecular dataset analyses no consensus about a generally applicable alpha diversity concept and no appropriate benchmarking of corresponding statistical indices exist yet. To overcome this, we listed criteria for the appropriateness of an index for such analyses and systematically scrutinised commonly employed ecological indices describing diversity, evenness and richness based on artificial and real molecular datasets. We identified appropriate indices warranting interstudy comparability and intuitive interpretability. The unified diversity concept based on 'effective numbers of types' provides the mathematical framework for describing community composition. Additionally, the Bray-Curtis dissimilarity as a beta-diversity index was found to reflect compositional changes. The employed statistical procedure is presented comprising commented R-scripts and example datasets for user-friendly trial application.
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Affiliation(s)
- Rico Lucas
- UFZ-Helmholtz Centre for Environmental Research, Department of Environmental Microbiology, Permoserstr. 15, 04318 Leipzig, Germany
| | - Jürgen Groeneveld
- UFZ-Helmholtz Centre for Environmental Research, Department of Ecological Modelling, Permoserstr. 15, 04318 Leipzig, Germany.,Institute of Forest Growth and Computer Science, Technische Universität Dresden, PO 1117, 01735 Tharandt, Germany
| | - Hauke Harms
- UFZ-Helmholtz Centre for Environmental Research, Department of Environmental Microbiology, Permoserstr. 15, 04318 Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig; Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Karin Johst
- UFZ-Helmholtz Centre for Environmental Research, Department of Ecological Modelling, Permoserstr. 15, 04318 Leipzig, Germany
| | - Karin Frank
- UFZ-Helmholtz Centre for Environmental Research, Department of Ecological Modelling, Permoserstr. 15, 04318 Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig; Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Sabine Kleinsteuber
- UFZ-Helmholtz Centre for Environmental Research, Department of Environmental Microbiology, Permoserstr. 15, 04318 Leipzig, Germany
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22
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De Vrieze J, Verstraete W. Perspectives for microbial community composition in anaerobic digestion: from abundance and activity to connectivity. Environ Microbiol 2016; 18:2797-809. [DOI: 10.1111/1462-2920.13437] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Jo De Vrieze
- Center for Microbial Ecology and Technology (CMET), Ghent University; Coupure Links 653 Gent B-9000 Belgium
| | - Willy Verstraete
- Center for Microbial Ecology and Technology (CMET), Ghent University; Coupure Links 653 Gent B-9000 Belgium
- Avecom NV, Industrieweg 122P; Wondelgem 9032 Belgium
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23
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Fra-Vázquez A, Morales N, Figueroa M, Val del Río A, Regueiro L, Campos J, Mosquera-Corral A. Bacterial community dynamics in long-term operation of a pilot plant using aerobic granular sludge to treat pig slurry. Biotechnol Prog 2016; 32:1212-1221. [DOI: 10.1002/btpr.2314] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 04/22/2016] [Indexed: 12/22/2022]
Affiliation(s)
- A. Fra-Vázquez
- Dept. of Chemical Engineering, Group of Environmental Engineering and Bioprocesses; Inst. of Technology, University of Santiago de Compostela; Santiago de Compostela 15705 Spain
| | - N. Morales
- Dept. of Chemical Engineering, Group of Environmental Engineering and Bioprocesses; Inst. of Technology, University of Santiago de Compostela; Santiago de Compostela 15705 Spain
| | - M. Figueroa
- Dept. of Chemical Engineering, Group of Environmental Engineering and Bioprocesses; Inst. of Technology, University of Santiago de Compostela; Santiago de Compostela 15705 Spain
| | - A. Val del Río
- Dept. of Chemical Engineering, Group of Environmental Engineering and Bioprocesses; Inst. of Technology, University of Santiago de Compostela; Santiago de Compostela 15705 Spain
| | - L. Regueiro
- Dept. of Chemical Engineering, Group of Environmental Engineering and Bioprocesses; Inst. of Technology, University of Santiago de Compostela; Santiago de Compostela 15705 Spain
| | - J.L. Campos
- Faculty of Engineering and Science; Universidad Adolfo Ibáñez; Avda. Padre Hurtado 750 Viña del Mar Chile
| | - A. Mosquera-Corral
- Dept. of Chemical Engineering, Group of Environmental Engineering and Bioprocesses; Inst. of Technology, University of Santiago de Compostela; Santiago de Compostela 15705 Spain
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24
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Prest EI, Hammes F, van Loosdrecht MCM, Vrouwenvelder JS. Biological Stability of Drinking Water: Controlling Factors, Methods, and Challenges. Front Microbiol 2016; 7:45. [PMID: 26870010 PMCID: PMC4740787 DOI: 10.3389/fmicb.2016.00045] [Citation(s) in RCA: 202] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 01/11/2016] [Indexed: 12/27/2022] Open
Abstract
Biological stability of drinking water refers to the concept of providing consumers with drinking water of same microbial quality at the tap as produced at the water treatment facility. However, uncontrolled growth of bacteria can occur during distribution in water mains and premise plumbing, and can lead to hygienic (e.g., development of opportunistic pathogens), aesthetic (e.g., deterioration of taste, odor, color) or operational (e.g., fouling or biocorrosion of pipes) problems. Drinking water contains diverse microorganisms competing for limited available nutrients for growth. Bacterial growth and interactions are regulated by factors, such as (i) type and concentration of available organic and inorganic nutrients, (ii) type and concentration of residual disinfectant, (iii) presence of predators, such as protozoa and invertebrates, (iv) environmental conditions, such as water temperature, and (v) spatial location of microorganisms (bulk water, sediment, or biofilm). Water treatment and distribution conditions in water mains and premise plumbing affect each of these factors and shape bacterial community characteristics (abundance, composition, viability) in distribution systems. Improved understanding of bacterial interactions in distribution systems and of environmental conditions impact is needed for better control of bacterial communities during drinking water production and distribution. This article reviews (i) existing knowledge on biological stability controlling factors and (ii) how these factors are affected by drinking water production and distribution conditions. In addition, (iii) the concept of biological stability is discussed in light of experience with well-established and new analytical methods, enabling high throughput analysis and in-depth characterization of bacterial communities in drinking water. We discussed, how knowledge gained from novel techniques will improve design and monitoring of water treatment and distribution systems in order to maintain good drinking water microbial quality up to consumer's tap. A new definition and methodological approach for biological stability is proposed.
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Affiliation(s)
- Emmanuelle I Prest
- Environmental Biotechnology Group, Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology Delft, Netherlands
| | - Frederik Hammes
- Department of Environmental Microbiology, Eawag - Swiss Federal Institute of Aquatic Science and Technology Dübendorf, Switzerland
| | - Mark C M van Loosdrecht
- Environmental Biotechnology Group, Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology Delft, Netherlands
| | - Johannes S Vrouwenvelder
- Environmental Biotechnology Group, Department of Biotechnology, Faculty of Applied Sciences, Delft University of TechnologyDelft, Netherlands; Division of Biological and Environmental Science and Engineering, Water Desalination and Reuse Center, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia; Wetsus - European Centre of Excellence for Sustainable Water TechnologyLeeuwarden, Netherlands
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25
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Cabrol L, Poly F, Malhautier L, Pommier T, Lerondelle C, Verstraete W, Lepeuple AS, Fanlo JL, Le Roux X. Management of Microbial Communities through Transient Disturbances Enhances the Functional Resilience of Nitrifying Gas-Biofilters to Future Disturbances. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:338-48. [PMID: 26651080 DOI: 10.1021/acs.est.5b02740] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Microbial communities have a key role for the performance of engineered ecosystems such as waste gas biofilters. Maintaining constant performance despite fluctuating environmental conditions is of prime interest, but it is highly challenging because the mechanisms that drive the response of microbial communities to disturbances still have to be disentangled. Here we demonstrate that the bioprocess performance and stability can be improved and reinforced in the face of disturbances, through a rationally predefined strategy of microbial resource management (MRM). This strategy was experimentally validated in replicated pilot-scale nitrifying gas-biofilters, for the two steps of nitrification. The associated biological mechanisms were unraveled through analysis of functions, abundances and community compositions for the major actors of nitrification in these biofilters, that is, ammonia-oxidizing bacteria (AOB) and Nitrobacter-like nitrite-oxidizers (NOB). Our MRM strategy, based on the application of successive, transient perturbations of increasing intensity, enabled to steer the nitrifier community in a favorable way through the selection of more resistant AOB and NOB sharing functional gene sequences close to those of, respectively, Nitrosomonas eutropha and Nitrobacter hamburgensis that are well adapted to high N load. The induced community shifts resulted in significant enhancement of nitrification resilience capacity following the intense perturbation.
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Affiliation(s)
- Léa Cabrol
- Laboratoire Génie de l'Environnement Industriel, Ecole des Mines d'Alès , Rue Jules Renard, 30100 Alès, France
- Veolia Environnement Recherche et Innovation, Chemin de la Digue, BP76, 78600, Maisons Laffitte, France
- Pontificia Universidad Católica de Valparaíso, Escuela de Ingeniería Bioquímica, Avenida Brasil 2185, Valparaíso, Chile
| | - Franck Poly
- Laboratoire d'Ecologie Microbienne, Université de Lyon, Université Lyon 1, CNRS, INRA, UMR CNRS 5557, USC INRA 1364, Bâtiment Gregor Mendel, 16, rue Raphael Dubois, 69622, Villeurbanne Cedex, France
| | - Luc Malhautier
- Laboratoire Génie de l'Environnement Industriel, Ecole des Mines d'Alès , Rue Jules Renard, 30100 Alès, France
| | - Thomas Pommier
- Laboratoire d'Ecologie Microbienne, Université de Lyon, Université Lyon 1, CNRS, INRA, UMR CNRS 5557, USC INRA 1364, Bâtiment Gregor Mendel, 16, rue Raphael Dubois, 69622, Villeurbanne Cedex, France
| | - Catherine Lerondelle
- Laboratoire d'Ecologie Microbienne, Université de Lyon, Université Lyon 1, CNRS, INRA, UMR CNRS 5557, USC INRA 1364, Bâtiment Gregor Mendel, 16, rue Raphael Dubois, 69622, Villeurbanne Cedex, France
| | - Willy Verstraete
- LabMET, Faculty Bio-Science Engineering, Ghent University , Coupure L 653, 9000 Gent, Belgium
| | - Anne-Sophie Lepeuple
- Veolia Environnement Recherche et Innovation, Chemin de la Digue, BP76, 78600, Maisons Laffitte, France
| | - Jean-Louis Fanlo
- Laboratoire Génie de l'Environnement Industriel, Ecole des Mines d'Alès , Rue Jules Renard, 30100 Alès, France
| | - Xavier Le Roux
- Laboratoire d'Ecologie Microbienne, Université de Lyon, Université Lyon 1, CNRS, INRA, UMR CNRS 5557, USC INRA 1364, Bâtiment Gregor Mendel, 16, rue Raphael Dubois, 69622, Villeurbanne Cedex, France
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Venkidusamy K, Megharaj M, Marzorati M, Lockington R, Naidu R. Enhanced removal of petroleum hydrocarbons using a bioelectrochemical remediation system with pre-cultured anodes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 539:61-69. [PMID: 26360455 DOI: 10.1016/j.scitotenv.2015.08.098] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 08/02/2015] [Accepted: 08/16/2015] [Indexed: 05/20/2023]
Abstract
Bioelectrochemical remediation (BER) systems such as microbial fuel cells (MFCs) have recently emerged as a green technology for the effective remediation of petroleum hydrocarbon contaminants (PH) coupled with simultaneous energy recovery. Recent research has shown that biofilms previously enriched for substrate degrading bacteria resulted in excellent performance in terms of substrate removal and electricity generation but the effects on hydrocarbon contaminant degradation were not examined. Here we investigate the differences between enriched biofilm anodes and freshly inoculated new anodes in diesel fed single chamber mediatorless microbial fuel cells (DMFC) using various techniques for the enhancement of PH contaminant remediation with concomitant electricity generation. An anodophilic microbial consortium previously selected for over a year through continuous culturing with a diesel concentration of about 800mgl(-1) and which now showed complete removal of this concentration of diesel within 30days was compared to that of a freshly inoculated new anode MFC (showing 83.4% removal of diesel) with a simultaneous power generation of 90.81mW/m(2) and 15.04mW/m(2) respectively. The behaviour of pre-cultured anodes at a higher concentration of PH (8000mgl(-1)) was also investigated. Scanning electron microscopy observation revealed a thick biofilm covering the pre-cultured anodic electrode but not the anode from the freshly inoculated MFC. High resolution imaging showed the presence of thin 60nm diametre pilus-like projections emanating from the cells. Anodic microbial community profiling confirmed that the selection for diesel degrading exoelectrogenic bacteria had occurred. Identification of a biodegradative gene (alkB) provided strong evidence of the catabolic pathway used for diesel degradation in the DMFCs.
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Affiliation(s)
- Krishnaveni Venkidusamy
- Centre for Environmental Risk Assessment and Remediation (CERAR), University of South, Australia; CRC for Contamination Assessment and Remediation of the Environment (CRCCARE), Mawson Lakes, SA5095, Australia
| | - Mallavarapu Megharaj
- Centre for Environmental Risk Assessment and Remediation (CERAR), University of South, Australia; CRC for Contamination Assessment and Remediation of the Environment (CRCCARE), Mawson Lakes, SA5095, Australia; Global Centre for Environmental Remediation, Faculty of Science and Information Technology, The University of Newcastle, Callaghan, NSW 2308, Australia.
| | - Massimo Marzorati
- Laboratory for Microbial Ecology and Technology (LabMET), Gent University, 9000 Gent, Belgium
| | - Robin Lockington
- Centre for Environmental Risk Assessment and Remediation (CERAR), University of South, Australia; CRC for Contamination Assessment and Remediation of the Environment (CRCCARE), Mawson Lakes, SA5095, Australia
| | - Ravi Naidu
- Centre for Environmental Risk Assessment and Remediation (CERAR), University of South, Australia; CRC for Contamination Assessment and Remediation of the Environment (CRCCARE), Mawson Lakes, SA5095, Australia; Global Centre for Environmental Remediation, Faculty of Science and Information Technology, The University of Newcastle, Callaghan, NSW 2308, Australia
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Monophyletic group of unclassified γ- Proteobacteria dominates in mixed culture biofilm of high-performing oxygen reducing biocathode. Bioelectrochemistry 2015; 106:167-76. [DOI: 10.1016/j.bioelechem.2015.04.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 04/01/2015] [Accepted: 04/05/2015] [Indexed: 12/31/2022]
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28
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Unveiling PHA-storing populations using molecular methods. Appl Microbiol Biotechnol 2015; 99:10433-46. [DOI: 10.1007/s00253-015-7010-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 09/10/2015] [Accepted: 09/14/2015] [Indexed: 10/23/2022]
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29
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Proctor CR, Hammes F. Drinking water microbiology — from measurement to management. Curr Opin Biotechnol 2015; 33:87-94. [DOI: 10.1016/j.copbio.2014.12.014] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 12/14/2014] [Accepted: 12/16/2014] [Indexed: 01/02/2023]
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Carballa M, Regueiro L, Lema JM. Microbial management of anaerobic digestion: exploiting the microbiome-functionality nexus. Curr Opin Biotechnol 2015; 33:103-11. [DOI: 10.1016/j.copbio.2015.01.008] [Citation(s) in RCA: 181] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 01/24/2015] [Accepted: 01/26/2015] [Indexed: 02/04/2023]
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31
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Community shifts in a well-operating agricultural biogas plant: how process variations are handled by the microbiome. Appl Microbiol Biotechnol 2015; 99:7791-803. [PMID: 25998656 DOI: 10.1007/s00253-015-6627-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 04/15/2015] [Accepted: 04/19/2015] [Indexed: 02/03/2023]
Abstract
This study provides a comprehensive, long-term microbiological study of a continuously operated, mesophilic, agricultural biogas plant fed with whole-crop silages of maize and rye, cattle manure and cattle slurry. The microbial community structure was accessed by high-throughput 16S rRNA gene amplicon sequencing. For the characterisation of the microbial dynamics, the community profiling method terminal restriction fragment length polymorphism (TRFLP) in combination with a cloning-sequencing approach as well as a LC-MS/MS approach for protein identification were applied. Our results revealed that the anaerobic digestion is a highly sensitive process: small variations in the process performance induce fluctuations in the microbial community composition and activity. In this context, it could be proven that certain microbial species were better adapted to changing process condition such as temperature (interspecies competition) and that there is a physiological compensation between different microorganisms so that the reactor efficiency was not adversely affected despite of structural and functional changes within the microbial community.
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32
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Liu J, Wang J, Gao G, Bartlam MG, Wang Y. Distribution and diversity of fungi in freshwater sediments on a river catchment scale. Front Microbiol 2015; 6:329. [PMID: 25954259 PMCID: PMC4404825 DOI: 10.3389/fmicb.2015.00329] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 04/01/2015] [Indexed: 11/16/2022] Open
Abstract
Fungal communities perform essential functions in biogeochemical cycles. However, knowledge of fungal community structural changes in river ecosystems is still very limited. In the present study, we combined culture-dependent and culture-independent methods to investigate fungal distribution and diversity in sediment on a regional scale in the Songhua River catchment, located in North-East Asia. A total of 147 samples over the whole river catchment were analyzed. The results showed that compared to the mainstream, the tributaries have a higher fungal community organization and culturable fungal concentration, but possess lower community dynamics as assessed by denaturing gradient gel electrophoresis (DGGE). Furthermore, phylogenetic analysis of DGGE bands showed that Ascomycota and Basidiomycota were the predominant community in the Songhua River catchment. Redundancy analysis revealed that longitude was the primary factor determining the variation of fungal community structure, and fungal biomass was mainly related to the total nutrient content. Our findings provide new insights into the characteristics of fungal community distribution in a temperate zone river at a regional scale, and demonstrate that fungal dispersal is restricted by geographical barriers in a whole river catchment.
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Affiliation(s)
- Jie Liu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University Tianjin, China
| | - Jianan Wang
- Department of Environmental Science and Engineering, Nankai University Binhai College Tianjin, China
| | - Guanghai Gao
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University Tianjin, China
| | - Mark G Bartlam
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University Tianjin, China
| | - Yingying Wang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University Tianjin, China
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Klang J, Theuerl S, Szewzyk U, Huth M, Tölle R, Klocke M. Dynamic variation of the microbial community structure during the long-time mono-fermentation of maize and sugar beet silage. Microb Biotechnol 2015; 8:764-75. [PMID: 25712194 PMCID: PMC4554465 DOI: 10.1111/1751-7915.12263] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 12/15/2014] [Accepted: 12/30/2014] [Indexed: 02/04/2023] Open
Abstract
This study investigated the development of the microbial community during a long-term (337 days) anaerobic digestion of maize and sugar beet silage, two feedstocks that significantly differ in their chemical composition. For the characterization of the microbial dynamics, the community profiling method terminal restriction fragment length polymorphism (TRFLP) in combination with a cloning-sequencing approach was applied. Our results revealed a specific adaptation of the microbial community to the supplied feedstocks. Based on the high amount of complex compounds, the anaerobic conversion rate of maize silage was slightly lower compared with the sugar beet silage. It was demonstrated that members from the phylum Bacteroidetes are mainly involved in the degradation of low molecular weight substances such as sugar, ethanol and acetate, the main compounds of the sugar beet silage. It was further shown that species of the genus Methanosaeta are highly sensitive against sudden stress situations such as a strong decrease in the ammonium nitrogen (NH4+-N) concentration or a drop of the pH value. In both cases, a functional compensation by members of the genera Methanoculleus and/or Methanosarcina was detected. However, the overall biomass conversion of both feedstocks proceeded efficiently as a steady state between acid production and consumption was recorded, which further resulted in an equal biogas yield.
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Affiliation(s)
- Johanna Klang
- Department Bioengineering, Leibniz Institute for Agricultural Engineering, Max Eyth Allee 100, Potsdam, 14469, Germany.,Department of Environmental Microbiology, Technische Universität Berlin, Ernst-Reuter-Platz 1, Berlin, 10587, Germany
| | - Susanne Theuerl
- Department Bioengineering, Leibniz Institute for Agricultural Engineering, Max Eyth Allee 100, Potsdam, 14469, Germany
| | - Ulrich Szewzyk
- Department of Environmental Microbiology, Technische Universität Berlin, Ernst-Reuter-Platz 1, Berlin, 10587, Germany
| | - Markus Huth
- Department of Crop and Animal Sciences, Humboldt-Universtät zu Berlin, Unter den Linden 6, Berlin, 10099, Germany
| | - Rainer Tölle
- Department of Crop and Animal Sciences, Humboldt-Universtät zu Berlin, Unter den Linden 6, Berlin, 10099, Germany
| | - Michael Klocke
- Department Bioengineering, Leibniz Institute for Agricultural Engineering, Max Eyth Allee 100, Potsdam, 14469, Germany
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34
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Deodorants and antiperspirants affect the axillary bacterial community. Arch Dermatol Res 2014; 306:701-10. [PMID: 25077920 DOI: 10.1007/s00403-014-1487-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 05/27/2014] [Accepted: 07/10/2014] [Indexed: 02/07/2023]
Abstract
The use of underarm cosmetics is common practice in the Western society to obtain better body odor and/or to prevent excessive sweating. A survey indicated that 95 % of the young adult Belgians generally use an underarm deodorant or antiperspirant. The effect of deodorants and antiperspirants on the axillary bacterial community was examined on nine healthy subjects, who were restrained from using deodorant/antiperspirant for 1 month. Denaturing gradient gel electrophoresis was used to investigate the individual microbial dynamics. The microbial profiles were unique for every person. A stable bacterial community was seen when underarm cosmetics were applied on a daily basis and when no underarm cosmetics were applied. A distinct community difference was seen when the habits were changed from daily use to no use of deodorant/antiperspirant and vice versa. The richness was higher when deodorants and antiperspirants were applied. Especially when antiperspirants were applied, the microbiome showed an increase in diversity. Antiperspirant usage led toward an increase of Actinobacteria, which is an unfavorable situation with respect to body odor development. These initial results show that axillary cosmetics modify the microbial community and can stimulate odor-producing bacteria.
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35
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Kerckhof FM, Courtens ENP, Geirnaert A, Hoefman S, Ho A, Vilchez-Vargas R, Pieper DH, Jauregui R, Vlaeminck SE, Van de Wiele T, Vandamme P, Heylen K, Boon N. Optimized cryopreservation of mixed microbial communities for conserved functionality and diversity. PLoS One 2014; 9:e99517. [PMID: 24937032 PMCID: PMC4061060 DOI: 10.1371/journal.pone.0099517] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 05/15/2014] [Indexed: 12/26/2022] Open
Abstract
The use of mixed microbial communities (microbiomes) for biotechnological applications has steadily increased over the past decades. However, these microbiomes are not readily available from public culture collections, hampering their potential for widespread use. The main reason for this lack of availability is the lack of an effective cryopreservation protocol. Due to this critical need, we evaluated the functionality as well as the community structure of three different types of microbiomes before and after cryopreservation with two cryoprotective agents (CPA). Microbiomes were selected based upon relevance towards applications: (1) a methanotrophic co-culture (MOB), with potential for mitigation of greenhouse gas emissions, environmental pollutants removal and bioplastics production; (2) an oxygen limited autotrophic nitrification/denitrification (OLAND) biofilm, with enhanced economic and ecological benefits for wastewater treatment, and (3) fecal material from a human donor, with potential applications for fecal transplants and pre/probiotics research. After three months of cryopreservation at −80°C, we found that metabolic activity, in terms of the specific activity recovery of MOB, aerobic ammonium oxidizing bacteria (AerAOB) and anaerobic AOB (AnAOB, anammox) in the OLAND mixed culture, resumes sooner when one of our selected CPA [dimethyl sulfoxide (DMSO) and DMSO plus trehalose and tryptic soy broth (DMSO+TT)] was added. However, the activity of the fecal community was not influenced by the CPA addition, although the preservation of the community structure (as determined by 16S rRNA gene sequencing) was enhanced by addition of CPA. In summary, we have evaluated a cryopreservation protocol that succeeded in preserving both community structure and functionality of value-added microbiomes. This will allow individual laboratories and culture collections to boost the use of microbiomes in biotechnological applications.
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Affiliation(s)
- Frederiek-Maarten Kerckhof
- Laboratory of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Emilie N. P. Courtens
- Laboratory of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Annelies Geirnaert
- Laboratory of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Sven Hoefman
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, Gent, Belgium
| | - Adrian Ho
- Laboratory of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Ramiro Vilchez-Vargas
- Laboratory of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Dietmar H. Pieper
- Microbial Interactions and Processes Research Group, Department of Medical Microbiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Ruy Jauregui
- Microbial Interactions and Processes Research Group, Department of Medical Microbiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Siegfried E. Vlaeminck
- Laboratory of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Tom Van de Wiele
- Laboratory of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, Gent, Belgium
| | - Kim Heylen
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, Gent, Belgium
| | - Nico Boon
- Laboratory of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
- * E-mail:
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Koch C, Harnisch F, Schröder U, Müller S. Cytometric fingerprints: evaluation of new tools for analyzing microbial community dynamics. Front Microbiol 2014; 5:273. [PMID: 24926290 PMCID: PMC4044693 DOI: 10.3389/fmicb.2014.00273] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 05/19/2014] [Indexed: 01/20/2023] Open
Abstract
Optical characteristics of individual bacterial cells of natural communities can be measured with flow cytometry (FCM) in high throughput. The resulting data are visualized in cytometric histograms. These histograms represent individual cytometric fingerprints of microbial communities, e.g., at certain time points or microenvironmental conditions. Up to now four tools for analyzing the variation in these cytometric fingerprints are available but have not yet been systematically compared regarding application: Dalmatian Plot, Cytometric Histogram Image Comparison (CHIC), Cytometric Barcoding (CyBar), and FlowFP. In this article these tools were evaluated concerning (i) the required experience of the operator in handling cytometric data sets, (ii) the detection level of changes, (iii) time demand for analysis, and (iv) software requirements. As an illustrative example, FCM was used to characterize the microbial community structure of electroactive microbial biofilms. Their cytometric fingerprints were determined, analyzed with all four tools, and correlated to experimental and functional parameters. The source of inoculum (four different types of wastewater samples) showed the strongest influence on the microbial community structure and biofilm performance while the choice of substrate (acetate or lactate) had no significant effect in the present study. All four evaluation tools were found suitable to monitor structural changes of natural microbial communities. The Dalmatian Plot was shown to be most sensitive to operator impact but nevertheless provided an overview on community shifts. CHIC, CyBar, and FlowFP showed less operator dependence and gave highly resolved information on community structure variation on different detection levels. In conclusion, experimental and productivity parameters correlated with the biofilm structures and practical process integration details were available from cytometric fingerprint analysis.
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Affiliation(s)
- Christin Koch
- Department of Environmental Microbiology, UFZ - Helmholtz-Centre for Environmental Research Leipzig, Germany
| | - Falk Harnisch
- Department of Environmental Microbiology, UFZ - Helmholtz-Centre for Environmental Research Leipzig, Germany ; Institute of Environmental and Sustainable Chemistry, TU Braunschweig Braunschweig, Germany
| | - Uwe Schröder
- Institute of Environmental and Sustainable Chemistry, TU Braunschweig Braunschweig, Germany
| | - Susann Müller
- Department of Environmental Microbiology, UFZ - Helmholtz-Centre for Environmental Research Leipzig, Germany
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Besmer MD, Weissbrodt DG, Kratochvil BE, Sigrist JA, Weyland MS, Hammes F. The feasibility of automated online flow cytometry for in-situ monitoring of microbial dynamics in aquatic ecosystems. Front Microbiol 2014; 5:265. [PMID: 24917858 PMCID: PMC4040452 DOI: 10.3389/fmicb.2014.00265] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 05/15/2014] [Indexed: 01/22/2023] Open
Abstract
Fluorescent staining coupled with flow cytometry (FCM) is often used for the monitoring, quantification and characterization of bacteria in engineered and environmental aquatic ecosystems including seawater, freshwater, drinking water, wastewater, and industrial bioreactors. However, infrequent grab sampling hampers accurate characterization and subsequent understanding of microbial dynamics in all of these ecosystems. A logic technological progression is high throughput and full automation of the sampling, staining, measurement, and data analysis steps. Here we assess the feasibility and applicability of automated FCM by means of actual data sets produced with prototype instrumentation. As proof-of-concept we demonstrate examples of microbial dynamics in (i) flowing tap water from a municipal drinking water supply network and (ii) river water from a small creek subject to two rainfall events. In both cases, automated measurements were done at 15-min intervals during 12-14 consecutive days, yielding more than 1000 individual data points for each ecosystem. The extensive data sets derived from the automated measurements allowed for the establishment of baseline data for each ecosystem, as well as for the recognition of daily variations and specific events that would most likely be missed (or miss-characterized) by infrequent sampling. In addition, the online FCM data from the river water was combined and correlated with online measurements of abiotic parameters, showing considerable potential for a better understanding of cause-and-effect relationships in aquatic ecosystems. Although several challenges remain, the successful operation of an automated online FCM system and the basic interpretation of the resulting data sets represent a breakthrough toward the eventual establishment of fully automated online microbiological monitoring technologies.
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Affiliation(s)
- Michael D Besmer
- Department of Environmental Microbiology, Eawag - Swiss Federal Institute for Aquatic Science and Technology Dübendorf, Switzerland ; Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich Zürich, Switzerland
| | - David G Weissbrodt
- Department of Environmental Microbiology, Eawag - Swiss Federal Institute for Aquatic Science and Technology Dübendorf, Switzerland ; Institute of Environmental Engineering, Chair of Process Engineering in Urban Water Management, ETH Zürich Zürich, Switzerland
| | - Bradley E Kratochvil
- Department of Environmental Microbiology, Eawag - Swiss Federal Institute for Aquatic Science and Technology Dübendorf, Switzerland
| | - Jürg A Sigrist
- Department of Environmental Microbiology, Eawag - Swiss Federal Institute for Aquatic Science and Technology Dübendorf, Switzerland
| | - Mathias S Weyland
- Department of Environmental Microbiology, Eawag - Swiss Federal Institute for Aquatic Science and Technology Dübendorf, Switzerland
| | - Frederik Hammes
- Department of Environmental Microbiology, Eawag - Swiss Federal Institute for Aquatic Science and Technology Dübendorf, Switzerland
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38
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Koch C, Müller S, Harms H, Harnisch F. Microbiomes in bioenergy production: From analysis to management. Curr Opin Biotechnol 2014; 27:65-72. [DOI: 10.1016/j.copbio.2013.11.006] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 11/15/2013] [Accepted: 11/17/2013] [Indexed: 11/26/2022]
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39
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Mishra D, Rhee YH. Microbial leaching of metals from solid industrial wastes. J Microbiol 2014; 52:1-7. [DOI: 10.1007/s12275-014-3532-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 11/27/2013] [Accepted: 11/28/2013] [Indexed: 02/05/2023]
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40
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De Roy K, Marzorati M, Van den Abbeele P, Van de Wiele T, Boon N. Synthetic microbial ecosystems: an exciting tool to understand and apply microbial communities. Environ Microbiol 2013; 16:1472-81. [PMID: 24274586 DOI: 10.1111/1462-2920.12343] [Citation(s) in RCA: 179] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 11/19/2013] [Indexed: 12/24/2022]
Abstract
Many microbial ecologists have described the composition of microbial communities in a plenitude of environments, which has greatly improved our basic understanding of microorganisms and ecosystems. However, the factors and processes that influence the behaviour and functionality of an ecosystem largely remain black boxes when using conventional approaches. Therefore, synthetic microbial ecology has gained a lot of interest in the last few years. Because of their reduced complexity and increased controllability, synthetic communities are often preferred over complex communities to examine ecological theories. They limit the factors that influence the microbial community to a minimum, allowing their management and identifying specific community responses. However, besides their use for basic research, synthetic ecosystems also found their way towards different applications, like industrial fermentation and bioremediation. Here, we review why and how synthetic microbial communities are applied for research purposes and for which applications they have been and could be successfully used.
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Affiliation(s)
- Karen De Roy
- Laboratory of Microbial Ecology and Technology (LabMET), Coupure Links 653, 9000, Gent, Belgium
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Exploration and prediction of interactions between methanotrophs and heterotrophs. Res Microbiol 2013; 164:1045-54. [DOI: 10.1016/j.resmic.2013.08.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 08/27/2013] [Indexed: 01/28/2023]
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Greenhouse gas emissions from rice microcosms amended with a plant microbial fuel cell. Appl Microbiol Biotechnol 2013; 98:3205-17. [DOI: 10.1007/s00253-013-5328-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2013] [Revised: 09/23/2013] [Accepted: 10/10/2013] [Indexed: 02/03/2023]
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Marzorati M, Negroni A, Fava F, Verstraete W, Boon N. Application of a molecular based approach for the early detection of short term 3-chloroaniline shock loads on activated sludge bacterial community and functionality. N Biotechnol 2013; 30:763-71. [DOI: 10.1016/j.nbt.2013.07.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 05/06/2013] [Accepted: 07/19/2013] [Indexed: 11/30/2022]
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Callewaert C, Kerckhof FM, Granitsiotis MS, Van Gele M, Van de Wiele T, Boon N. Characterization of Staphylococcus and Corynebacterium clusters in the human axillary region. PLoS One 2013; 8:e70538. [PMID: 23950955 PMCID: PMC3741381 DOI: 10.1371/journal.pone.0070538] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 06/18/2013] [Indexed: 12/28/2022] Open
Abstract
The skin microbial community is regarded as essential for human health and well-being, but likewise plays an important role in the formation of body odor in, for instance, the axillae. Few molecular-based research was done on the axillary microbiome. This study typified the axillary microbiome of a group of 53 healthy subjects. A profound view was obtained of the interpersonal, intrapersonal and temporal diversity of the human axillary microbiota. Denaturing gradient gel electrophoresis (DGGE) and next generation sequencing on 16S rRNA gene region were combined and used as extent to each other. Two important clusters were characterized, where Staphylococcus and Corynebacterium species were the abundant species. Females predominantly clustered within the Staphylococcus cluster (87%, n = 17), whereas males clustered more in the Corynebacterium cluster (39%, n = 36). The axillary microbiota was unique to each individual. Left-right asymmetry occurred in about half of the human population. For the first time, an elaborate study was performed on the dynamics of the axillary microbiome. A relatively stable axillary microbiome was noticed, although a few subjects evolved towards another stable community. The deodorant usage had a proportional linear influence on the species diversity of the axillary microbiome.
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Affiliation(s)
- Chris Callewaert
- Laboratory of Microbial Ecology and Technology, Ghent University, Gent, Belgium
| | | | - Michael S. Granitsiotis
- Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Research Unit Environmental Genomics, Neuherberg, Germany
| | | | - Tom Van de Wiele
- Laboratory of Microbial Ecology and Technology, Ghent University, Gent, Belgium
| | - Nico Boon
- Laboratory of Microbial Ecology and Technology, Ghent University, Gent, Belgium
- * E-mail:
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Croese E, Keesman KJ, Widjaja-Greefkes AHCA, Geelhoed JS, Plugge CM, Sleutels THJA, Stams AJM, Euverink GJW. Relating MEC population dynamics to anode performance from DGGE and electrical data. Syst Appl Microbiol 2013; 36:408-16. [PMID: 23830069 DOI: 10.1016/j.syapm.2013.05.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 05/24/2013] [Accepted: 05/25/2013] [Indexed: 10/26/2022]
Abstract
The microbial electrolysis cell (MEC) is a promising system for H2 production, but little is known about the active microbial population in MEC systems. Therefore, the microbial community of five different MEC graphite felt anodes was analyzed using denaturing gradient gel electrophoresis (DGGE) profiling. The results showed that the bacterial population was very diverse and there were substantial differences between microorganisms in anolyte and anode samples. The archaeal population in the anolyte and at the anodes, and between the different MEC anodes, was very similar. SEM and FISH imaging showed that Archaea were mainly present in the spaces between the electrode fibers and Bacteria were present at the fiber surface, which suggested that Bacteria were the main microorganisms involved in MEC electrochemical activity. Redundancy analysis (RDA) and QR factorization-based estimation (QRE) were used to link the composition of the bacterial community to electrochemical performance of the MEC. The operational mode of the MECs and their consequent effects on current density and anode resistance on the populations were significant. The results showed that the community composition was most strongly correlated with current density. The DGGE band mostly correlated with current represented a Clostridium sticklandii strain, suggesting that this species had a major role in current from acetate generation at the MEC anodes. The combination of RDA and QRE seemed especially promising for obtaining an insight into the part of the microbial population actively involved in electrode interaction in the MEC.
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Affiliation(s)
- Elsemiek Croese
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
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De Vrieze J, Verstraete W, Boon N. Repeated pulse feeding induces functional stability in anaerobic digestion. Microb Biotechnol 2013; 6:414-24. [PMID: 23302421 PMCID: PMC3917476 DOI: 10.1111/1751-7915.12025] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2012] [Accepted: 11/30/2012] [Indexed: 01/29/2023] Open
Abstract
Anaerobic digestion is an environmental key technology in the future bio-based economy. To achieve functional stability, a minimal microbial community diversity is required. This microbial community should also have a certain ‘elasticity’, i.e. the ability to rapidly adapt to suboptimal conditions or stress. In this study it was evaluated whether a higher degree of functional stability could be achieved by changing the feeding pattern, which can change the evenness, dynamics and richness of the bacterial community. The first reactor (CSTRstable) was fed on daily basis, whereas the second reactor (CSTRdynamic) was fed every 2 days. Average biogas production was 0.30 l CH4 l−1 day−1 in both reactors, although daily variation was up to four times higher in the CSTRdynamic compared with the CSTRstable during the first 50 days. Bacterial analysis revealed that this CSTRdynamic had a two times higher degree of bacterial community dynamics. The CSTRdynamic also appeared to be more tolerant to an organic shock load of 8 g COD l−1 and ammonium levels up to 8000 mg TAN l−1. These results suggest that the regular application of a limited pulse of organic material and/or a variation in the substrate composition might promote higher functional stability in anaerobic digestion.
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Affiliation(s)
- Jo De Vrieze
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, B-9000, Gent, Belgium
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Chi XQ, Zhang JJ, Zhao S, Zhou NY. Bioaugmentation with a consortium of bacterial nitrophenol-degraders for remediation of soil contaminated with three nitrophenol isomers. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2013; 172:33-41. [PMID: 22982551 DOI: 10.1016/j.envpol.2012.08.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 05/25/2012] [Accepted: 08/04/2012] [Indexed: 06/01/2023]
Abstract
A consortium consisting of para-nitrophenol utilizer Pseudomonas sp. strain WBC-3, meta-nitrophenol utilizer Cupriavidus necator JMP134 and ortho-nitrophenol utilizer Alcaligenes sp. strain NyZ215 was inoculated into soil contaminated with three nitrophenol isomers for bioaugmentation. Accelerated removal of all nitrophenols was achieved in inoculated soils compared to un-inoculated soils, with complete removal of nitrophenols in inoculated soils occurring between 2 and 16 days. Real-time polymerase chain reaction (PCR) targeting nitrophenol-degradation functional genes indicated that the three strains survived and were stable over the course of the incubation period. The abundance of total indigenous bacteria (measured by 16S rRNA gene real-time PCR) was slightly negatively impacted by the nitrophenol contamination. Denaturing gradient gel electrophoresis profiles of total and group-specific indigenous community suggested a dynamic change in species richness occurred during the bioaugmentation process. Furthermore, Pareto-Lorenz curves and Community organization parameters indicated that the bioaugmentation process had little impact on species evenness within the microbial community.
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Affiliation(s)
- Xiang-Qun Chi
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
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Comparing metabolic functionalities, community structures, and dynamics of herbicide-degrading communities cultivated with different substrate concentrations. Appl Environ Microbiol 2012; 79:367-75. [PMID: 23124226 DOI: 10.1128/aem.02536-12] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Two 4-chloro-2-methylphenoxyacetic acid (MCPA)-degrading enrichment cultures selected from an aquifer on low (0.1 mg liter(-1)) or high (25 mg liter(-1)) MCPA concentrations were compared in terms of metabolic activity, community composition, population growth, and single cell physiology. Different community compositions and major shifts in community structure following exposure to different MCPA concentrations were observed using both 16S rRNA gene denaturing gradient gel electrophoresis fingerprinting and pyrosequencing. The communities also differed in their MCPA-mineralizing activities. The enrichments selected on low concentrations mineralized MCPA with shorter lag phases than those selected on high concentrations. Flow cytometry measurements revealed that mineralization led to cell growth. The presence of low-nucleic acid-content bacteria (LNA bacteria) was correlated with mineralization activity in cultures selected on low herbicide concentrations. This suggests that LNA bacteria may play a role in degradation of low herbicide concentrations in aquifers impacted by agriculture. This study shows that subpopulations of herbicide-degrading bacteria that are adapted to different pesticide concentrations can coexist in the same environment and that using a low herbicide concentration enables enrichment of apparently oligotrophic subpopulations.
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Selection of associated heterotrophs by methane-oxidizing bacteria at different copper concentrations. Antonie van Leeuwenhoek 2012; 103:527-37. [DOI: 10.1007/s10482-012-9835-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2012] [Accepted: 10/17/2012] [Indexed: 01/29/2023]
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50
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Marzorati M, Maignien L, Verhelst A, Luta G, Sinnott R, Kerckhof FM, Boon N, Van de Wiele T, Possemiers S. Barcoded pyrosequencing analysis of the microbial community in a simulator of the human gastrointestinal tract showed a colon region-specific microbiota modulation for two plant-derived polysaccharide blends. Antonie van Leeuwenhoek 2012; 103:409-20. [DOI: 10.1007/s10482-012-9821-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 09/18/2012] [Indexed: 01/01/2023]
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