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Hubau A, Joulian C, Tris H, Pino-Herrera D, Becquet C, Guezennec AG. Fe(III) bioreduction kinetics in anaerobic batch and continuous stirred tank reactors with acidophilic bacteria relevant for bioleaching of limonitic laterites. Front Microbiol 2024; 15:1358788. [PMID: 38533329 PMCID: PMC10964485 DOI: 10.3389/fmicb.2024.1358788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/19/2024] [Indexed: 03/28/2024] Open
Abstract
In the framework of the H2020 project CROCODILE, the recovery of Co from oxidized ores by reductive bioleaching has been studied. The objective was to reduce Fe(III) to Fe(II) to enhance the dissolution of Co from New-Caledonian limonitic laterites, mainly composed of goethite and Mn oxides. This study focused on the Fe(III) bioreduction which is a relevant reaction of this process. In the first step, biomass growth was sustained by aerobic bio-oxidation of elemental sulfur. In the second step, the biomass anaerobically reduced Fe(III) to Fe(II). The last step, which is not in the scope of this study, was the reduction of limonites and the dissolution of metals. This study aimed at assessing the Fe(III) bioreduction rate at 35°C with a microbial consortium composed predominantly of Sulfobacillus (Sb.) species as the iron reducers and Acidithiobacillus (At.) caldus. It evaluated the influence of the biomass concentration on the Fe(III) bioreduction rate and yield, both in batch and continuous mode. The influence of the composition of the growth medium on the bioreduction rate was assessed in continuous mode. A mean Fe(III) bioreduction rate of 1.7 mg·L-1·h-1 was measured in batch mode, i.e., 13 times faster than the abiotic control (0.13 mg·L-1·h-1). An increase in biomass concentrations in the liquid phase from 4 × 108 cells·mL-1 to 3 × 109 cells·mL-1 resulted in an increase of the mean Fe(III) bioreduction rate from 1.7 to 10 mg·L-1·h-1. A test in continuous stirred tank reactors at 35°C resulted in further optimization of the Fe(III) bioreduction rate which reached 20 mg·L-1·h-1. A large excess of nutrients enables to obtain higher kinetics. The determination of this kinetics is essential for the design of a reductive bioleaching process.
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Luo Y, Cui X, Cheruba E, Chua YK, Ng C, Tan RZ, Tan KK, Cheow LF. SAMBA: A Multicolor Digital Melting PCR Platform for Rapid Microbiome Profiling. SMALL METHODS 2022; 6:e2200185. [PMID: 35652511 DOI: 10.1002/smtd.202200185] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 04/27/2022] [Indexed: 06/15/2023]
Abstract
During the past decade, breakthroughs in sequencing technology have provided the basis for studies of the myriad ways in which microbial communities in and on the human body influence human health and disease. In almost every medical specialty, there is now a growing interest in accurate and quantitative profiling of the microbiota for use in diagnostic and therapeutic applications. However, the current next-generation sequencing approach for microbiome profiling is costly, requires laborious library preparation, and is challenging to scale up for routine diagnostics. Split, Amplify, and Melt analysis of BActeria-community (SAMBA), a novel multicolor digital melting polymerase chain reaction platform with unprecedented multiplexing capability is presented, and the capability to distinguish and quantify 16 bacteria species in mixtures is demonstrated. Subsequently, SAMBA is applied to measure the compositions of bacteria in the gut microbiome to identify microbial dysbiosis related to colorectal cancer. This rapid, low cost, and high-throughput approach will enable the implementation of microbiome diagnostics in clinical laboratories and routine medical practice.
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Affiliation(s)
- Yongqiang Luo
- Department of Biomedical Engineering & Institute for Health Innovation and Technology, National University of Singapore, Singapore, 119077, Singapore
| | - Xu Cui
- Department of Biomedical Engineering & Institute for Health Innovation and Technology, National University of Singapore, Singapore, 119077, Singapore
| | - Elsie Cheruba
- Department of Biomedical Engineering & Institute for Health Innovation and Technology, National University of Singapore, Singapore, 119077, Singapore
| | - Yong Kang Chua
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Charmaine Ng
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Rui Zhen Tan
- Engineering Cluster, Singapore Institute of Technology, Singapore, 138683, Singapore
| | - Ker-Kan Tan
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Division of Colorectal Surgery, National University Hospital, Singapore, 119074, Singapore
| | - Lih Feng Cheow
- Department of Biomedical Engineering & Institute for Health Innovation and Technology, National University of Singapore, Singapore, 119077, Singapore
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Goss-Souza D, Tsai SM, Rodrigues JLM, Klauberg-Filho O, Sousa JP, Baretta D, Mendes LW. Biogeographic responses and niche occupancy of microbial communities following long-term land-use change. Antonie Van Leeuwenhoek 2022; 115:1129-1150. [DOI: 10.1007/s10482-022-01761-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 06/29/2022] [Indexed: 10/17/2022]
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Jeon J, Cho K, Kang J, Park S, Uchenna Esther Ada O, Park J, Song M, Viet Ly Q, Bae H. Combined machine learning and biomolecular analysis for stability assessment of anaerobic ammonium oxidation under salt stress. BIORESOURCE TECHNOLOGY 2022; 355:127206. [PMID: 35477105 DOI: 10.1016/j.biortech.2022.127206] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 04/17/2022] [Accepted: 04/19/2022] [Indexed: 06/14/2023]
Abstract
In this study, the stability of the total nitrogen removal efficiency (TNRE) was modeled using an artificial neural network (ANN)-based binary classification model for the anaerobic ammonium oxidation (AMX) process under saline conditions. The TNRE was stabilized to 80.2 ± 11.4% at the final phase under the salinity of 1.0 ± 0.02%. The results of terminal restriction fragment length polymorphism (T-RFLP) analysis showed the predominance of Candidatus Jettenia genus. Real-time quantitative PCR analysis revealed the average abundance of Ca. Jettenia and Kuenenia spp. increased in 3.2 ± 5.4 × 108 and 2.0 ± 2.2 × 105 copies/mL, respectively. The prediction accuracy using operational parameters with data augmentation was 88.2%. However, integration with T-RFLP and real-time qPCR signals improved the prediction accuracy by 97.1%. This study revealed the feasible application of machine learning and biomolecular signals to the stability prediction of the AMX process under increased salinity.
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Affiliation(s)
- Junbeom Jeon
- Department of Civil and Environmental Engineering, Pusan National University, Busan 46241, Republic of Korea.
| | - Kyungjin Cho
- Center for Water Cycle Research, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea; Division of Energy and Environment Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea.
| | - Jinkyu Kang
- Institute for Environment and Energy, Pusan National University, Busan 46241, Republic of Korea.
| | - Suin Park
- Department of Civil and Environmental Engineering, Pusan National University, Busan 46241, Republic of Korea.
| | - Okpete Uchenna Esther Ada
- Department of Civil and Environmental Engineering, Pusan National University, Busan 46241, Republic of Korea; Department of Precision Medicine, Step Forward Personalized Medicine (SPMED), Busan 46508, Republic of Korea
| | - Jihye Park
- Department of Civil and Environmental Engineering, Pusan National University, Busan 46241, Republic of Korea.
| | - Minsu Song
- Department of Civil and Environmental Engineering, Pusan National University, Busan 46241, Republic of Korea.
| | - Quang Viet Ly
- Institute of Environmental Engineering & Nano-Technology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Hyokwan Bae
- Department of Civil and Environmental Engineering, Pusan National University, Busan 46241, Republic of Korea; Institute for Environment and Energy, Pusan National University, Busan 46241, Republic of Korea.
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Campolino ML, de Paula Lana UG, Gomes EA, Coelho AM, de Sousa SM. Phosphate fertilization affects rhizosphere microbiome of maize and sorghum genotypes. Braz J Microbiol 2022; 53:1371-1383. [PMID: 35391636 PMCID: PMC9433508 DOI: 10.1007/s42770-022-00747-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 03/30/2022] [Indexed: 11/26/2022] Open
Abstract
Despite the lower reactivity of natural phosphates compared to soluble fertilizers, their P bioavailability can increase over the cultivation years, due to the physicochemical processes and the activity of soil microbiota. Therefore, this work aimed to evaluate the α and β diversity of the rhizosphere microbiota of maize and sorghum genotypes grown under different sources and doses of phosphate fertilizers. Four commercial maize and four sorghum genotypes were grown under field conditions with three levels of triple superphosphate (TSP) and two types of rock phosphate sources: phosphorite (RockP) and bayóvar (RP) during two seasons. Maize and sorghum presented a significant difference on the genetic β diversity of both rhizosferic bacterial and arbuscular mycorrhizal fungi. Moreover, P doses within each phosphate source formed two distinct groups for maize and sorghum, and six bacterial phyla were identified in both crops with significant difference in the relative abundance of Firmicutes and Proteobacteria. It was observed that RockP fertilization increased Firmicutes population while Proteobacteria was the most abundant phylum after TSP fertilization in maize. In sorghum, a significant impact of fertilization was observed on the Acidobacteria and Proteobacteria phyla. TSP fertilization increased the Acidobacteria population compared to no fertilized (P0) and RockP while Proteobacteria abundance in RockP was reduced compared to P0 and TSP, indicating a shift toward a more copiotrophic community. Our results suggested that the reactivity of P source is the predominant factor in bacterial community' structures in the maize and sorghum rhizosphere from the evaluated genotypes, followed by P source.
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Affiliation(s)
| | | | | | | | - Sylvia Morais de Sousa
- Universidade Federal de São João del Rei, Sete Lagoas, MG, Brazil.
- Embrapa Milho e Sorgo, Sete Lagoas, MG, 35701-970, Brazil.
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Verstraete W, Yanuka‐Golub K, Driesen N, De Vrieze J. Engineering microbial technologies for environmental sustainability: choices to make. Microb Biotechnol 2022; 15:215-227. [PMID: 34875143 PMCID: PMC8719809 DOI: 10.1111/1751-7915.13986] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 11/21/2021] [Indexed: 11/27/2022] Open
Abstract
Microbial technologies have provided solutions to key challenges in our daily lives for over a century. In the debate about the ongoing climate change and the need for planetary sustainability, microbial ecology and microbial technologies are rarely considered. Nonetheless, they can bring forward vital solutions to decrease and even prevent long-term effects of climate change. The key to the success of microbial technologies is an effective, target-oriented microbiome management. Here, we highlight how microbial technologies can play a key role in both natural, i.e. soils and aquatic ecosystems, and semi-natural or even entirely human-made, engineered ecosystems, e.g. (waste) water treatment and bodily systems. First, we set forward fundamental guidelines for effective soil microbial resource management, especially with respect to nutrient loss and greenhouse gas abatement. Next, we focus on closing the water circle, integrating resource recovery. We also address the essential interaction of the human and animal host with their respective microbiomes. Finally, we set forward some key future potentials, such as microbial protein and the need to overcome microphobia for microbial products and services. Overall, we conclude that by relying on the wisdom of the past, we can tackle the challenges of our current era through microbial technologies.
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Affiliation(s)
- Willy Verstraete
- Center for Microbial Ecology and Technology (CMET)Faculty of Bioscience EngineeringGhent UniversityCoupure Links 653GentB‐9000Belgium
- Avecom NVIndustrieweg 122PWondelgem9032Belgium
| | - Keren Yanuka‐Golub
- The Institute of Applied ResearchThe Galilee SocietyP.O. Box 437Shefa‐AmrIsrael
| | | | - Jo De Vrieze
- Center for Microbial Ecology and Technology (CMET)Faculty of Bioscience EngineeringGhent UniversityCoupure Links 653GentB‐9000Belgium
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Dalby FR, Nikolausz M, Hansen MJ, Feilberg A. Effects of combined tannic acid/fluoride on sulfur transformations and methanogenic pathways in swine manure. PLoS One 2021; 16:e0257759. [PMID: 34555107 PMCID: PMC8459979 DOI: 10.1371/journal.pone.0257759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 09/10/2021] [Indexed: 01/04/2023] Open
Abstract
Livestock manure emits reduced sulfur compounds and methane, which affect nature and the climate. These gases are efficiently mitigated by addition of a tannic acid-sodium fluoride combination inhibitor (TA-NaF), and to some extent by acidification. In this paper, TA-NaF treatment was performed on swine manure to study the treatment influence on methanogenic pathways and sulfur transformation pathways in various laboratory experiments. Stable carbon isotope labeling revealed that both untreated and TA-NaF treated swine manures were dominated by hydrogenotrophic methanogenesis. However, in supplementary experiments in wastewater sludge, TA-NaF clearly inhibited acetoclastic methanogenesis, whereas acidification inhibited hydrogenotrophic methanogenesis. In swine manure, TA-NaF inhibited s-amino acid catabolism to a larger extent than sulfate reduction. Conversely, acidification reduced sulfate reduction activity more than s-amino acid degradation. TA-NaF treatment had no significant effect on methanogenic community structure, which was surprising considering clear effects on isotope ratios of methane and carbon dioxide. Halophile sulfate reducers adapted well to TA-NaF treatment, but the community change also depended on temperature. The combined experimental work resulted in a proposed inhibition scheme for sulfur transformations and methanogenic pathways as affected by TA-NaF and acidification in swine manure and in other inocula.
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Affiliation(s)
- Frederik Rask Dalby
- Department of Engineering, Air Quality Engineering, Aarhus University, Aarhus N, Denmark
| | - Marcell Nikolausz
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Michael Jørgen Hansen
- Department of Engineering, Air Quality Engineering, Aarhus University, Aarhus N, Denmark
| | - Anders Feilberg
- Department of Engineering, Air Quality Engineering, Aarhus University, Aarhus N, Denmark
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Altaie AM, Saddik B, Alsaegh MA, Soliman SSM, Hamoudi R, Samaranayake LP. Prevalence of unculturable bacteria in the periapical abscess: A systematic review and meta-analysis. PLoS One 2021; 16:e0255485. [PMID: 34351963 PMCID: PMC8341601 DOI: 10.1371/journal.pone.0255485] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 07/18/2021] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVE To assess the prevalence of unculturable bacteria in periapical abscess, radicular cyst, and periapical granuloma. METHODS PubMed, Scopus, Science Direct, and Ovid databases were systematically searched from January 1990 to May 2020. All the included studies were cross-sectional design. The risk of bias was assessed using Joanna Briggs Institute check-list. Heterogeneity was described using meta-regression and mixed-effects model for lesion, country, and sequence technique moderators. Funnel plot and unweighted Egger's regression test were used to estimate the publication bias. Microbiome data on diversity, abundance, and frequency of unculturable bacteria in the periapical lesions were reviewed, analysed, and the principal component analysis (PCA) was performed. RESULTS A total of 13 studies out of 14,780, were selected for the final analysis. These studies focused on the prevalence of unculturable bacteria in periapical abscesses and related lesions. Approximately 13% (95% CI: 7-23%) of the cumulative number of bacteria derived from periapical abscesses was unculturable. Country moderator significantly (P = 0.05) affects the diversity summary proportion. While the pooled frequency of unculturable bacteria was 8%; 95% CI: 5, 14%, the estimate of the pooled abundance of unculturable bacteria was 5%; 95% CI: 2, 12% with a significant (P = 0.05) country moderator that affects the abundance summary proportion. Of the 62 unculturable bacteria, 35 were subjected to PCA and Peptostreptococcus sp. oral clone CK035 was the most abundant species in periapical abscesses. Hybridization techniques were found to be the most reliable molecular methods in detecting the abundance and frequency of unculturable bacteria. CONCLUSION The significant prevalence of unculturable bacteria in the periapical abscess, suggests that they are likely to play, a yet unknown, critical role in the pathogenesis and progression of the disease. Further research remains to be done to confirm their specific contributions in the virulence and disease progression.
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Affiliation(s)
- Alaa Muayad Altaie
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, UAE
- Department of Oral and Craniofacial Health Sciences, College of Dental Medicine, University of Sharjah, Sharjah, UAE
| | - Basema Saddik
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, UAE
- Department of Family and Community Medicine, College of Medicine, University of Sharjah, Sharjah, UAE
| | - Mohammed Amjed Alsaegh
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, UAE
- Department of Oral and Craniofacial Health Sciences, College of Dental Medicine, University of Sharjah, Sharjah, UAE
| | - Sameh S. M. Soliman
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, UAE
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, UAE
| | - Rifat Hamoudi
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, UAE
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, UAE
- Division of Surgery and Interventional Science, University College London, London, United Kingdom
- * E-mail: (RH); (LPS)
| | - Lakshman P. Samaranayake
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, UAE
- Department of Oral and Craniofacial Health Sciences, College of Dental Medicine, University of Sharjah, Sharjah, UAE
- * E-mail: (RH); (LPS)
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Hassa J, Klang J, Benndorf D, Pohl M, Hülsemann B, Mächtig T, Effenberger M, Pühler A, Schlüter A, Theuerl S. Indicative Marker Microbiome Structures Deduced from the Taxonomic Inventory of 67 Full-Scale Anaerobic Digesters of 49 Agricultural Biogas Plants. Microorganisms 2021; 9:1457. [PMID: 34361893 PMCID: PMC8307424 DOI: 10.3390/microorganisms9071457] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/01/2021] [Accepted: 07/03/2021] [Indexed: 11/24/2022] Open
Abstract
There are almost 9500 biogas plants in Germany, which are predominantly operated with energy crops and residues from livestock husbandry over the last two decades. In the future, biogas plants must be enabled to use a much broader range of input materials in a flexible and demand-oriented manner. Hence, the microbial communities will be exposed to frequently varying process conditions, while an overall stable process must be ensured. To accompany this transition, there is the need to better understand how biogas microbiomes respond to management measures and how these responses affect the process efficiency. Therefore, 67 microbiomes originating from 49 agricultural, full-scale biogas plants were taxonomically investigated by 16S rRNA gene amplicon sequencing. These microbiomes were separated into three distinct clusters and one group of outliers, which are characterized by a specific distribution of 253 indicative taxa and their relative abundances. These indicative taxa seem to be adapted to specific process conditions which result from a different biogas plant operation. Based on these results, it seems to be possible to deduce/assess the general process condition of a biogas digester based solely on the microbiome structure, in particular on the distribution of specific indicative taxa, and without knowing the corresponding operational and chemical process parameters. Perspectively, this could allow the development of detection systems and advanced process models considering the microbial diversity.
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Affiliation(s)
- Julia Hassa
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany; (J.H.); (A.P.); (A.S.)
- Department Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy, Max-Eyth-Allee 100, 14469 Potsdam, Germany;
| | - Johanna Klang
- Department Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy, Max-Eyth-Allee 100, 14469 Potsdam, Germany;
| | - Dirk Benndorf
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany;
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
- Microbiology, Anhalt University of Applied Sciences, Bernburger Straße 55, 06366 Köthen, Germany
| | - Marcel Pohl
- Biochemical Conversion Department, DBFZ Deutsches Biomasseforschungszentrum Gemeinnützige GmbH, Torgauer Straße 116, 04347 Leipzig, Germany;
| | - Benedikt Hülsemann
- The State Institute of Agricultural Engineering and Bioenergy, University of Hohenheim, Garbenstraße 9, 70599 Stuttgart, Germany;
| | - Torsten Mächtig
- Institute of Agricultural Engineering, Kiel University, Max-Eyth-Str. 6, 24118 Kiel, Germany;
| | - Mathias Effenberger
- Institute for Agricultural Engineering and Animal Husbandry, Bavarian State Research Center for Agriculture, Vöttinger Str. 36, 85354 Freising, Germany;
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany; (J.H.); (A.P.); (A.S.)
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany; (J.H.); (A.P.); (A.S.)
| | - Susanne Theuerl
- Department Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy, Max-Eyth-Allee 100, 14469 Potsdam, Germany;
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Dzofou Ngoumelah D, Harnisch F, Kretzschmar J. Benefits of Age-Improved Resistance of Mature Electroactive Biofilm Anodes in Anaerobic Digestion. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:8258-8266. [PMID: 34096274 DOI: 10.1021/acs.est.0c07320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Anaerobic digestion (AD) and microbial electrochemical technologies (MET) can be combined in manifold ways. Recent studies show negative influences of AD effluents on the performance of pre-grown Geobacter spp.-dominated biofilm anodes. In this study, it was investigated how such biofilm anodes are affected by AD effluents. Therefore, experiments using AD effluents in different concentrations (0-100%) in combination with biofilms of different ages were performed. Furthermore, the activity of methanogens was inhibited and minimized by application of 2-bromoethanesulfonate (2-BES) and microfiltration, respectively. Biofilms pre-grown for 5 weeks show higher resistance against AD effluents compared to biofilms pre-grown for only 3 weeks. Nevertheless, adaptation of biofilms to AD effluents was not successful. Biofilm activity in terms of coulombic efficiency and maximum current density (jmax) dropped by factor 32.2 ± 3.2 and 38.9 ± 8.4, respectively. The application of 2-BES and microfiltration had positive effects on the biofilm activity. The results support the assumption that methanogens or further compounds not studied here, for example, protozoans, which may have been inhibited or removed by 2-BES application or microfiltration, have an immediate influence on the stability of Geobacter spp.-dominated biofilms and may limit their practical application in AD environments.
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Affiliation(s)
- Daniel Dzofou Ngoumelah
- Biochemical Conversion Department, DBFZ Deutsches Biomasseforschungszentrum gemeinnützige GmbH (German Biomass Research Centre), Torgauer Straße 116, 04347 Leipzig, Germany
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Germany
| | - Falk Harnisch
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Germany
| | - Jörg Kretzschmar
- Biochemical Conversion Department, DBFZ Deutsches Biomasseforschungszentrum gemeinnützige GmbH (German Biomass Research Centre), Torgauer Straße 116, 04347 Leipzig, Germany
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11
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Quejigo JR, Korth B, Kuchenbuch A, Harnisch F. Redox Potential Heterogeneity in Fixed-Bed Electrodes Leads to Microbial Stratification and Inhomogeneous Performance. CHEMSUSCHEM 2021; 14:1155-1165. [PMID: 33387375 PMCID: PMC7986606 DOI: 10.1002/cssc.202002611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/28/2020] [Indexed: 06/12/2023]
Abstract
Bed electrodes provide high electrode area-to-volume ratios represent a promising configuration for transferring bioelectrochemical systems close to industrial applications. Nevertheless, the intrinsic electrical resistance leads to poor polarization behavior. Therefore, the distribution of Geobacter spp. and their electrochemical performance within exemplary fixed-bed electrodes are investigated. A minimally invasive sampling system allows characterization of granules from different spatial locations of bed electrodes. Cyclic voltammetry of single granules (n=63) demonstrates that the major share of electroactivity (134.3 mA L-1 ) is achieved by approximately 10 % of the bed volume, specifically that being close to the current collector. Nevertheless, analysis of the microbial community reveals that Geobacter spp. dominated all sampled granules. These findings clearly demonstrate the need for engineered bed electrodes to improve electron exchange between microorganisms and granules.
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Affiliation(s)
- Jose Rodrigo Quejigo
- Department of Environmental MicrobiologyHelmholtz Centre for Environmental Research GmbH – UFZPermoser Str. 1504318LeipzigGermany
| | - Benjamin Korth
- Department of Environmental MicrobiologyHelmholtz Centre for Environmental Research GmbH – UFZPermoser Str. 1504318LeipzigGermany
| | - Anne Kuchenbuch
- Department of Environmental MicrobiologyHelmholtz Centre for Environmental Research GmbH – UFZPermoser Str. 1504318LeipzigGermany
| | - Falk Harnisch
- Department of Environmental MicrobiologyHelmholtz Centre for Environmental Research GmbH – UFZPermoser Str. 1504318LeipzigGermany
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Saha S, Basak B, Hwang JH, Salama ES, Chatterjee PK, Jeon BH. Microbial Symbiosis: A Network towards Biomethanation. Trends Microbiol 2020; 28:968-984. [DOI: 10.1016/j.tim.2020.03.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/20/2020] [Accepted: 03/25/2020] [Indexed: 11/28/2022]
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13
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Singh A, Nylander JAA, Schnürer A, Bongcam-Rudloff E, Müller B. High-Throughput Sequencing and Unsupervised Analysis of Formyltetrahydrofolate Synthetase (FTHFS) Gene Amplicons to Estimate Acetogenic Community Structure. Front Microbiol 2020; 11:2066. [PMID: 32983047 PMCID: PMC7481360 DOI: 10.3389/fmicb.2020.02066] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 08/05/2020] [Indexed: 11/17/2022] Open
Abstract
The formyltetrahydrofolate synthetase (FTHFS) gene is a molecular marker of choice to study the diversity of acetogenic communities. However, current analyses are limited due to lack of a high-throughput sequencing approach for FTHFS gene amplicons and a dedicated bioinformatics pipeline for data analysis, including taxonomic annotation and visualization of the sequence data. In the present study, we combined the barcode approach for multiplexed sequencing with unsupervised data analysis to visualize acetogenic community structure. We used samples from a biogas digester to develop proof-of-principle for our combined approach. We successfully generated high-throughput sequence data for the partial FTHFS gene and performed unsupervised data analysis using the novel bioinformatics pipeline “AcetoScan” presented in this study, which resulted in taxonomically annotated OTUs, phylogenetic tree, abundance plots and diversity indices. The results demonstrated that high-throughput sequencing can be used to sequence the FTHFS amplicons from a pool of samples, while the analysis pipeline AcetoScan can be reliably used to process the raw sequence data and visualize acetogenic community structure. The method and analysis pipeline described in this paper can assist in the identification and quantification of known or potentially new acetogens. The AcetoScan pipeline is freely available at https://github.com/abhijeetsingh1704/AcetoScan.
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Affiliation(s)
- Abhijeet Singh
- Anaerobic Microbiology and Biotechnology Group, Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Johan A A Nylander
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,National Bioinformatics Infrastructure Sweden, SciLifeLab, Uppsala, Sweden
| | - Anna Schnürer
- Anaerobic Microbiology and Biotechnology Group, Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Erik Bongcam-Rudloff
- SLU-Global Bioinformatics Centre, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Bettina Müller
- Anaerobic Microbiology and Biotechnology Group, Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
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14
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Aho VTE, Tolonen T, Haverinen J, Jaakkola M, Paulin L, Auvinen P, Laine MM. Survey of microbes in industrial-scale second-generation bioethanol production for better process knowledge and operation. Appl Microbiol Biotechnol 2020; 104:8049-8064. [PMID: 32785760 DOI: 10.1007/s00253-020-10818-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 06/30/2020] [Accepted: 08/05/2020] [Indexed: 11/24/2022]
Abstract
The microbes present in bioethanol production processes have been previously studied in laboratory-scale experiments, but there is a lack of information on full-scale industrial processes. In this study, the microbial communities of three industrial bioethanol production processes were characterized using several methods. The samples originated from second-generation bioethanol plants that produce fuel ethanol from biowaste, food industry side streams, or sawdust. Amplicon sequencing targeting bacteria, archaea, and fungi was used to explore the microbes present in biofuel production and anaerobic digestion of wastewater and sludge. Biofilm-forming lactic acid bacteria and wild yeasts were identified in fermentation samples of a full-scale plant that uses biowaste as feedstock. During the 20-month monitoring period, the anaerobic digester adapted to the bioethanol process waste with a shift in methanogen profile indicating acclimatization to high concentrations of ammonia. Amplicon sequencing does not specifically target living microbes. The same is true for indirect parameters, such as low pH, metabolites, or genes of lactic acid bacteria. Since rapid identification of living microbes would be indispensable for process management, a commercial method was tested that detects them by measuring the rRNA of selected microbial groups. Small-scale testing indicated that the method gives results comparable with plate counts and microscopic counting, especially for bacterial quantification. The applicability of the method was verified in an industrial bioethanol plant, inspecting the clean-in-place process quality and detecting viability during yeast separation. The results supported it as a fast and promising tool for monitoring microbes throughout industrial bioethanol processes.
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Affiliation(s)
- Velma T E Aho
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Department of Neurology, Helsinki University Hospital, Helsinki, Finland
| | - Tiina Tolonen
- Unit of Measurement Technology, Kajaani University Consortium, University of Oulu, Kajaani, Finland
| | - Jasmiina Haverinen
- Unit of Measurement Technology, Kajaani University Consortium, University of Oulu, Kajaani, Finland
| | - Mari Jaakkola
- Unit of Measurement Technology, Kajaani University Consortium, University of Oulu, Kajaani, Finland
| | - Lars Paulin
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Petri Auvinen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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15
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Theuerl S, Klang J, Hülsemann B, Mächtig T, Hassa J. Microbiome Diversity and Community-Level Change Points within Manure-based small Biogas Plants. Microorganisms 2020; 8:microorganisms8081169. [PMID: 32752188 PMCID: PMC7464807 DOI: 10.3390/microorganisms8081169] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 07/21/2020] [Accepted: 07/30/2020] [Indexed: 12/21/2022] Open
Abstract
Efforts to integrate biogas plants into bioeconomy concepts will lead to an expansion of manure-based (small) biogas plants, while their operation is challenging due to critical characteristics of some types of livestock manure. For a better process understanding, in this study, three manure-based small biogas plants were investigated with emphasis on microbiome diversity. Due to varying digester types, feedstocks, and process conditions, 16S rRNA gene amplicon sequencing showed differences in the taxonomic composition. Dynamic variations of each investigated biogas plant microbiome over time were analyzed by terminal restriction fragment length polymorphism (TRFLP), whereby nonmetric multidimensional scaling (NMDS) revealed two well-running systems, one of them with a high share of chicken manure, and one unstable system. By using Threshold Indicator Taxa Analysis (TITAN), community-level change points at ammonium and ammonia concentrations of 2.25 g L-1 and 193 mg L-1 or volatile fatty acid concentrations of 0.75 g L-1were reliably identified which are lower than the commonly reported thresholds for critical process stages based on chemical parameters. Although a change in the microbiome structure does not necessarily indicate an upcoming critical process stage, the recorded community-level change points might be a first indication to carefully observe the process.
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Affiliation(s)
- Susanne Theuerl
- Department Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy, Max-Eyth-Allee 100, 14469 Potsdam, Germany; (J.K.); or (J.H.)
- Correspondence: ; Tel.: +49-331-5699-900
| | - Johanna Klang
- Department Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy, Max-Eyth-Allee 100, 14469 Potsdam, Germany; (J.K.); or (J.H.)
| | - Benedikt Hülsemann
- University of Hohenheim, The State Institute of Agricultural Engineering and Bioenergy, 70599 Stuttgart, Germany;
| | - Torsten Mächtig
- Kiel University, Institute of Agricultural Engineering, 24098 Kiel, Germany;
| | - Julia Hassa
- Department Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy, Max-Eyth-Allee 100, 14469 Potsdam, Germany; (J.K.); or (J.H.)
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld University, 33615 Bielefeld, Germany
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16
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De Vrieze J. The next frontier of the anaerobic digestion microbiome: From ecology to process control. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2020; 3:100032. [PMID: 36159602 PMCID: PMC9488066 DOI: 10.1016/j.ese.2020.100032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/29/2020] [Accepted: 05/05/2020] [Indexed: 05/11/2023]
Abstract
The anaerobic digestion process has been one of the key processes for renewable energy recovery from organic waste streams for over a century. The anaerobic digestion microbiome is, through the continuous development of novel techniques, evolving from a black box to a well-defined consortium, but we are not there yet. In this perspective, I provide my view on the current status and challenges of the anaerobic digestion microbiome, as well as the opportunities and solutions to exploit it. I consider identification and fingerprinting of the anaerobic digestion microbiome as complementary tools to monitor the anaerobic digestion microbiome. However, data availability, method-inherent biases and correct taxa identification hamper the accuracy and reproducibility of anaerobic digestion microbiome characterization. Standardisation of microbiome research in anaerobic digestion and other engineered systems will be essential in the coming decades, for which I proposed some targeted solutions. These will bring anaerobic digestion from a single-purpose energy-recovery technology to a versatile process for integrated resource recovery. It is my opinion that the exploitation of the microbiome will be a driver of innovation, and that it has a key role to play in the bio-based economy of the decades to come.
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17
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De Vrieze J, De Mulder T, Matassa S, Zhou J, Angenent LT, Boon N, Verstraete W. Stochasticity in microbiology: managing unpredictability to reach the Sustainable Development Goals. Microb Biotechnol 2020; 13:829-843. [PMID: 32311222 PMCID: PMC7264747 DOI: 10.1111/1751-7915.13575] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/04/2020] [Accepted: 03/25/2020] [Indexed: 01/06/2023] Open
Abstract
Pure (single) cultures of microorganisms and mixed microbial communities (microbiomes) have been important for centuries in providing renewable energy, clean water and food products to human society and will continue to play a crucial role to pursue the Sustainable Development Goals. To use microorganisms effectively, microbial engineered processes require adequate control. Microbial communities are shaped by manageable deterministic processes, but also by stochastic processes, which can promote unforeseeable variations and adaptations. Here, we highlight the impact of stochasticity in single culture and microbiome engineering. First, we discuss the concepts and mechanisms of stochasticity in relation to microbial ecology of single cultures and microbiomes. Second, we discuss the consequences of stochasticity in relation to process performance and human health, which are reflected in key disadvantages and important opportunities. Third, we propose a suitable decision tool to deal with stochasticity in which monitoring of stochasticity and setting the boundaries of stochasticity by regulators are central aspects. Stochasticity may give rise to some risks, such as the presence of pathogens in microbiomes. We argue here that by taking the necessary precautions and through clever monitoring and interpretation, these risks can be mitigated.
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Affiliation(s)
- Jo De Vrieze
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000, Gent, Belgium
| | | | - Silvio Matassa
- Department of Civil, Architectural and Environmental Engineering, University of Naples Federico II, via Claudio 21, 80125, Naples, Italy
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Largus T Angenent
- Center for Applied Geosciences, University of Tübingen, Tübingen, Germany
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000, Gent, Belgium
| | - Willy Verstraete
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000, Gent, Belgium
- Avecom NV, Industrieweg 122P, Wondelgem, 9032, Belgium
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18
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Genetic and Metabolic Diversity of Soil Microbiome in Response to Exogenous Organic Matter Amendments. AGRONOMY-BASEL 2020. [DOI: 10.3390/agronomy10040546] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Loss of organic matter content of cultivated soils is observed in many regions of Europe. The possibility of using organic waste as a soil additive that enriches the soil with organic matter and essential components is important in soil quality protection and waste management. This research concerned the influence of six organic wastes—two industrial composts, three digestates and meat bone meal—on soil microbial properties. The study of functional microbial diversity concerns the determination of the catabolic capacity of bacterial, fungal and anaerobic communities in relation to carbon substrates in metabolic profiling plates (Biolog® ECO, FF, AN (Biolog Inc., Hayward, CA, USA)). The assessment of genetic diversity was made on the basis of analysis of the restriction profile of ammonia-oxidizing archaea. Additionally, soil dehydrogenases activity was determined. The research showed that the type of organic waste used had an influence on the microbiological parameters. The application of exogenous organic matter caused increases in functional and genetic microbial diversity. The nature of the noted changes was short term and periodic. The values of the microbiological parameters in soils with organic waste were similar to those of the control samples. This indicates an improved microbiological balance and stability of the soil environment after the application of exogenous organic matter.
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19
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Ali S, Saldias S, Weerasuriya N, Delaney K, Kandasamy S, Lazarovits G. Corn microbial diversity and its relationship to yield. Can J Microbiol 2020; 66:457-473. [PMID: 32155347 DOI: 10.1139/cjm-2020-0002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
This study aimed to identify possible relationships between corn (Zea mays L.) productivity and its endosphere microbial community. Any insights would be used to develop testable hypotheses at the farm level. Sap was collected from 14 fields in 2014 and 10 fields in 2017, with a yield range of 10.1 to 21.7 tonnes per hectare (t/ha). The microbial sap communities were analyzed using terminal restriction fragment length polymorphism (TRFLP) and identified using an internal pure culture reference database and BLAST. This technique is rapid and inexpensive and is suitable for use at the grower level. Diversity, richness, and normalized abundances of each bacterial population in corn sap samples were evaluated to link the microbiome of a specific field to its yield. A negative trend was observed (r = -0.60), with higher-yielding fields having lower terminal restriction fragment (TRF) richness. A partial least square regression analysis of TRF intensity and binary data from 2014 identified 10 TRFs (bacterial genera) that positively, or negatively, correlated with corn yields, when either absent or present at certain levels or ratios. Using these observations, a model was developed that accommodated criteria for each of the 10 microbes and assigned a score for each field out of 10. Data collected in 2014 showed that sites with higher model scores were highly correlated with larger yields (r = 0.83). This correlation was also seen when the 2017 data set was used (r = 0.87). We were able to conclude that a positive significant effect was seen with the model score and yield (adjusted R2 = 0.67, F[1,22] = 46.7, p < 0.001) when combining 2014 and 2017 data. The results of this study are being expanded to identify the key microbes in the corn sap community that potentially impact corn yield, regardless of corn variety, geographic factors, or edaphic factors.
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Affiliation(s)
- Shimaila Ali
- A&L Biologicals, Agroecological Research Services Centre, 2136 Jetstream Road, London, ON N5V 3P5, Canada
| | - Soledad Saldias
- A&L Biologicals, Agroecological Research Services Centre, 2136 Jetstream Road, London, ON N5V 3P5, Canada
| | - Nimalka Weerasuriya
- A&L Biologicals, Agroecological Research Services Centre, 2136 Jetstream Road, London, ON N5V 3P5, Canada.,Department of Biology, University of Western Ontario, 1151 Richmond Street, London, ON N6A 3K7, Canada
| | - Kristen Delaney
- A&L Biologicals, Agroecological Research Services Centre, 2136 Jetstream Road, London, ON N5V 3P5, Canada
| | - Saveetha Kandasamy
- A&L Biologicals, Agroecological Research Services Centre, 2136 Jetstream Road, London, ON N5V 3P5, Canada
| | - George Lazarovits
- A&L Biologicals, Agroecological Research Services Centre, 2136 Jetstream Road, London, ON N5V 3P5, Canada.,Department of Biology, University of Western Ontario, 1151 Richmond Street, London, ON N6A 3K7, Canada
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20
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Juottonen H. Disentangling the effects of methanogen community and environment on peatland greenhouse gas production by a reciprocal transplant experiment. Funct Ecol 2020. [DOI: 10.1111/1365-2435.13536] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Heli Juottonen
- Department of Biosciences, General Microbiology University of Helsinki Helsinki Finland
- Natural Resources Institute Finland Helsinki Finland
- Department of Biological and Environmental Sciences University of Jyväskylä Jyväskylä Finland
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21
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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: 0.8] [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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22
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Abstract
The microbiome residing in anaerobic digesters drives the anaerobic digestion (AD) process to convert various feedstocks to biogas as a renewable source of energy. This microbiome has been investigated in numerous studies in the last century. The early studies used cultivation-based methods and analysis to identify the four guilds (or functional groups) of microorganisms. Molecular biology techniques overcame the limitations of cultivation-based methods and allowed the identification of unculturable microorganisms, revealing the high diversity of microorganisms involved in AD. In the past decade, omics technologies, including metataxonomics, metagenomics, metatranscriptomics, metaproteomics, and metametabolomics, have been or start to be used in comprehensive analysis and studies of biogas-producing microbiomes. In this chapter, we reviewed the utilities and limitations of these analysis methods, techniques, and technologies when they were used in studies of biogas-producing microbiomes, as well as the new information on diversity, composition, metabolism, and syntrophic interactions of biogas-producing microbiomes. We also discussed the current knowledge gaps and the research needed to further improve AD efficiency and stability.
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23
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Nexus between the microbial diversity level and the stress tolerance within the biogas process. Anaerobe 2019; 56:8-16. [DOI: 10.1016/j.anaerobe.2019.01.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 12/19/2018] [Accepted: 01/05/2019] [Indexed: 11/21/2022]
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24
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Schmidt J, Krohn S, Buenger L, Zeller K, Schneider H, Treuheit M, Kaiser T, Ziebolz D, Berg T, Haak R. Molecular characterization of intact cell-derived and cell-free bacterial DNA from carious dentine samples. J Microbiol Methods 2019; 158:33-43. [DOI: 10.1016/j.mimet.2019.01.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 01/17/2019] [Accepted: 01/18/2019] [Indexed: 01/22/2023]
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25
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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: 9.0] [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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