1
|
Doloman A, Besteman MS, Sanders MG, Sousa DZ. Methanogenic partner influences cell aggregation and signalling of Syntrophobacterium fumaroxidans. Appl Microbiol Biotechnol 2024; 108:127. [PMID: 38229305 DOI: 10.1007/s00253-023-12955-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/15/2023] [Accepted: 12/01/2023] [Indexed: 01/18/2024]
Abstract
For several decades, the formation of microbial self-aggregates, known as granules, has been extensively documented in the context of anaerobic digestion. However, current understanding of the underlying microbial-associated mechanisms responsible for this phenomenon remains limited. This study examined morphological and biochemical changes associated with cell aggregation in model co-cultures of the syntrophic propionate oxidizing bacterium Syntrophobacterium fumaroxidans and hydrogenotrophic methanogens, Methanospirillum hungatei or Methanobacterium formicicum. Formerly, we observed that when syntrophs grow for long periods with methanogens, cultures tend to form aggregates visible to the eye. In this study, we maintained syntrophic co-cultures of S. fumaroxidans with either M. hungatei or M. formicicum for a year in a fed-batch growth mode to stimulate aggregation. Millimeter-scale aggregates were observed in both co-cultures within the first 5 months of cultivation. In addition, we detected quorum sensing molecules, specifically N-acyl homoserine lactones, in co-culture supernatants preceding the formation of macro-aggregates (with diameter of more than 20 μm). Comparative transcriptomics revealed higher expression of genes related to signal transduction, polysaccharide secretion and metal transporters in the late-aggregation state co-cultures, compared to the initial ones. This is the first study to report in detail both biochemical and physiological changes associated with the aggregate formation in syntrophic methanogenic co-cultures. KEYPOINTS: • Syntrophic co-cultures formed mm-scale aggregates within 5 months of fed-batch cultivation. • N-acyl homoserine lactones were detected during the formation of aggregates. • Aggregated co-cultures exhibited upregulated expression of adhesins- and polysaccharide-associated genes.
Collapse
Affiliation(s)
- Anna Doloman
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708, WE, Wageningen, The Netherlands.
| | - Maaike S Besteman
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708, WE, Wageningen, The Netherlands
| | - Mark G Sanders
- Laboratory of Food Chemistry, Wageningen University, Bornse Weilanden 9, 6708, WG, Wageningen, The Netherlands
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708, WE, Wageningen, The Netherlands
- Centre for Living Technologies, Eindhoven-Wageningen-Utrecht Alliance, Princetonlaan 6, 3584, CB, Utrecht, The Netherlands
| |
Collapse
|
2
|
Allaart MT, Korkontzelos C, Sousa DZ, Kleerebezem R. A novel experimental method to determine substrate uptake kinetics of gaseous substrates applied to the carbon monoxide-fermenting Clostridium autoethanogenum. Biotechnol Bioeng 2024; 121:1325-1335. [PMID: 38265153 DOI: 10.1002/bit.28652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 01/25/2024]
Abstract
Syngas fermentation has gained momentum over the last decades. The cost-efficient design of industrial-scale bioprocesses is highly dependent on quantitative microbial growth data. Kinetic and stoichiometric models for syngas-converting microbes exist, but accurate experimental validation of the derived parameters is lacking. Here, we describe a novel experimental approach for measuring substrate uptake kinetics of gas-fermenting microbes using the model microorganism Clostridium autoethanogenum. One-hour disturbances of a steady-state chemostat bioreactor with increased CO partial pressures (up to 1.2 bar) allowed for measurement of biomass-specific CO uptake- and CO2 production rates (q CO ${q}_{{CO}}$ ,q CO 2 ${q}_{{{CO}}_{2}}$ ) using off-gas analysis. At a pCO of 1.2 bar, aq CO ${q}_{{CO}}$ of -119 ± 1 mmol g-1 X h-1 was measured. This value is 1.8-3.5-fold higher than previously reported experimental and kinetic modeling results for syngas fermenters. Analysis of the catabolic flux distribution reveals a metabolic shift towards ethanol production at the expense of acetate at pCO ≥ $\ge $ 0.6 atm, likely to be mediated by acetate availability and cellular redox state. We characterized this metabolic shift as acetogenic overflow metabolism. These results provide key mechanistic understanding of the factors steering the product spectrum of CO fermentation in C. autoethanogenum and emphasize the importance of dedicated experimental validation of kinetic parameters.
Collapse
Affiliation(s)
| | | | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Robbert Kleerebezem
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| |
Collapse
|
3
|
Egas RA, Kurth JM, Boeren S, Sousa DZ, Welte CU, Sánchez-Andrea I. A novel mechanism for dissimilatory nitrate reduction to ammonium in Acididesulfobacillus acetoxydans. mSystems 2024; 9:e0096723. [PMID: 38323850 PMCID: PMC10949509 DOI: 10.1128/msystems.00967-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 12/25/2023] [Indexed: 02/08/2024] Open
Abstract
The biological route of nitrate reduction has important implications for the bioavailability of nitrogen within ecosystems. Nitrate reduction via nitrite, either to ammonium (ammonification) or to nitrous oxide or dinitrogen (denitrification), determines whether nitrogen is retained within the system or lost as a gas. The acidophilic sulfate-reducing bacterium (aSRB) Acididesulfobacillus acetoxydans can perform dissimilatory nitrate reduction to ammonium (DNRA). While encoding a Nar-type nitrate reductase, A. acetoxydans lacks recognized nitrite reductase genes. In this study, A. acetoxydans was cultivated under conditions conducive to DNRA. During cultivations, we monitored the production of potential nitrogen intermediates (nitrate, nitrite, nitric oxide, hydroxylamine, and ammonium). Resting cell experiments were performed with nitrate, nitrite, and hydroxylamine to confirm their reduction to ammonium, and formed intermediates were tracked. To identify the enzymes involved in DNRA, comparative transcriptomics and proteomics were performed with A. acetoxydans growing under nitrate- and sulfate-reducing conditions. Nitrite is likely reduced to ammonia by the previously undescribed nitrite reductase activity of the NADH-linked sulfite reductase AsrABC, or by a putatively ferredoxin-dependent homolog of the nitrite reductase NirA (DEACI_1836), or both. We identified enzymes and intermediates not previously associated with DNRA and nitrosative stress in aSRB. This increases our knowledge about the metabolism of this type of bacteria and helps the interpretation of (meta)genome data from various ecosystems on their DNRA potential and the nitrogen cycle.IMPORTANCENitrogen is crucial to any ecosystem, and its bioavailability depends on microbial nitrogen-transforming reactions. Over the recent years, various new nitrogen-transforming reactions and pathways have been identified, expanding our view on the nitrogen cycle and metabolic versatility. In this study, we elucidate a novel mechanism employed by Acididesulfobacillus acetoxydans, an acidophilic sulfate-reducing bacterium, to reduce nitrate to ammonium. This finding underscores the diverse physiological nature of dissimilatory reduction to ammonium (DNRA). A. acetoxydans was isolated from acid mine drainage, an extremely acidic environment where nitrogen metabolism is poorly studied. Our findings will contribute to understanding DNRA potential and variations in extremely acidic environments.
Collapse
Affiliation(s)
- Reinier A. Egas
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Julia M. Kurth
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Microcosm Earth Centre, Philipps-Universität Marburg & Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, The Netherlands
| | - Diana Z. Sousa
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, Utrecht, The Netherlands
| | - Cornelia U. Welte
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Irene Sánchez-Andrea
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Department of Environmental Sciences for Sustainability, IE University, Segovia, Spain
| |
Collapse
|
4
|
Doloman A, de Bruin S, van Loosdrecht MCM, Sousa DZ, Lin Y. Coupling extracellular glycan composition with metagenomic data in papermill and brewery anaerobic granular sludges. Water Res 2024; 252:121240. [PMID: 38330717 DOI: 10.1016/j.watres.2024.121240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/12/2024] [Accepted: 01/29/2024] [Indexed: 02/10/2024]
Abstract
Glycans are crucial for the structure and function of anaerobic granular sludge in wastewater treatment. Yet, there is limited knowledge regarding the microorganisms and biosynthesis pathways responsible for glycan production. In this study, we analysed samples from anaerobic granular sludges treating papermill and brewery wastewater, examining glycans composition and using metagenome-assembled genomes (MAGs) to explore potential biochemical pathways associated with their production. Uronic acids were the predominant constituents of the glycans in extracellular polymeric substances (EPS) produced by the anaerobic granular sludges, comprising up to 60 % of the total polysaccharide content. MAGs affiliated with Anaerolineacae, Methanobacteriaceae and Methanosaetaceae represented the majority of the microbial community (30-50 % of total reads per MAG). Based on the analysis of MAGs, it appears that Anaerolinea sp. and members of the Methanobacteria class are involved in the production of exopolysaccharides within the analysed granular sludges. These findings shed light on the functional roles of microorganisms in glycan production in industrial anaerobic wastewater treatment systems.
Collapse
Affiliation(s)
- Anna Doloman
- Laboratory of Microbiology, Wageningen University & Research, the Netherlands.
| | | | - Mark C M van Loosdrecht
- Department of Biotechnology, TU Delft, the Netherlands; Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Denmark
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, the Netherlands; Centre for Living Technologies, EWUU Alliance, the Netherlands
| | - Yuemei Lin
- Department of Biotechnology, TU Delft, the Netherlands
| |
Collapse
|
5
|
Friedeheim L, Boeren S, Sánchez-Andrea I, Stams AJM, Sousa DZ. Alcohol dehydrogenase system acts as the sole pathway for methanol oxidation in Desulfofundulus kuznetsovii strain TPOSR. Antonie Van Leeuwenhoek 2024; 117:47. [PMID: 38427176 PMCID: PMC10907483 DOI: 10.1007/s10482-024-01937-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 01/28/2024] [Indexed: 03/02/2024]
Abstract
Desulfofundulus kuznetsovii is a thermophilic, spore-forming sulphate-reducing bacterium in the family Peptococcaceae. In this study, we describe a newly isolated strain of D. kuznetsovii, strain TPOSR, and compare its metabolism to the type strain D. kuznetsovii 17T. Both strains grow on a large variety of alcohols, such as methanol, ethanol and propane-diols, coupled to the reduction of sulphate. Strain 17T metabolizes methanol via two routes, one involving a cobalt-dependent methyl transferase and the other using a cobalt-independent alcohol dehydrogenase. However, strain TPOSR, which shares 97% average nucleotide identity with D. kuznetsovii strain 17T, lacks several genes from the methyl transferase operon found in strain 17T. The gene encoding the catalytically active methyl transferase subunit B is missing, indicating that strain TPOSR utilizes the alcohol dehydrogenase pathway exclusively. Both strains grew with methanol during cobalt starvation, but growth was impaired. Strain 17T was more sensitive to cobalt deficiency, due to the repression of its methyl transferase system. Our findings shed light on the metabolic diversity of D. kuznetsovii and their metabolic differences of encoding one or two routes for the conversion of methanol.
Collapse
Affiliation(s)
- Lukas Friedeheim
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University and Research, Wageningen, The Netherlands
| | - Irene Sánchez-Andrea
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands.
| |
Collapse
|
6
|
Egas RA, Sahonero-Canavesi DX, Bale NJ, Koenen M, Yildiz Ç, Villanueva L, Sousa DZ, Sánchez-Andrea I. Acetic acid stress response of the acidophilic sulfate reducer Acididesulfobacillus acetoxydans. Environ Microbiol 2024; 26:e16565. [PMID: 38356112 DOI: 10.1111/1462-2920.16565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 12/12/2023] [Indexed: 02/16/2024]
Abstract
Acid mine drainage (AMD) waters are a severe environmental threat, due to their high metal content and low pH (pH <3). Current technologies treating AMD utilize neutrophilic sulfate-reducing microorganisms (SRMs), but acidophilic SRM could offer advantages. As AMDs are low in organics these processes require electron donor addition, which is often incompletely oxidized into organic acids (e.g., acetic acid). At low pH, acetic acid is undissociated and toxic to microorganisms. We investigated the stress response of the acetotrophic Acididesulfobacillus acetoxydans to acetic acid. A. acetoxydans was cultivated in bioreactors at pH 5.0 (optimum). For stress experiments, triplicate reactors were spiked until 7.5 mM of acetic acid and compared with (non-spiked) triplicate reactors for physiological, transcriptomic, and membrane lipid changes. After acetic acid spiking, the optical density initially dropped, followed by an adaptation phase during which growth resumed at a lower growth rate. Transcriptome analysis revealed a downregulation of genes involved in glutamate and aspartate synthesis following spiking. Membrane lipid analysis revealed a decrease in iso and anteiso fatty acid relative abundance; and an increase of acetyl-CoA as a fatty acid precursor. These adaptations allow A. acetoxydans to detoxify acetic acid, creating milder conditions for other microorganisms in AMD environments.
Collapse
Affiliation(s)
- Reinier A Egas
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Diana X Sahonero-Canavesi
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Texel, Den Burg, The Netherlands
| | - Nicole J Bale
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Texel, Den Burg, The Netherlands
| | - Michel Koenen
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Texel, Den Burg, The Netherlands
| | - Çağlar Yildiz
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Texel, Den Burg, The Netherlands
- Department of Earth Sciences, Utrecht University, Utrecht, The Netherlands
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, Utrecht, The Netherlands
| | - Irene Sánchez-Andrea
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Environmental Sciences and Sustainability Department, Science & Technology School, IE University, Segovia, Spain
| |
Collapse
|
7
|
Cantera S, Rodríguez E, Santaella Vecchini N, López JC, García-Encina PA, Sousa DZ, Muñoz R. Resilience and robustness of alphaproteobacterial methanotrophs upon methane feast-famine scenarios. Environ Res 2023; 239:117376. [PMID: 37832766 DOI: 10.1016/j.envres.2023.117376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/27/2023] [Accepted: 10/10/2023] [Indexed: 10/15/2023]
Abstract
Most of methane (CH4) emissions contain low CH4 concentrations and typically occur at irregular intervals, which hinders the implementation and performance of methane abatement processes. This study aimed at understanding the metabolic mechanisms that allow methane oxidizing bacteria (MOB) to survive for long periods of time under methane starvation. To this aim, we used an omics-approach and studied the diversity and metabolism of MOB and non-MOB in bioreactors exposed to low CH4 concentrations under feast-famine cycles of 5 days and supplied with nutrient-rich broth. The 16S rRNA and the pmoA transcripts revealed that the most abundant and active MOB during feast and famine conditions belonged to the alphaproteobacterial genus Methylocystis (91-65%). The closest Methylocystis species were M. parvus and M. echinoides. Nitrifiers and denitrifiers were the most representative non-MOB communities, which likely acted as detoxifiers of the system. During starvation periods, the induced activity of CH4 oxidation was not lost, with the particulate methane monooxygenase of alphaproteobacterial MOB playing a key role in energy production. The polyhydroxyalkanoate and nitrification metabolisms of MOB had also an important role during feast-famine cycles, maintaining cell viability when CH4 concentrations were negligible. This research shows that there is an emergence and resilience of conventional alphaproteobacterial MOB, being the genus Methylocystis a centrepiece in environments exposed to dilute and intermittent methane emissions. This knowledge can be applied to the operation of bioreactors subjected to the treatment of dilute and discontinuous emissions via controlled bioaugmentation.
Collapse
Affiliation(s)
- Sara Cantera
- Institute of Sustainable Processes, University of Valladolid, Dr. Mergelina s/n., Valladolid, 47011, Spain; Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708WE, Wageningen, the Netherlands.
| | - Elisa Rodríguez
- Institute of Sustainable Processes, University of Valladolid, Dr. Mergelina s/n., Valladolid, 47011, Spain; Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina s/n., Valladolid, 47011, Spain
| | - Nicolás Santaella Vecchini
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708WE, Wageningen, the Netherlands
| | - Juan Carlos López
- Institute of Sustainable Processes, University of Valladolid, Dr. Mergelina s/n., Valladolid, 47011, Spain; Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina s/n., Valladolid, 47011, Spain
| | - Pedro A García-Encina
- Institute of Sustainable Processes, University of Valladolid, Dr. Mergelina s/n., Valladolid, 47011, Spain; Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina s/n., Valladolid, 47011, Spain
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708WE, Wageningen, the Netherlands
| | - Raul Muñoz
- Institute of Sustainable Processes, University of Valladolid, Dr. Mergelina s/n., Valladolid, 47011, Spain; Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina s/n., Valladolid, 47011, Spain.
| |
Collapse
|
8
|
Olavarria K, Becker MV, Sousa DZ, van Loosdrecht MC, Wahl SA. Design and thermodynamic analysis of a pathway enabling anaerobic production of poly-3-hydroxybutyrate in Escherichia coli. Synth Syst Biotechnol 2023; 8:629-639. [PMID: 37823039 PMCID: PMC10562921 DOI: 10.1016/j.synbio.2023.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 09/14/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023] Open
Abstract
Utilizing anaerobic metabolisms for the production of biotechnologically relevant products presents potential advantages, such as increased yields and reduced energy dissipation. However, lower energy dissipation may indicate that certain reactions are operating closer to their thermodynamic equilibrium. While stoichiometric analyses and genetic modifications are frequently employed in metabolic engineering, the use of thermodynamic tools to evaluate the feasibility of planned interventions is less documented. In this study, we propose a novel metabolic engineering strategy to achieve an efficient anaerobic production of poly-(R)-3-hydroxybutyrate (PHB) in the model organism Escherichia coli. Our approach involves re-routing of two-thirds of the glycolytic flux through non-oxidative glycolysis and coupling PHB synthesis with NADH re-oxidation. We complemented our stoichiometric analysis with various thermodynamic approaches to assess the feasibility and the bottlenecks in the proposed engineered pathway. According to our calculations, the main thermodynamic bottleneck are the reactions catalyzed by the acetoacetyl-CoA β-ketothiolase (EC 2.3.1.9) and the acetoacetyl-CoA reductase (EC 1.1.1.36). Furthermore, we calculated thermodynamically consistent sets of kinetic parameters to determine the enzyme amounts required for sustaining the conversion fluxes. In the case of the engineered conversion route, the protein pool necessary to sustain the desired fluxes could account for 20% of the whole cell dry weight.
Collapse
Affiliation(s)
- Karel Olavarria
- Laboratory of Microbiology, Wageningen University and Research, Stippenenweg 4, 6708 WE, Wageningen, The Netherlands
- Centre for Living Technologies, Eindhoven-Wageningen-Utrecht Alliance, Princetonlaan 6, 3584 CB, Utrecht, The Netherlands
| | - Marco V. Becker
- Department of Biotechnology, Applied Sciences Faculty, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Diana Z. Sousa
- Laboratory of Microbiology, Wageningen University and Research, Stippenenweg 4, 6708 WE, Wageningen, The Netherlands
- Centre for Living Technologies, Eindhoven-Wageningen-Utrecht Alliance, Princetonlaan 6, 3584 CB, Utrecht, The Netherlands
| | - Mark C.M. van Loosdrecht
- Department of Biotechnology, Applied Sciences Faculty, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - S. Aljoscha Wahl
- Lehrstuhl für Bioverfahrenstechnik, Friedrich-Alexander-Universität, Paul-Gordan-Strasse 3, 91052, Erlangen, Germany
| |
Collapse
|
9
|
Diender M, Dykstra JC, Parera Olm I, Kengen SWM, Stams AJM, Sousa DZ. The role of ethanol oxidation during carboxydotrophic growth of Clostridium autoethanogenum. Microb Biotechnol 2023; 16:2082-2093. [PMID: 37814497 PMCID: PMC10616641 DOI: 10.1111/1751-7915.14338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 09/05/2023] [Indexed: 10/11/2023] Open
Abstract
The Wood-Ljungdahl pathway is an ancient metabolic route used by acetogenic carboxydotrophs to convert CO into acetate, and some cases ethanol. When produced, ethanol is generally seen as an end product of acetogenic metabolism, but here we show that it acts as an important intermediate and co-substrate during carboxydotrophic growth of Clostridium autoethanogenum. Depending on CO availability, C. autoethanogenum is able to rapidly switch between ethanol production and utilization, hereby optimizing its carboxydotrophic growth. The importance of the aldehyde ferredoxin:oxidoreductase (AOR) route for ethanol production in carboxydotrophic acetogens is known; however, the role of the bifunctional alcohol dehydrogenase AdhE (Ald-Adh) route in ethanol metabolism remains largely unclear. We show that the mutant strain C. autoethanogenum ∆adhE1a, lacking the Ald subunit of the main bifunctional aldehyde/alcohol dehydrogenase (AdhE, CAETHG_3747), has poor ethanol oxidation capabilities, with a negative impact on biomass yield. This indicates that the Adh-Ald route plays a major role in ethanol oxidation during carboxydotrophic growth, enabling subsequent energy conservation via substrate-level phosphorylation using acetate kinase. Subsequent chemostat experiments with C. autoethanogenum show that the wild type, in contrast to ∆adhE1a, is more resilient to sudden changes in CO supply and utilizes ethanol as a temporary storage for reduction equivalents and energy during CO-abundant conditions, reserving these 'stored assets' for more CO-limited conditions. This shows that the direction of the ethanol metabolism is very dynamic during carboxydotrophic acetogenesis and opens new insights in the central metabolism of C. autoethanogenum and similar acetogens.
Collapse
Affiliation(s)
- Martijn Diender
- Laboratory of MicrobiologyWageningen University & ResearchWageningenThe Netherlands
- Centre for Living TechnologiesEindhoven‐Wageningen‐Utrecht AllianceUtrechtThe Netherlands
| | - James C. Dykstra
- Laboratory of MicrobiologyWageningen University & ResearchWageningenThe Netherlands
| | - Ivette Parera Olm
- Laboratory of MicrobiologyWageningen University & ResearchWageningenThe Netherlands
- Centre for Living TechnologiesEindhoven‐Wageningen‐Utrecht AllianceUtrechtThe Netherlands
| | - Servé W. M. Kengen
- Laboratory of MicrobiologyWageningen University & ResearchWageningenThe Netherlands
| | - Alfons J. M. Stams
- Laboratory of MicrobiologyWageningen University & ResearchWageningenThe Netherlands
- Centre of Biological EngineeringUniversity of MinhoBragaPortugal
| | - Diana Z. Sousa
- Laboratory of MicrobiologyWageningen University & ResearchWageningenThe Netherlands
- Centre for Living TechnologiesEindhoven‐Wageningen‐Utrecht AllianceUtrechtThe Netherlands
| |
Collapse
|
10
|
Allaart MT, Fox BB, Nettersheim IHMS, Pabst M, Sousa DZ, Kleerebezem R. Physiological and stoichiometric characterization of ethanol-based chain elongation in the absence of short-chain carboxylic acids. Sci Rep 2023; 13:17370. [PMID: 37833311 PMCID: PMC10576071 DOI: 10.1038/s41598-023-43682-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
Hexanoate is a valuable chemical that can be produced by microorganisms that convert short-chain- to medium-chain carboxylic acids through a process called chain elongation. These microorganisms usually produce mixtures of butyrate and hexanoate from ethanol and acetate, but direct conversion of ethanol to hexanoate is theoretically possible. Steering microbial communities to ethanol-only elongation to hexanoate circumvents the need for acetate addition and simplifies product separation. The biological feasibility of ethanol elongation to hexanoate was validated in batch bioreactor experiments with a Clostridium kluyveri-dominated enrichment culture incubated with ethanol, acetate and butyrate in different ratios. Frequent liquid sampling combined with high-resolution off-gas measurements allowed to monitor metabolic behavior. In experiments with an initial ethanol-to-acetate ratio of 6:1, acetate depletion occurred after ± 35 h of fermentation, which triggered a metabolic shift to direct conversion of ethanol to hexanoate despite the availability of butyrate (± 40 mCmol L-1). When only ethanol and no external electron acceptor was supplied, stable ethanol to hexanoate conversion could be maintained until 60-90 mCmol L-1 of hexanoate was produced. After this, transient production of either acetate and butyrate or butyrate and hexanoate was observed, requiring a putative reversal of the Rnf complex. This was not observed before acetate depletion or in presence of low concentrations (40-60 mCmol L-1) of butyrate, suggesting a stabilizing or regulatory role of butyrate or butyrate-related catabolic intermediates. This study sheds light on previously unknown versatility of chain elongating microbes and provides new avenues for optimizing (waste) bioconversion for hexanoate production.
Collapse
Affiliation(s)
| | - Bartholomeus B Fox
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | | | - Martin Pabst
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Robbert Kleerebezem
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| |
Collapse
|
11
|
Chen LM, de Bruin S, Pronk M, Sousa DZ, van Loosdrecht MCM, Lin Y. Sialylation and Sulfation of Anionic Glycoconjugates Are Common in the Extracellular Polymeric Substances of Both Aerobic and Anaerobic Granular Sludges. Environ Sci Technol 2023; 57:13217-13225. [PMID: 37604486 PMCID: PMC10483923 DOI: 10.1021/acs.est.2c09586] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 06/14/2023] [Accepted: 08/07/2023] [Indexed: 08/23/2023]
Abstract
Anaerobic and aerobic granular sludge processes are widely applied in wastewater treatment. In these systems, microorganisms grow in dense aggregates due to the production of extracellular polymeric substances (EPS). This study investigates the sialylation and sulfation of anionic glyconconjugates in anaerobic and aerobic granular sludges collected from full-scale wastewater treatment processes. Size exclusion chromatography revealed a wide molecular weight distribution (3.5 to >5500 kDa) of the alkaline-extracted EPS. The high-molecular weight fraction (>5500 kDa), comprising 16.9-27.4% of EPS, was dominant with glycoconjugates. Mass spectrometry analysis and quantification assays identified nonulosonic acids (NulOs, e.g., bacterial sialic acids) and sulfated groups contributing to the negative charge in all EPS fractions. NulOs were predominantly present in the high-molecular weight fraction (47.2-84.3% of all detected NulOs), while sulfated glycoconjugates were distributed across the molecular weight fractions. Microorganisms, closely related to genera found in the granular sludge communities, contained genes responsible for NulO and sulfate group synthesis or transfer. The similar distribution patterns of sialylation and sulfation of the anionic glycoconjugates in the EPS samples indicate that these two glycoconjugate modifications commonly occur in the EPS of aerobic and anaerobic granular sludges.
Collapse
Affiliation(s)
- Le Min Chen
- Department
of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Stefan de Bruin
- Department
of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Mario Pronk
- Department
of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
- Royal
HaskoningDHV, Laan 1914
35, Amersfoort 3800 AL, The Netherlands
| | - Diana Z. Sousa
- Laboratory
of Microbiology, Wageningen University &
Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands
| | - Mark C. M. van Loosdrecht
- Department
of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Yuemei Lin
- Department
of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| |
Collapse
|
12
|
Parera Olm I, Sousa DZ. Upgrading dilute ethanol to odd-chain carboxylic acids by a synthetic co-culture of Anaerotignum neopropionicum and Clostridium kluyveri. Biotechnol Biofuels Bioprod 2023; 16:83. [PMID: 37194097 DOI: 10.1186/s13068-023-02336-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/03/2023] [Indexed: 05/18/2023]
Abstract
BACKGROUND Dilute ethanol streams generated during fermentation of biomass or syngas can be used as feedstocks for the production of higher value products. In this study, we describe a novel synthetic microbial co-culture that can effectively upgrade dilute ethanol streams to odd-chain carboxylic acids (OCCAs), specifically valerate and heptanoate. The co-culture consists of two strict anaerobic microorganisms: Anaerotignum neopropionicum, a propionigenic bacterium that ferments ethanol, and Clostridium kluyveri, well-known for its chain-elongating metabolism. In this co-culture, A. neopropionicum grows on ethanol and CO2 producing propionate and acetate, which are then utilised by C. kluyveri for chain elongation with ethanol as the electron donor. RESULTS A co-culture of A. neopropionicum and C. kluyveri was established in serum bottles with 50 mM ethanol, leading to the production of valerate (5.4 ± 0.1 mM) as main product of ethanol-driven chain elongation. In a continuous bioreactor supplied with 3.1 g ethanol L-1 d-1, the co-culture exhibited high ethanol conversion (96.6%) and produced 25% (mol/mol) valerate, with a steady-state concentration of 8.5 mM and a rate of 5.7 mmol L-1 d-1. In addition, up to 6.5 mM heptanoate was produced at a rate of 2.9 mmol L-1 d-1. Batch experiments were also conducted to study the individual growth of the two strains on ethanol. A. neopropionicum showed the highest growth rate when cultured with 50 mM ethanol (μmax = 0.103 ± 0.003 h-1) and tolerated ethanol concentrations of up to 300 mM. Cultivation experiments with C. kluyveri showed that propionate and acetate were used simultaneously for chain elongation. However, growth on propionate alone (50 mM and 100 mM) led to a 1.8-fold reduction in growth rate compared to growth on acetate. Our results also revealed sub-optimal substrate use by C. kluyveri during odd-chain elongation, where excessive ethanol was oxidised to acetate. CONCLUSIONS This study highlights the potential of synthetic co-cultivation in chain elongation processes to target the production of OCCAs. Furthermore, our findings shed light on to the metabolism of odd-chain elongation by C. kluyveri.
Collapse
Affiliation(s)
- Ivette Parera Olm
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands.
- Centre for Living Technologies, Eindhoven-Wageningen-Utrecht Alliance, Utrecht, The Netherlands.
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Centre for Living Technologies, Eindhoven-Wageningen-Utrecht Alliance, Utrecht, The Netherlands
| |
Collapse
|
13
|
Santaella NV, Sousa DZ, Stams AJM. Moorella caeni sp. nov., isolated from thermophilic anaerobic sludge from a methanol-fed reactor. Int J Syst Evol Microbiol 2023; 73. [PMID: 37234030 DOI: 10.1099/ijsem.0.005905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023] Open
Abstract
Strain AMPT has been previously suggested as a strain of the species Moorella thermoacetica Jiang et al. 2009 (based on the high 16S rRNA gene identity, 98.3 %). However, genome-based phylogenetic analysis of strain AMPT reveals that this bacterium is in fact a novel species of the genus Moorella. Genome relatedness indices between strain AMPT and Moorella thermoacetica DSM 521T were below the minimum threshold values required to consider them members of the same species (digital DNA-DNA hybridization, 52.2 % (<70%); average nucleotide identity, 93.2 % (<95%)). Based on phylogenetic and phenotypic results we recommend that strain AMPT (DSM 21394T=JCM 35360T) should be classified as representing new species, for which we propose the name Moorella caeni sp. nov.
Collapse
Affiliation(s)
- Nicolás Vecchini Santaella
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708WE Wageningen, Netherlands
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708WE Wageningen, Netherlands
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708WE Wageningen, Netherlands
| |
Collapse
|
14
|
Cantera S, Di Benedetto F, Tumulero BF, Sousa DZ. Microbial conversion of carbon dioxide and hydrogen into the fine chemicals hydroxyectoine and ectoine. Bioresour Technol 2023; 374:128753. [PMID: 36801441 DOI: 10.1016/j.biortech.2023.128753] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/11/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
This study explores a novel conversion of CO2 into the chemicals hydroxyectoine and ectoine, which are compounds with high retail values in the pharmaceutical industry. Firstly, 11 species of microbes able to use CO2 and H2 and that have the genes for ectoines synthesis (ectABCD) were identified through literature search and genomic mining. Laboratory tests were then conducted to ascertain the capacity of these microbes to produce ectoines from CO2. Results showed that the most promising bacteria for CO2 to ectoines bioconversion areHydrogenovibrio marinus, Rhodococcus opacus, and Hydrogenibacillus schlegelii.Upon salinity and H2/CO2/O2 ratio optimization,H. marinus accumulated 85 mg of ectoine g biomass-1. Interestingly, R.opacusand H. schlegelii mainly produced hydroxyectoine (53 and 62 mg g biomass-1), which has a higher commercial value. Overall, these results constitute the first proof of a novel valorization platform of CO2 and lay the foundation for a new economic niche aimed at CO2 recircularization into pharmaceuticals.
Collapse
Affiliation(s)
- Sara Cantera
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, the Netherlands.
| | - Francesca Di Benedetto
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, the Netherlands
| | - Ben F Tumulero
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, the Netherlands
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, the Netherlands
| |
Collapse
|
15
|
Allaart MT, Diender M, Sousa DZ, Kleerebezem R. Overflow metabolism at the thermodynamic limit of life: How carboxydotrophic acetogens mitigate carbon monoxide toxicity. Microb Biotechnol 2023; 16:697-705. [PMID: 36632026 PMCID: PMC10034630 DOI: 10.1111/1751-7915.14212] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/29/2022] [Accepted: 01/01/2023] [Indexed: 01/13/2023] Open
Abstract
Carboxydotrophic metabolism is gaining interest due to its applications in gas fermentation technology, enabling the conversion of carbon monoxide to fuels and commodities. Acetogenic carboxydotrophs play a central role in current gas fermentation processes. In contrast to other energy-rich microbial substrates, CO is highly toxic, which makes it a challenging substrate to utilize. Instantaneous scavenging of CO upon entering the cell is required to mitigate its toxicity. Experiments conducted with Clostridium autoethanogenum at different biomass-specific growth rates show that elevated ethanol production occurs at increasing growth rates. The increased allocation of electrons towards ethanol at higher growth rates strongly suggests that C. autoethanogenum employs a form of overflow metabolism to cope with high dissolved CO concentrations. We argue that this overflow branch enables acetogens to efficiently use CO at highly variable substrate influxes by increasing the conversion rate almost instantaneously when required to remove toxic substrate and promote growth. In this perspective, we will address the case study of C. autoethanogenum grown solely on CO and syngas mixtures to assess how it employs acetate reduction to ethanol as a form of overflow metabolism.
Collapse
Affiliation(s)
| | - Martijn Diender
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Robbert Kleerebezem
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| |
Collapse
|
16
|
Dykstra JC, van Oort J, Yazdi AT, Vossen E, Patinios C, van der Oost J, Sousa DZ, Kengen SWM. Metabolic engineering of Clostridium autoethanogenum for ethyl acetate production from CO. Microb Cell Fact 2022; 21:243. [DOI: 10.1186/s12934-022-01964-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 10/18/2022] [Indexed: 11/25/2022] Open
Abstract
Abstract
Background
Ethyl acetate is a bulk chemical traditionally produced via energy intensive chemical esterification. Microbial production of this compound offers promise as a more sustainable alternative process. So far, efforts have focused on using sugar-based feedstocks for microbial ester production, but extension to one-carbon substrates, such as CO and CO2/H2, is desirable. Acetogens present a promising microbial platform for the production of ethyl esters from these one-carbon substrates.
Results
We engineered the acetogen C. autoethanogenum to produce ethyl acetate from CO by heterologous expression of an alcohol acetyltransferase (AAT), which catalyzes the formation of ethyl acetate from acetyl-CoA and ethanol. Two AATs, Eat1 from Kluyveromyces marxianus and Atf1 from Saccharomyces cerevisiae, were expressed in C. autoethanogenum. Strains expressing Atf1 produced up to 0.2 mM ethyl acetate. Ethyl acetate production was barely detectable (< 0.01 mM) for strains expressing Eat1. Supplementation of ethanol was investigated as potential boost for ethyl acetate production but resulted only in a 1.5-fold increase (0.3 mM ethyl acetate). Besides ethyl acetate, C. autoethanogenum expressing Atf1 could produce 4.5 mM of butyl acetate when 20 mM butanol was supplemented to the growth medium.
Conclusions
This work offers for the first time a proof-of-principle that autotrophic short chain ester production from C1-carbon feedstocks is possible and offers leads on how this approach can be optimized in the future.
Collapse
|
17
|
de Bruin S, Vasquez-Cardenas D, Sarbu SM, Meysman FJR, Sousa DZ, van Loosdrecht MCM, Lin Y. Sulfated glycosaminoglycan-like polymers are present in an acidophilic biofilm from a sulfidic cave. Sci Total Environ 2022; 829:154472. [PMID: 35276175 DOI: 10.1016/j.scitotenv.2022.154472] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/21/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Sulfated glycosaminoglycans (sGAG) are negatively charged extracellular polymeric substances that occur in biofilms from various environments. Yet, it remains unclear whether these polymers are acquired from the external environment or produced by microbes in the biofilm. To resolve this, we analyzed the presence of sGAGs in samples of an acidophilic biofilm collected from Sulfur Cave in Puturosu Mountain (Romania), an environment that is largely inaccessible to contamination. A maximum of 55.16 ± 2.06 μg sGAG-like polymers were recovered per mg of EPS. Enzymatic treatment with chondroitinase ABC resulted in a decrease of the mass of these polymers, suggesting the structure of the recovered sGAG is similar to chondroitin. Subsequent FT-IR analysis of these polymers revealed absorbance bands at 1230 cm-1, 1167 cm-1 and 900 cm-1, indicating a possible presence of polysaccharides and sulfate. Analysis of genomic sequences closely related to those predominant in the acidophilic biofilm, contained genes coding for sulfotransferase (an enzyme needed for the production of sGAG), which supports the hypothesis of microbial synthesis of sGAGs within the biofilm.
Collapse
Affiliation(s)
- S de Bruin
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands.
| | - D Vasquez-Cardenas
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands; Department of Biology, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - S M Sarbu
- Department of Biological Sciences, California State University, 400 West 1st St, Chico, CA 95926-515, USA; Emil G. Racoviță Institute, Babeș-Bolyai University, Clinicilor 5-7, 400006 Cluj-Napoca, Romania
| | - F J R Meysman
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands; Department of Biology, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - D Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands
| | - M C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Y Lin
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| |
Collapse
|
18
|
Cantera S, Sousa DZ, Sánchez-Andrea I. Enhanced ectoines production by carbon dioxide capture: A step further towards circular economy. J CO2 UTIL 2022. [DOI: 10.1016/j.jcou.2022.102009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
|
19
|
Benito-Vaquerizo S, Parera Olm I, de Vroet T, Schaap PJ, Sousa DZ, Martins Dos Santos VAP, Suarez-Diez M. Genome-scale metabolic modelling enables deciphering ethanol metabolism via the acrylate pathway in the propionate-producer Anaerotignum neopropionicum. Microb Cell Fact 2022; 21:116. [PMID: 35710409 PMCID: PMC9205015 DOI: 10.1186/s12934-022-01841-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/26/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Microbial production of propionate from diluted streams of ethanol (e.g., deriving from syngas fermentation) is a sustainable alternative to the petrochemical production route. Yet, few ethanol-fermenting propionigenic bacteria are known, and understanding of their metabolism is limited. Anaerotignum neopropionicum is a propionate-producing bacterium that uses the acrylate pathway to ferment ethanol and CO2 to propionate and acetate. In this work, we used computational and experimental methods to study the metabolism of A. neopropionicum and, in particular, the pathway for conversion of ethanol into propionate. RESULTS Our work describes iANEO_SB607, the first genome-scale metabolic model (GEM) of A. neopropionicum. The model was built combining the use of automatic tools with an extensive manual curation process, and it was validated with experimental data from this and published studies. The model predicted growth of A. neopropionicum on ethanol, lactate, sugars and amino acids, matching observed phenotypes. In addition, the model was used to implement a dynamic flux balance analysis (dFBA) approach that accurately predicted the fermentation profile of A. neopropionicum during batch growth on ethanol. A systematic analysis of the metabolism of A. neopropionicum combined with model simulations shed light into the mechanism of ethanol fermentation via the acrylate pathway, and revealed the presence of the electron-transferring complexes NADH-dependent reduced ferredoxin:NADP+ oxidoreductase (Nfn) and acryloyl-CoA reductase-EtfAB, identified for the first time in this bacterium. CONCLUSIONS The realisation of the GEM iANEO_SB607 is a stepping stone towards the understanding of the metabolism of the propionate-producer A. neopropionicum. With it, we have gained insight into the functioning of the acrylate pathway and energetic aspects of the cell, with focus on the fermentation of ethanol. Overall, this study provides a basis to further exploit the potential of propionigenic bacteria as microbial cell factories.
Collapse
Affiliation(s)
- Sara Benito-Vaquerizo
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, Wageningen, 6708WE, The Netherlands
| | - Ivette Parera Olm
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, Wageningen, 6708WE, The Netherlands
| | - Thijs de Vroet
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, Wageningen, 6708WE, The Netherlands
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, Wageningen, 6708WE, The Netherlands
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, Wageningen, 6708WE, The Netherlands.,Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, Vening Meinesz building C, Princetonlaan 6, Utrecht, 3584 CB, The Netherlands
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, Wageningen, 6708WE, The Netherlands.,Bioprocess Engineering, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, Wageningen, 6708WE, The Netherlands.
| |
Collapse
|
20
|
Holohan BC, Duarte MS, Szabo-Corbacho MA, Cavaleiro AJ, Salvador AF, Pereira MA, Ziels RM, Frijters CTMJ, Pacheco-Ruiz S, Carballa M, Sousa DZ, Stams AJM, O'Flaherty V, van Lier JB, Alves MM. Principles, Advances, and Perspectives of Anaerobic Digestion of Lipids. Environ Sci Technol 2022; 56:4749-4775. [PMID: 35357187 DOI: 10.1021/acs.est.1c08722] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Several problems associated with the presence of lipids in wastewater treatment plants are usually overcome by removing them ahead of the biological treatment. However, because of their high energy content, waste lipids are interesting yet challenging pollutants in anaerobic wastewater treatment and codigestion processes. The maximal amount of waste lipids that can be sustainably accommodated, and effectively converted to methane in anaerobic reactors, is limited by several problems including adsorption, sludge flotation, washout, and inhibition. These difficulties can be circumvented by appropriate feeding, mixing, and solids separation strategies, provided by suitable reactor technology and operation. In recent years, membrane bioreactors and flotation-based bioreactors have been developed to treat lipid-rich wastewater. In parallel, the increasing knowledge on the diversity of complex microbial communities in anaerobic sludge, and on interspecies microbial interactions, contributed to extend the knowledge and to understand more precisely the limits and constraints influencing the anaerobic biodegradation of lipids in anaerobic reactors. This critical review discusses the most important principles underpinning the degradation process and recent key discoveries and outlines the current knowledge coupling fundamental and applied aspects. A critical assessment of knowledge gaps in the field is also presented by integrating sectorial perspectives of academic researchers and of prominent developers of anaerobic technology.
Collapse
Affiliation(s)
- B Conall Holohan
- Microbial Ecology Laboratory, Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland, Galway H91 TK33, Ireland
- NVP Energy Ltd., IDA Technology and Business Park, Mervue, Galway H91 TK33, Ireland
| | - M Salomé Duarte
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- LABBELS - Associate Laboratory, 4710-057 Braga, Guimarães, Portugal
| | - M Alejandra Szabo-Corbacho
- Department of Environmental Engineering and Water Technology, IHE Delft Institute for Water Education, Westvest 7, 2611 AX Delft, The Netherlands
| | - Ana J Cavaleiro
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- LABBELS - Associate Laboratory, 4710-057 Braga, Guimarães, Portugal
| | - Andreia F Salvador
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- LABBELS - Associate Laboratory, 4710-057 Braga, Guimarães, Portugal
| | - M Alcina Pereira
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- LABBELS - Associate Laboratory, 4710-057 Braga, Guimarães, Portugal
| | - Ryan M Ziels
- Department of Civil Engineering, The University of British Columbia, 6250 Applied Science Lane, Vancouver, BC V6T 1Z 4, Canada
| | | | - Santiago Pacheco-Ruiz
- Biothane, Veolia Water Technologies, Tanthofdreef 21, 2623 EW Delft, The Netherlands
| | - Marta Carballa
- CRETUS, Department of Chemical Engineering, Universidad de Santiago de Compostela, 15705 Santiago de Compostela, Spain
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE, Wageningen, The Netherlands
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE, Wageningen, The Netherlands
| | - Vincent O'Flaherty
- Microbial Ecology Laboratory, Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland, Galway H91 TK33, Ireland
| | - Jules B van Lier
- Department of Environmental Engineering and Water Technology, IHE Delft Institute for Water Education, Westvest 7, 2611 AX Delft, The Netherlands
- Section Sanitary Engineering, CEG Faculty, Delft University of Technology, 2628 CN, Delft, The Netherlands
| | - M Madalena Alves
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- LABBELS - Associate Laboratory, 4710-057 Braga, Guimarães, Portugal
| |
Collapse
|
21
|
Sánchez-Andrea I, van der Graaf CM, Hornung B, Bale NJ, Jarzembowska M, Sousa DZ, Rijpstra WIC, Sinninghe Damsté JS, Stams AJM. Acetate Degradation at Low pH by the Moderately Acidophilic Sulfate Reducer Acididesulfobacillus acetoxydans gen. nov. sp. nov. Front Microbiol 2022; 13:816605. [PMID: 35391737 PMCID: PMC8982180 DOI: 10.3389/fmicb.2022.816605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 01/31/2022] [Indexed: 11/19/2022] Open
Abstract
In acid drainage environments, biosulfidogenesis by sulfate-reducing bacteria (SRB) attenuates the extreme conditions by enabling the precipitation of metals as their sulfides, and the neutralization of acidity through proton consumption. So far, only a handful of moderately acidophilic SRB species have been described, most of which are merely acidotolerant. Here, a novel species within a novel genus of moderately acidophilic SRB is described, Acididesulfobacillus acetoxydans gen. nov. sp. nov. strain INE, able to grow at pH 3.8. Bioreactor studies with strain INE at optimum (5.0) and low (3.9) pH for growth showed that strain INE alkalinized its environment, and that this was more pronounced at lower pH. These studies also showed the capacity of strain INE to completely oxidize organic acids to CO2, which is uncommon among acidophilic SRB. Since organic acids are mainly in their protonated form at low pH, which increases their toxicity, their complete oxidation may be an acid stress resistance mechanism. Comparative proteogenomic and membrane lipid analysis further indicated that the presence of saturated ether-bound lipids in the membrane, and their relative increase at lower pH, was a protection mechanism against acid stress. Interestingly, other canonical acid stress resistance mechanisms, such as a Donnan potential and increased active charge transport, did not appear to be active.
Collapse
Affiliation(s)
- Irene Sánchez-Andrea
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
- *Correspondence: Irene Sánchez-Andrea,
| | | | - Bastian Hornung
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands
| | - Nicole J. Bale
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
| | - Monika Jarzembowska
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Diana Z. Sousa
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - W. Irene C. Rijpstra
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
| | - Alfons J. M. Stams
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| |
Collapse
|
22
|
Allaart MT, Stouten GR, Sousa DZ, Kleerebezem R. Product Inhibition and pH Affect Stoichiometry and Kinetics of Chain Elongating Microbial Communities in Sequencing Batch Bioreactors. Front Bioeng Biotechnol 2021; 9:693030. [PMID: 34235138 PMCID: PMC8256265 DOI: 10.3389/fbioe.2021.693030] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 05/25/2021] [Indexed: 11/13/2022] Open
Abstract
Anaerobic microbial communities can produce carboxylic acids of medium chain length (e.g., caproate, caprylate) by elongating short chain fatty acids through reversed β-oxidation. Ethanol is a common electron donor for this process. The influence of environmental conditions on the stoichiometry and kinetics of ethanol-based chain elongation remains elusive. Here, a sequencing batch bioreactor setup with high-resolution off-gas measurements was used to identify the physiological characteristics of chain elongating microbial communities enriched on acetate and ethanol at pH 7.0 ± 0.2 and 5.5 ± 0.2. Operation at both pH-values led to the development of communities that were highly enriched (>50%, based on 16S rRNA gene amplicon sequencing) in Clostridium kluyveri related species. At both pH-values, stably performing cultures were characterized by incomplete substrate conversion and decreasing biomass-specific hydrogen production rates during an operational cycle. The process stoichiometries obtained at both pH-values were different: at pH 7.0, 71 ± 6% of the consumed electrons were converted to caproate, compared to only 30 ± 5% at pH 5.5. Operating at pH 5.5 led to a decrease in the biomass yield, but a significant increase in the biomass-specific substrate uptake rate, suggesting that the organisms employ catabolic overcapacity to deal with energy losses associated to product inhibition. These results highlight that chain elongating conversions rely on a delicate balance between substrate uptake- and product inhibition kinetics.
Collapse
Affiliation(s)
| | | | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Robbert Kleerebezem
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| |
Collapse
|
23
|
Kleerebezem R, Sousa DZ. Editorial overview: Microbial community engineering. Curr Opin Biotechnol 2021; 67:vi-ix. [PMID: 33745678 DOI: 10.1016/j.copbio.2021.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Robbert Kleerebezem
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands.
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708WE Wageningen, The Netherlands.
| |
Collapse
|
24
|
Abstract
Despite the surge of microbial genome data, experimental testing is important to confirm inferences about the cell biology, ecological roles and evolution of microorganisms. As the majority of archaeal and bacterial diversity remains uncultured and poorly characterized, culturing is a priority. The growing interest in and need for efficient cultivation strategies has led to many rapid methodological and technological advances. In this Review, we discuss common barriers that can hamper the isolation and culturing of novel microorganisms and review emerging, innovative methods for targeted or high-throughput cultivation. We also highlight recent examples of successful cultivation of novel archaea and bacteria, and suggest key microorganisms for future cultivation attempts.
Collapse
Affiliation(s)
- William H Lewis
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Guillaume Tahon
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Patricia Geesink
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands.
| |
Collapse
|
25
|
Fischer PQ, Sánchez‐Andrea I, Stams AJM, Villanueva L, Sousa DZ. Anaerobic microbial methanol conversion in marine sediments. Environ Microbiol 2021; 23:1348-1362. [PMID: 33587796 PMCID: PMC8048578 DOI: 10.1111/1462-2920.15434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 01/15/2023]
Abstract
Methanol is an ubiquitous compound that plays a role in microbial processes as a carbon and energy source, intermediate in metabolic processes or as end product in fermentation. In anoxic environments, methanol can act as the sole carbon and energy source for several guilds of microorganisms: sulfate-reducing microorganisms, nitrate-reducing microorganisms, acetogens and methanogens. In marine sediments, these guilds compete for methanol as their common substrate, employing different biochemical pathways. In this review, we will give an overview of current knowledge of the various ways in which methanol reaches marine sediments, the ecology of microorganisms capable of utilizing methanol and their metabolism. Furthermore, through a metagenomic analysis, we shed light on the unknown diversity of methanol utilizers in marine sediments which is yet to be explored.
Collapse
Affiliation(s)
- Peter Q. Fischer
- Laboratory of MicrobiologyWageningen University & Research, Stippeneng 4Wageningen6708 WEThe Netherlands
- Department of Marine Microbiology and BiogeochemistryRoyal Netherlands Institute for Sea Research, P.O. Box 59Den BurgTexel7197 ABThe Netherlands
| | - Irene Sánchez‐Andrea
- Laboratory of MicrobiologyWageningen University & Research, Stippeneng 4Wageningen6708 WEThe Netherlands
| | - Alfons J. M. Stams
- Laboratory of MicrobiologyWageningen University & Research, Stippeneng 4Wageningen6708 WEThe Netherlands
- Centre of Biological EngineeringUniversity of Minho, Campus de GualtarBraga4710‐057Portugal
| | - Laura Villanueva
- Department of Marine Microbiology and BiogeochemistryRoyal Netherlands Institute for Sea Research, P.O. Box 59Den BurgTexel7197 ABThe Netherlands
- Faculty of GeosciencesUtrecht University, Princetonlaan 8aUtrecht3584 CBThe Netherlands
| | - Diana Z. Sousa
- Laboratory of MicrobiologyWageningen University & Research, Stippeneng 4Wageningen6708 WEThe Netherlands
| |
Collapse
|
26
|
Diender M, Parera Olm I, Sousa DZ. Synthetic co-cultures: novel avenues for bio-based processes. Curr Opin Biotechnol 2021; 67:72-79. [PMID: 33517194 DOI: 10.1016/j.copbio.2021.01.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/23/2020] [Accepted: 01/07/2021] [Indexed: 02/06/2023]
Abstract
In nature, microorganisms live in multi-species communities allowing microbial interactions. These interactions are lost upon establishing a pure culture, increasing the metabolic burden and limiting the metabolic potential of the isolated microbe. In the past years, synthetic microbial co-cultivation, using well-defined consortia of two or more microbes, was increasingly explored for innovative applications in biotechnology. As such, interspecies interactions take place without the complexity of an open mixed culture, minimizing undesired side reactions. Ultimately, synthetic co-cultivation allows to take well-characterized microbes 'off-the-shelf' to create ecosystems with improved process capabilities. This review highlights some of the recent developments on co-cultivation, focusing on waste-to-chemicals conversions. It also addresses fundamental knowledge on microbial interactions deriving from these studies, which is important to further develop our ability to engineer functional co-cultures for bioproduction.
Collapse
Affiliation(s)
- Martijn Diender
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Ivette Parera Olm
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
| |
Collapse
|
27
|
Alves JI, Salvador AF, Castro AR, Zheng Y, Nijsse B, Atashgahi S, Sousa DZ, Stams AJM, Alves MM, Cavaleiro AJ. Long-Chain Fatty Acids Degradation by Desulfomonile Species and Proposal of " Candidatus Desulfomonile Palmitatoxidans". Front Microbiol 2021; 11:539604. [PMID: 33391191 PMCID: PMC7773648 DOI: 10.3389/fmicb.2020.539604] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 11/24/2020] [Indexed: 11/13/2022] Open
Abstract
Microbial communities with the ability to convert long-chain fatty acids (LCFA) coupled to sulfate reduction can be important in the removal of these compounds from wastewater. In this work, an enrichment culture, able to oxidize the long-chain fatty acid palmitate (C16 : 0) coupled to sulfate reduction, was obtained from anaerobic granular sludge. Microscopic analysis of this culture, designated HP culture, revealed that it was mainly composed of one morphotype with a typical collar-like cell wall invagination, a distinct morphological feature of the Desulfomonile genus. 16S rRNA gene amplicon and metagenome-assembled genome (MAG) indeed confirmed that the abundant phylotype in HP culture belong to Desulfomonile genus [ca. 92% 16S rRNA gene sequences closely related to Desulfomonile spp.; and ca. 82% whole genome shotgun (WGS)]. Based on similar cell morphology and average nucleotide identity (ANI) (77%) between the Desulfomonile sp. in HP culture and the type strain Desulfomonile tiedjei strain DCB-1T, we propose a novel species designated as "Candidatus Desulfomonile palmitatoxidans." This bacterium shares 94.3 and 93.6% 16S rRNA gene identity with Desulfomonile limimaris strain DCB-MT and D. tiedjei strain DCB-1T, respectively. Based on sequence abundance of Desulfomonile-morphotype in HP culture, its predominance in the microscopic observations, and presence of several genes coding for enzymes involved in LCFA degradation, the proposed species "Ca. Desulfomonile palmitatoxidans" most probably plays an important role in palmitate degradation in HP culture. Analysis of the growth of HP culture and D. tiedjei strain DCB-1T with short- (butyrate), medium- (caprylate) and long-chain fatty acids (palmitate, stearate, and oleate) showed that both cultures degraded all fatty acids coupled to sulfate reduction, except oleate that was only utilized by HP culture. In the absence of sulfate, neither HP culture, nor D. tiedjei strain DCB-1T degraded palmitate when incubated with Methanobacterium formicicum as a possible methanogenic syntrophic partner. Unlike D. tiedjei strain DCB-1T, "Ca. Desulfomonile palmitatoxidans" lacks reductive dehalogenase genes in its genome, and HP culture was not able to grow by organohalide respiration. An emended description of the genus Desulfomonile is proposed. Our study reveals an unrecognized LCFA degradation feature of the Desulfomonile genus.
Collapse
Affiliation(s)
- Joana I Alves
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | | | - A Rita Castro
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Ying Zheng
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Bart Nijsse
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands.,Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Diana Z Sousa
- Centre of Biological Engineering, University of Minho, Braga, Portugal.,Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Alfons J M Stams
- Centre of Biological Engineering, University of Minho, Braga, Portugal.,Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - M Madalena Alves
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Ana J Cavaleiro
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| |
Collapse
|
28
|
Plugge CM, Sousa DZ. Special Issue "Anaerobes in Biogeochemical Cycles". Microorganisms 2020; 9:microorganisms9010023. [PMID: 33374655 PMCID: PMC7822419 DOI: 10.3390/microorganisms9010023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 12/03/2020] [Indexed: 11/16/2022] Open
|
29
|
Alves JI, Visser M, Arantes AL, Nijsse B, Plugge CM, Alves MM, Stams AJM, Sousa DZ. Effect of Sulfate on Carbon Monoxide Conversion by a Thermophilic Syngas-Fermenting Culture Dominated by a Desulfofundulus Species. Front Microbiol 2020; 11:588468. [PMID: 33304333 PMCID: PMC7701048 DOI: 10.3389/fmicb.2020.588468] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 10/19/2020] [Indexed: 11/13/2022] Open
Abstract
A syngas-degrading enrichment culture, culture T-Syn, was dominated by a bacterium closely related to Desulfofundulus australicus strain AB33T (98% 16S rRNA gene sequence identity). Culture T-Syn could convert high CO concentrations (from pCO ≈ 34 kPa to pCO ≈ 170 kPa), both in the absence and in the presence of sulfate as external electron acceptor. The products formed from CO conversion were H2 and acetate. With sulfate, a lower H2/acetate ratio was observed in the product profile, but CO conversion rates were similar to those in the absence of sulfate. The ability of D. australicus strain AB33T to use CO was also investigated. D. australicus strain AB33T uses up to 40% CO (pCO ≈ 68 kPa) with sulfate and up to 20% CO (pCO ≈ 34 kPa) without sulfate. Comparison of the metagenome-assembled genome (MAG) of the Desulfofundulus sp. from T-Syn culture with the genome of D. australicus strain AB33T revealed high similarity, with an ANI value of 99% and only 32 unique genes in the genome of the Desulfofundulus sp. T-Syn. So far, only Desulfotomaculum nigrificans strain CO-1-SRB had been described to grow with CO with and without sulfate. This work further shows the carboxydotrophic potential of Desulfofundulus genus for CO conversion, both in sulfate-rich and low-sulfate environments.
Collapse
Affiliation(s)
- Joana I Alves
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Michael Visser
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Ana L Arantes
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Bart Nijsse
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands
| | - Caroline M Plugge
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - M Madalena Alves
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Alfons J M Stams
- Centre of Biological Engineering, University of Minho, Braga, Portugal.,Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Diana Z Sousa
- Centre of Biological Engineering, University of Minho, Braga, Portugal.,Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| |
Collapse
|
30
|
Benito-Vaquerizo S, Diender M, Parera Olm I, Martins Dos Santos VAP, Schaap PJ, Sousa DZ, Suarez-Diez M. Modeling a co-culture of Clostridium autoethanogenum and Clostridium kluyveri to increase syngas conversion to medium-chain fatty-acids. Comput Struct Biotechnol J 2020; 18:3255-3266. [PMID: 33240469 PMCID: PMC7658664 DOI: 10.1016/j.csbj.2020.10.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 10/01/2020] [Accepted: 10/02/2020] [Indexed: 12/17/2022] Open
Abstract
We model a co-culture of C. autoethanogenum and C. kluyveri for syngas fermentation. Biomass species ratio affects ethanol and acetate profiles in the co-culture. The model predicts that addition of succinate increases caproate production. Genetic interventions in C. autoethanogenum could increase caproate production.
Microbial fermentation of synthesis gas (syngas) is becoming more attractive for sustainable production of commodity chemicals. To date, syngas fermentation focuses mainly on the use of Clostridium species for the production of small organic molecules such as ethanol and acetate. The co-cultivation of syngas-fermenting microorganisms with chain-elongating bacteria can expand the range of possible products, allowing, for instance, the production of medium-chain fatty acids (MCFA) and alcohols from syngas. To explore these possibilities, we report herein a genome-scale, constraint-based metabolic model to describe growth of a co-culture of Clostridium autoethanogenum and Clostridium kluyveri on syngas for the production of valuable compounds. Community flux balance analysis was used to gain insight into the metabolism of the two strains and their interactions, and to reveal potential strategies enabling production of butyrate and hexanoate. The model suggests that one strategy to optimize the production of medium-chain fatty-acids from syngas would be the addition of succinate. According to the prediction, addition of succinate would increase the pool of crotonyl-CoA and the ethanol/acetate uptake ratio in C. kluyveri, resulting in a flux of up to 60% of electrons into hexanoate. Another potential way to further optimize butyrate and hexanoate production would be an increase of C. autoethanogenum ethanol production. Blocking either acetaldehyde dehydrogenase or formate dehydrogenase (ferredoxin) activity or formate transport, in the C. autoethanogenum metabolic model could potentially lead to an up to 150% increase in ethanol production.
Collapse
Affiliation(s)
- Sara Benito-Vaquerizo
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Martijn Diender
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Ivette Parera Olm
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| |
Collapse
|
31
|
Sánchez-Andrea I, Guedes IA, Hornung B, Boeren S, Lawson CE, Sousa DZ, Bar-Even A, Claassens NJ, Stams AJM. The reductive glycine pathway allows autotrophic growth of Desulfovibrio desulfuricans. Nat Commun 2020; 11:5090. [PMID: 33037220 PMCID: PMC7547702 DOI: 10.1038/s41467-020-18906-7] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 09/14/2020] [Indexed: 12/30/2022] Open
Abstract
Six CO2 fixation pathways are known to operate in photoautotrophic and chemoautotrophic microorganisms. Here, we describe chemolithoautotrophic growth of the sulphate-reducing bacterium Desulfovibrio desulfuricans (strain G11) with hydrogen and sulphate as energy substrates. Genomic, transcriptomic, proteomic and metabolomic analyses reveal that D. desulfuricans assimilates CO2 via the reductive glycine pathway, a seventh CO2 fixation pathway. In this pathway, CO2 is first reduced to formate, which is reduced and condensed with a second CO2 to generate glycine. Glycine is further reduced in D. desulfuricans by glycine reductase to acetyl-P, and then to acetyl-CoA, which is condensed with another CO2 to form pyruvate. Ammonia is involved in the operation of the pathway, which is reflected in the dependence of the autotrophic growth rate on the ammonia concentration. Our study demonstrates microbial autotrophic growth fully supported by this highly ATP-efficient CO2 fixation pathway.
Collapse
Affiliation(s)
- Irene Sánchez-Andrea
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
| | - Iame Alves Guedes
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Bastian Hornung
- Leids Universitair Medisch Centrum (LUMC), Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Christopher E Lawson
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Arren Bar-Even
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Nico J Claassens
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
- Center of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
| |
Collapse
|
32
|
Sorokin DY, Diender M, Merkel AY, Koenen M, Bale NJ, Pabst M, Sinninghe Damsté JS, Sousa DZ. Natranaerofaba carboxydovora gen. nov., sp. nov., an extremely haloalkaliphilic CO-utilizing acetogen from a hypersaline soda lake representing a novel deep phylogenetic lineage in the class 'Natranaerobiia'. Environ Microbiol 2020; 23:3460-3476. [PMID: 32955149 PMCID: PMC8359318 DOI: 10.1111/1462-2920.15241] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/15/2020] [Accepted: 09/17/2020] [Indexed: 01/02/2023]
Abstract
An anaerobic enrichment with CO from sediments of hypersaline soda lakes resulted in a methane‐forming binary culture, whereby CO was utilized by a bacterium and not the methanogenic partner. The bacterial isolate ANCO1 forms a deep‐branching phylogenetic lineage at the level of a new family within the class ‘Natranaerobiia’. It is an extreme haloalkaliphilic and moderate thermophilic acetogen utilizing CO, formate, pyruvate and lactate as electron donors and thiosulfate, nitrate (reduced to ammonia) and fumarate as electron acceptors. The genome of ANCO1 encodes a full Wood–Ljungdahl pathway allowing for CO oxidation and acetogenic conversion of pyruvate. A locus encoding Nap nitrate reductase/NrfA ammonifying nitrite reductase is also present. Thiosulfate respiration is encoded by a Phs/Psr‐like operon. The organism obviously relies on Na‐based bioenergetics, since the genome encodes for the Na+‐Rnf complex, Na+‐F1F0 ATPase and Na+‐translocating decarboxylase. Glycine betaine serves as a compatible solute. ANCO1 has an unusual membrane polar lipid composition dominated by diethers, more common among archaea, probably a result of adaptation to multiple extremophilic conditions. Overall, ANCO1 represents a unique example of a triple extremophilic CO‐oxidizing anaerobe and is classified as a novel genus and species Natranaerofaba carboxydovora in a novel family Natranaerofabacea.
Collapse
Affiliation(s)
- Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia.,Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Martijn Diender
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Alexander Y Merkel
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Michel Koenen
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, Den Burg, The Netherlands
| | - Nicole J Bale
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, Den Burg, The Netherlands
| | - Martin Pabst
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Jaap S Sinninghe Damsté
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, Den Burg, The Netherlands.,Department of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| |
Collapse
|
33
|
Cavaleiro AJ, Guedes AP, Silva SA, Arantes AL, Sequeira JC, Salvador AF, Sousa DZ, Stams AJM, Alves MM. Effect of Sub-Stoichiometric Fe(III) Amounts on LCFA Degradation by Methanogenic Communities. Microorganisms 2020; 8:microorganisms8091375. [PMID: 32906848 PMCID: PMC7564256 DOI: 10.3390/microorganisms8091375] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/01/2020] [Accepted: 09/04/2020] [Indexed: 02/06/2023] Open
Abstract
Long-chain fatty acids (LCFA) are common contaminants in municipal and industrial wastewater that can be converted anaerobically to methane. A low hydrogen partial pressure is required for LCFA degradation by anaerobic bacteria, requiring the establishment of syntrophic relationships with hydrogenotrophic methanogens. However, high LCFA loads can inhibit methanogens, hindering biodegradation. Because it has been suggested that anaerobic degradation of these compounds may be enhanced by the presence of alternative electron acceptors, such as iron, we investigated the effect of sub-stoichiometric amounts of Fe(III) on oleate (C18:1 LCFA) degradation by suspended and granular methanogenic sludge. Fe(III) accelerated oleate biodegradation and hydrogenotrophic methanogenesis in the assays with suspended sludge, with H2-consuming methanogens coexisting with iron-reducing bacteria. On the other hand, acetoclastic methanogenesis was delayed by Fe(III). These effects were less evident with granular sludge, possibly due to its higher initial methanogenic activity relative to suspended sludge. Enrichments with close-to-stoichiometric amounts of Fe(III) resulted in a microbial community mainly composed of Geobacter, Syntrophomonas, and Methanobacterium genera, with relative abundances of 83-89%, 3-6%, and 0.2-10%, respectively. In these enrichments, oleate was biodegraded to acetate and coupled to iron-reduction and methane production, revealing novel microbial interactions between syntrophic LCFA-degrading bacteria, iron-reducing bacteria, and methanogens.
Collapse
Affiliation(s)
- Ana J. Cavaleiro
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (A.P.G.); (S.A.S.); (A.L.A.); (J.C.S.); (A.F.S.); (D.Z.S.); (A.J.M.S.); (M.M.A.)
- Correspondence: ; Tel.: +35-1253604423
| | - Ana P. Guedes
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (A.P.G.); (S.A.S.); (A.L.A.); (J.C.S.); (A.F.S.); (D.Z.S.); (A.J.M.S.); (M.M.A.)
| | - Sérgio A. Silva
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (A.P.G.); (S.A.S.); (A.L.A.); (J.C.S.); (A.F.S.); (D.Z.S.); (A.J.M.S.); (M.M.A.)
| | - Ana L. Arantes
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (A.P.G.); (S.A.S.); (A.L.A.); (J.C.S.); (A.F.S.); (D.Z.S.); (A.J.M.S.); (M.M.A.)
| | - João C. Sequeira
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (A.P.G.); (S.A.S.); (A.L.A.); (J.C.S.); (A.F.S.); (D.Z.S.); (A.J.M.S.); (M.M.A.)
| | - Andreia F. Salvador
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (A.P.G.); (S.A.S.); (A.L.A.); (J.C.S.); (A.F.S.); (D.Z.S.); (A.J.M.S.); (M.M.A.)
| | - Diana Z. Sousa
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (A.P.G.); (S.A.S.); (A.L.A.); (J.C.S.); (A.F.S.); (D.Z.S.); (A.J.M.S.); (M.M.A.)
- Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands
| | - Alfons J. M. Stams
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (A.P.G.); (S.A.S.); (A.L.A.); (J.C.S.); (A.F.S.); (D.Z.S.); (A.J.M.S.); (M.M.A.)
- Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands
| | - M. Madalena Alves
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (A.P.G.); (S.A.S.); (A.L.A.); (J.C.S.); (A.F.S.); (D.Z.S.); (A.J.M.S.); (M.M.A.)
| |
Collapse
|
34
|
Magalhães CP, Ribeiro JA, Guedes AP, Arantes AL, Sousa DZ, Stams AJM, Alves MM, Cavaleiro AJ. Co-cultivation of Thermoanaerobacter strains with a methanogenic partner enhances glycerol conversion. Microb Biotechnol 2020; 13:962-973. [PMID: 32154666 PMCID: PMC7264899 DOI: 10.1111/1751-7915.13506] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 10/07/2019] [Accepted: 10/13/2019] [Indexed: 11/30/2022] Open
Abstract
Glycerol-rich waste streams produced by the biodiesel, bioethanol and oleochemical industries can be treated and valorized by anaerobic microbial communities to produce methane. As current knowledge of the microorganisms involved in thermophilic glycerol conversion to methane is scarce, thermophilic glycerol-degrading methanogenic communities were enriched. A co-culture of Thermoanaerobacter and Methanothermobacter species was obtained, pointing to a non-obligately syntrophic glycerol degradation. This hypothesis was further studied by incubating Thermoanaerobacter brockii subsp. finnii and T. wiegelii with glycerol (10 mM) in pure culture and with different hydrogenotrophic methanogens. The presence of the methanogen accelerated glycerol fermentation by the two Thermoanaerobacter strains up to 3.3 mM day-1 , corresponding to 12 times higher volumetric glycerol depletion rates in the methanogenic co-cultures than in the pure bacterial cultures. The catabolic pathways of glycerol conversion were identified by genome analysis of the two Thermoanaerobacter strains. NADH and reduced ferredoxin formed in the pathway are linked to proton reduction, which becomes thermodynamically favourable when the hydrogen partial pressure is kept low by the hydrogenotrophic methanogenic partner.
Collapse
Affiliation(s)
| | - Joaquim A. Ribeiro
- Centre of Biological EngineeringUniversity of MinhoBragaPortugal
- Present address:
Optimizer ‐ Serviços e Consultadoria Informática Lda.PortoPortugal
| | - Ana P. Guedes
- Centre of Biological EngineeringUniversity of MinhoBragaPortugal
- Present address:
Agricultural Superior School of Ponte de LimaPolytechnic Institute of Viana do CasteloViana do CasteloPortugal
| | - Ana L. Arantes
- Centre of Biological EngineeringUniversity of MinhoBragaPortugal
| | - Diana Z. Sousa
- Centre of Biological EngineeringUniversity of MinhoBragaPortugal
- Laboratory of MicrobiologyWageningen University and ResearchWageningenThe Netherlands
| | - Alfons J. M. Stams
- Centre of Biological EngineeringUniversity of MinhoBragaPortugal
- Laboratory of MicrobiologyWageningen University and ResearchWageningenThe Netherlands
| | - Maria M. Alves
- Centre of Biological EngineeringUniversity of MinhoBragaPortugal
| | | |
Collapse
|
35
|
Paulo LM, Hidayat MR, Moretti G, Stams AJM, Sousa DZ. Effect of nickel, cobalt, and iron on methanogenesis from methanol and cometabolic conversion of 1,2-dichloroethene by Methanosarcina barkeri. Biotechnol Appl Biochem 2020; 67:744-750. [PMID: 32282086 PMCID: PMC7687089 DOI: 10.1002/bab.1925] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 03/17/2020] [Indexed: 01/28/2023]
Abstract
Methanogens are responsible for the last step in anaerobic digestion (AD), in which methane (a biofuel) is produced. Some methanogens can cometabolize chlorinated pollutants, contributing for their removal during AD. Methanogenic cofactors involved in cometabolic reductive dechlorination, such as F430 and cobalamin, contain metal ions (nickel, cobalt, iron) in their structure. We hypothesized that the supplementation of trace metals could improve methane production and the cometabolic dechlorination of 1,2‐dichloroethene (DCE) by pure cultures of Methanosarcina barkeri. Nickel, cobalt, and iron were added to cultures of M. barkeri growing on methanol and methanol plus DCE. Metal amendment improved DCE dechlorination to vinyl chloride (VC): assays with 20 µM of Fe3+ showed the highest final concentration of VC (5× higher than in controls without Fe3+), but also in assays with 5.5 µM of Co2+ and 5 µM of Ni2+ VC formation was improved (3.5–4× higher than in controls without the respective metals). Dosing of metals could be useful to improve anaerobic removal of chlorinated compounds, and more importantly decrease the detrimental effect of DCE on methane production in anaerobic digesters.
Collapse
Affiliation(s)
- Lara M Paulo
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Mohamad R Hidayat
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Giulio Moretti
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands.,Laboratory of Microbiology, MESVA Department, University of L'Aquila, Via Vetoio Coppito (AQ), Italy
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| |
Collapse
|
36
|
Arantes AL, Moreira JPC, Diender M, Parshina SN, Stams AJM, Alves MM, Alves JI, Sousa DZ. Enrichment of Anaerobic Syngas-Converting Communities and Isolation of a Novel Carboxydotrophic Acetobacterium wieringae Strain JM. Front Microbiol 2020; 11:58. [PMID: 32082285 PMCID: PMC7006291 DOI: 10.3389/fmicb.2020.00058] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 01/13/2020] [Indexed: 11/13/2022] Open
Abstract
Syngas is a substrate for the anaerobic bioproduction of fuels and valuable chemicals. In this study, anaerobic sludge was used for microbial enrichments with synthetic syngas and acetate as main substrates. The objectives of this study were to identify microbial networks (in enrichment cultures) for the conversion of syngas to added-value products, and to isolate robust, non-fastidious carboxydotrophs. Enrichment cultures produced methane and propionate, this last one an unusual product from syngas fermentation. A bacterium closely related to Acetobacterium wieringae was identified as most prevalent (87% relative abundance) in the enrichments. Methanospirillum sp. and propionate-producing bacteria clustering within the genera Anaerotignum and Pelobacter were also found. Further on, strain JM, was isolated and was found to be 99% identical (16S rRNA gene) to A. wieringae DSM 1911T. Digital DNA-DNA hybridization (dDDH) value between the genomes of strain JM and A. wieringae was 77.1%, indicating that strain JM is a new strain of A. wieringae. Strain JM can grow on carbon monoxide (100% CO, total pressure 170 kPa) without yeast extract or formate, producing mainly acetate. Remarkably, conversion of CO by strain JM showed shorter lag phase than in cultures of A. wieringae DSM 1911T, and about four times higher amount of CO was consumed in 7 days. Genome analysis suggests that strain JM uses the Wood-Ljungdahl pathway for the conversion of one carbon compounds (CO, formate, CO2/H2). Genes encoding bifurcational enzyme complexes with similarity to the bifurcational formate dehydrogenase (Fdh) of Clostridium autoethanogenum are present, and possibly relate to the higher tolerance to CO of strain JM compared to other Acetobacterium species. A. wieringae DSM 1911T grew on CO in medium containing 1 mM formate.
Collapse
Affiliation(s)
- Ana L Arantes
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands.,Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - João P C Moreira
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands.,Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Martijn Diender
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Sofiya N Parshina
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands.,Laboratory of Microbiology of Anthropogenic Habitats of Winogradsky Institute of Microbiology, Federal State Institution (Fundamentals of Biotechnology) of the Russian Academy of Sciences, Moscow, Russia
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands.,Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - M Madalena Alves
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Joana I Alves
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| |
Collapse
|
37
|
Strepis N, Naranjo HD, Meier-Kolthoff J, Göker M, Shapiro N, Kyrpides N, Klenk HP, Schaap PJ, Stams AJM, Sousa DZ. Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species. BMC Genomics 2020; 21:24. [PMID: 31914924 PMCID: PMC6950789 DOI: 10.1186/s12864-019-6410-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 12/18/2019] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND The genus Trichococcus currently contains nine species: T. flocculiformis, T. pasteurii, T. palustris, T. collinsii, T. patagoniensis, T. ilyis, T. paludicola, T. alkaliphilus, and T. shcherbakoviae. In general, Trichococcus species can degrade a wide range of carbohydrates. However, only T. pasteurii and a non-characterized strain of Trichococcus, strain ES5, have the capacity of converting glycerol to mainly 1,3-propanediol. Comparative genomic analysis of Trichococcus species provides the opportunity to further explore the physiological potential and uncover novel properties of this genus. RESULTS In this study, a genotype-phenotype comparative analysis of Trichococcus strains was performed. The genome of Trichococcus strain ES5 was sequenced and included in the comparison with the other nine type strains. Genes encoding functions related to e.g. the utilization of different carbon sources (glycerol, arabinan and alginate), antibiotic resistance, tolerance to low temperature and osmoregulation could be identified in all the sequences analysed. T. pasteurii and Trichococcus strain ES5 contain a operon with genes encoding necessary enzymes for 1,3-PDO production from glycerol. All the analysed genomes comprise genes encoding for cold shock domains, but only five of the Trichococcus species can grow at 0 °C. Protein domains associated to osmoregulation mechanisms are encoded in the genomes of all Trichococcus species, except in T. palustris, which had a lower resistance to salinity than the other nine studied Trichococcus strains. CONCLUSIONS Genome analysis and comparison of ten Trichococcus strains allowed the identification of physiological traits related to substrate utilization and environmental stress resistance (e.g. to cold and salinity). Some substrates were used by single species, e.g. alginate by T. collinsii and arabinan by T. alkaliphilus. Strain ES5 may represent a subspecies of Trichococcus flocculiformis and contrary to the type strain (DSM 2094T), is able to grow on glycerol with the production of 1,3-propanediol.
Collapse
Affiliation(s)
- Nikolaos Strepis
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Henry D. Naranjo
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Jan Meier-Kolthoff
- Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Markus Göker
- Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Nicole Shapiro
- DOE Joint Genome Institute, 2800 Mitchell Drive 100, CA, Walnut Creek, CA 94598 USA
| | - Nikos Kyrpides
- DOE Joint Genome Institute, 2800 Mitchell Drive 100, CA, Walnut Creek, CA 94598 USA
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
- School of Biology, Newcastle University, Ridley Building 2, Newcastle, NE1 7RU UK
| | - Peter J. Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Alfons J. M. Stams
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Diana Z. Sousa
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| |
Collapse
|
38
|
Ziels RM, Nobu MK, Sousa DZ. Elucidating Syntrophic Butyrate-Degrading Populations in Anaerobic Digesters Using Stable-Isotope-Informed Genome-Resolved Metagenomics. mSystems 2019; 4:e00159-19. [PMID: 31387934 PMCID: PMC6687939 DOI: 10.1128/msystems.00159-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 07/12/2019] [Indexed: 11/20/2022] Open
Abstract
Linking the genomic content of uncultivated microbes to their metabolic functions remains a critical challenge in microbial ecology. Resolving this challenge has implications for improving our management of key microbial interactions in biotechnologies such as anaerobic digestion, which relies on slow-growing syntrophic and methanogenic communities to produce renewable methane from organic waste. In this study, we combined DNA stable-isotope probing (SIP) with genome-centric metagenomics to recover the genomes of populations enriched in 13C after growing on [13C]butyrate. Differential abundance analysis of recovered genomic bins across the SIP metagenomes identified two metagenome-assembled genomes (MAGs) that were significantly enriched in heavy [13C]DNA. Phylogenomic analysis assigned one MAG to the genus Syntrophomonas and the other MAG to the genus Methanothrix. Metabolic reconstruction of the annotated genomes showed that the Syntrophomonas genome encoded all the enzymes for beta-oxidizing butyrate, as well as several mechanisms for interspecies electron transfer via electron transfer flavoproteins, hydrogenases, and formate dehydrogenases. The Syntrophomonas genome shared low average nucleotide identity (<95%) with any cultured representative species, indicating that it is a novel species that plays a significant role in syntrophic butyrate degradation within anaerobic digesters. The Methanothrix genome contained the complete pathway for acetoclastic methanogenesis, indicating that it was enriched in 13C from syntrophic acetate transfer. This study demonstrates the potential of stable-isotope-informed genome-resolved metagenomics to identify in situ interspecies metabolic cooperation within syntrophic consortia important to anaerobic waste treatment as well as global carbon cycling.IMPORTANCE Predicting the metabolic potential and ecophysiology of mixed microbial communities remains a major challenge, especially for slow-growing anaerobes that are difficult to isolate. Unraveling the in situ metabolic activities of uncultured species may enable a more descriptive framework to model substrate transformations by microbiomes, which has broad implications for advancing the fields of biotechnology, global biogeochemistry, and human health. Here, we investigated the in situ function of mixed microbiomes by combining stable-isotope probing with metagenomics to identify the genomes of active syntrophic populations converting butyrate, a C4 fatty acid, into methane within anaerobic digesters. This approach thus moves beyond the mere presence of metabolic genes to resolve "who is doing what" by obtaining confirmatory assimilation of the labeled substrate into the DNA signature. Our findings provide a framework to further link the genomic identities of uncultured microbes with their ecological function within microbiomes driving many important biotechnological and global processes.
Collapse
Affiliation(s)
- Ryan M Ziels
- Department of Civil Engineering, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington, USA
| | - Masaru K Nobu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| |
Collapse
|
39
|
Parada J, Rubilar O, Sousa DZ, Martínez M, Fernández-Baldo MA, Tortella GR. Short term changes in the abundance of nitrifying microorganisms in a soil-plant system simultaneously exposed to copper nanoparticles and atrazine. Sci Total Environ 2019; 670:1068-1074. [PMID: 31018422 DOI: 10.1016/j.scitotenv.2019.03.221] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 03/14/2019] [Accepted: 03/14/2019] [Indexed: 06/09/2023]
Abstract
Copper nanoparticles (NCu) may co-exist with other pollutants in agricultural soils, such as pesticides. However, this has been little evaluated yet. Thus, possible effects of the simultaneous applications of pesticides and NCu on biogeochemical cycles are expected, for example on the nitrogen cycle. Therefore, the aim of this work was to evaluate the effect of simultaneous application of the herbicide atrazine (ATZ) and NCu on the abundance of total bacteria and nitrifying communities: ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Moreover, the ATZ dissipation was evaluated. A soil-plant system containing ATZ at field dose (3 mg a.i. kg-1) was mixed with two doses of NCu (0.05% or 0.15% w/w). Changes in the abundance of 16S rRNA and ammonia monooxygenase (amoA) genes of AOA and AOB were evaluated by real-time quantitative PCR (qPCR) at three sampling times (1, 15 and 30 days). The residual ATZ and nitrate production were also measured. The results showed significant differences in microbial composition and abundance over the 30 days of the experiment. Particularly, an initial decrease was observed in total bacterial abundance due to the presence of ATZ and NCu respect to ATZ alone (~60%). The abundance of AOA was also remarkably reduced (~85%), but these communities gradually recovered towards the end of the experiment. Conversely, AOB abundance initially increased (>100%) and remained mainly unaltered in soil exposed to ATZ and NCu 0.15% w/w, where nitrate formation was also constant. Moreover, NCu decreased the ATZ dissipation, which was translated in a 2-fold increase on the ATZ half-life values (T1/2). This study demonstrates that the simultaneous presence of NCu and ATZ may represent a risk for the total bacteria present in soil and sensitive microorganisms such as nitrifying communities, and changes in the dissipation of the pesticide could influence this process.
Collapse
Affiliation(s)
- J Parada
- Doctoral Program in Sciences of Natural Resources, Universidad de La Frontera, Temuco, Chile
| | - O Rubilar
- Departamento de Ingeniería Química, Universidad de La Frontera, Temuco, Chile; Centro de Excelencia en Investigación Biotecnológica Aplicada al Medio Ambiente (CIBAMA), Temuco, Chile
| | - D Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - M Martínez
- Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - M A Fernández-Baldo
- INQUISAL, Departamento de Química, Universidad Nacional de San Luis, CONICET, Chacabuco 917, D5700BWS San Luis, Argentina
| | - G R Tortella
- Departamento de Ingeniería Química, Universidad de La Frontera, Temuco, Chile; Centro de Excelencia en Investigación Biotecnológica Aplicada al Medio Ambiente (CIBAMA), Temuco, Chile.
| |
Collapse
|
40
|
Guzman JJL, Sousa DZ, Angenent LT. Development of a Bioelectrochemical System as a Tool to Enrich H 2-Producing Syntrophic Bacteria. Front Microbiol 2019; 10:110. [PMID: 30804906 PMCID: PMC6370660 DOI: 10.3389/fmicb.2019.00110] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 01/18/2019] [Indexed: 01/23/2023] Open
Abstract
Syntrophic microbial partnerships are found in many environments and play critical roles in wastewater treatment, global nutrient cycles, and gut systems. An important type of syntrophy for the anaerobic conversion of carboxylic acids is H2 syntrophy. In this type of microbial partnership, dissolved H2 is produced by a bacterium and rapidly consumed by an archeon (methanogen), resulting in methane gas. This is referred to as interspecies H2 transfer, and some conversions rely on this mechanism to become thermodynamically feasible. For this reason, syntrophic partners are often not possible to separate in the lab, which hampers the full understanding of their physiology. Bioelectrochemical systems (BESs) may show promise to ultimately separate and study the behavior of the syntrophic bacterium by employing an abiotic H2 oxidation reaction at the anode, actively removing dissolved H2. Here, we performed a proof-of-concept study to ascertain whether an H2-removing anode can: (1) provide a growth advantage for the syntrophic bacterium; and (2) compete with the methanogenic partner. A mathematical model was developed to design a BES to perform competition experiments. Indeed, the operated BES demonstrated the ability to provide a growth advantage to the syntrophic bacterium Syntrophus aciditrophicus compared to its methanogenic partner Methanospirillum hungatei when grown in co-culture. Further, the BES provided the never-before isolated Syntrophomonas zehnderi with a growth advantage compared to Methanobacterium formicicum. Our results demonstrate a potential to use this BES to enrich H2-sensitive syntrophic bacteria, and gives prospects for the development of an effective method for the separation of obligate syntrophs.
Collapse
Affiliation(s)
- Juan J L Guzman
- Biological and Environmental Engineering Department, Cornell University, Ithaca, NY, United States
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Largus T Angenent
- Centrum for Applied Geosciences, University of Tübingen, Tübingen, Germany
| |
Collapse
|
41
|
Parshina SN, Strepis N, Aalvink S, Nozhevnikova AN, Stams AJM, Sousa DZ. Trichococcus shcherbakoviae sp. nov., isolated from a laboratory-scale anaerobic EGSB bioreactor operated at low temperature. Int J Syst Evol Microbiol 2019; 69:529-534. [PMID: 30605071 DOI: 10.1099/ijsem.0.003193] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
A new species of the genus Trichococcus, strain Art1T, was isolated from a psychrotolerant syntrophic propionate-oxidizing consortium, obtained before from a low-temperature EGSB reactor fed with a mixture of VFAs (acetate, propionate and butyrate). The 16S rRNA gene sequence of strain Art1T was highly similar to those of other Trichococcus species (99.7-99.9 %) but digital DNA-DNA hybridization values were lower than those recommended for the delineation of a novel species, indicating that strain Art1T is a novel species of the genus Trichococcus. Cells of strain Art1T are non-motile cocci with a diameter of 0.5-2.0 µm and were observed singularly, in pairs, short chains and irregular conglomerates. Cells of Art1T stained Gram-positive and produced extracellular polymeric substances . Growth was optimal at pH 6-7.5 and cells could grow in a temperature range of from -2 to 30 °C (optimum 25-30 °C). Strain Art1T can degrade several carbohydrates, and the main products from glucose fermentation are lactate, acetate, formate and ethanol. The genomic DNA G+C content of strain Art1T is 46.7 %. The major components of the cellular fatty acids are C16 : 1 ω9c, C16 : 0 and C18 : 1 ω9c. Based on genomic and physiological characteristics of strain Art1T, a new species of the genus Trichococcus, Trichococcusshcherbakoviae, is proposed. The type strain of Trichococcusshcherbakoviae is Art1T (=DSM 107162T = VKM B-3260T).
Collapse
Affiliation(s)
- Sofiya Nikolaevna Parshina
- 1Laboratory of Microbiology of Anthropogenic Habitats of Winogradsky Institute of Microbiology, Federal State Institution «Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences», Leninsky prosp. 33, b.2, 119071 Moscow, Russia.,2Laboratory of Microbiology, Wageningen University and Research, 6708 WE Wageningen, The Netherlands
| | - Nikolaos Strepis
- 2Laboratory of Microbiology, Wageningen University and Research, 6708 WE Wageningen, The Netherlands.,3Laboratory of Systems and Synthetic Biology, Wageningen University and Research, 6708 WE Stippeneng, The Netherlands
| | - Steven Aalvink
- 2Laboratory of Microbiology, Wageningen University and Research, 6708 WE Wageningen, The Netherlands
| | - Alla N Nozhevnikova
- 1Laboratory of Microbiology of Anthropogenic Habitats of Winogradsky Institute of Microbiology, Federal State Institution «Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences», Leninsky prosp. 33, b.2, 119071 Moscow, Russia
| | - Alfons J M Stams
- 2Laboratory of Microbiology, Wageningen University and Research, 6708 WE Wageningen, The Netherlands
| | - Diana Z Sousa
- 2Laboratory of Microbiology, Wageningen University and Research, 6708 WE Wageningen, The Netherlands
| |
Collapse
|
42
|
Sánchez-Andrea I, Florentino AP, Semerel J, Strepis N, Sousa DZ, Stams AJM. Co-culture of a Novel Fermentative Bacterium, Lucifera butyrica gen. nov. sp. nov., With the Sulfur Reducer Desulfurella amilsii for Enhanced Sulfidogenesis. Front Microbiol 2018; 9:3108. [PMID: 30631314 PMCID: PMC6315149 DOI: 10.3389/fmicb.2018.03108] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 11/30/2018] [Indexed: 11/28/2022] Open
Abstract
Biosulfidogenesis can be used to remediate low pH and high metal content waters such as acid mine drainage and recover the present metals. The selection of a cheap electron donor for the process is important for the economic viability. In this work we isolated a novel versatile acidotolerant fermentative bacterium (strain ALET) that is able to use a great variety of substrates including glycerol. Strain ALET is an obligate anaerobe, and cells are motile, rod-shaped, spore-forming, and stain Gram-positive. Growth occurred in a pH range from 3.5 to 7 (optimum 5.5), and temperature range from 25 to 40°C (optimum 37°C). It grows by fermentation of sugars, organic acids and glycerol. It has the ability to use thiosulfate, iron and DMSO as electron acceptors. Its genome is 4.7 Mb with 5122 protein-coding sequences, and a G+C content of 46.9 mol%. Based on 16S rRNA gene sequence analysis, the closest cultured species is Propionispora hippei (91.4% 16S rRNA gene identity) from the Sporomusaceae family (Selenomonadales order, Negativicutes class, Firmicutes phylum). Based on the distinctive physiological and phylogenetic characteristics of strain ALET, a new genus and species Lucifera butyrica gen. nov., sp. nov., is proposed. The type strain is ALET (=JCM 19373T = DSM 27520T). Strain ALET is an incomplete oxidizer and acetate, among other products, accumulates during glycerol conversion. Strain ALET was used to extend the substrate range for sulfur reduction by constructing co-cultures with the acetate oxidizer and sulfur reducer Desulfurella amilsii. The co-culture was tested with glycerol as substrate in batch and chemostat experiments. Acetate formed by fermentation of glycerol by strain ALET resulted in sulfur reduction by D. amilsii. The co-culture strategy offers good perspectives to use a wide range of cost-efficient substrates, including glycerol, to produce sulfide by specialized sulfur reducers. The recovery of heavy metals from metalliferous streams may become economically feasible by this approach. Note: The locus tag for the genes encoded in Lucifera butyrica is LUCI_∗. To avoid repetition of the prefix along the text, the locus tags are represented by the specific identifier.
Collapse
Affiliation(s)
| | | | - Jeltzlin Semerel
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | - Nikolaos Strepis
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands.,Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, Netherlands
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands.,Centre of Biological Engineering, University of Minho, Braga, Portugal
| |
Collapse
|
43
|
Hidalgo-Ahumada CAP, Nobu MK, Narihiro T, Tamaki H, Liu WT, Kamagata Y, Stams AJM, Imachi H, Sousa DZ. Novel energy conservation strategies and behaviour of Pelotomaculum schinkii driving syntrophic propionate catabolism. Environ Microbiol 2018; 20:4503-4511. [PMID: 30126076 DOI: 10.1111/1462-2920.14388] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 08/02/2018] [Accepted: 08/15/2018] [Indexed: 11/29/2022]
Abstract
Under methanogenic conditions, short-chain fatty acids are common byproducts from degradation of organic compounds and conversion of these acids is an important component of the global carbon cycle. Due to the thermodynamic difficulty of propionate degradation, this process requires syntrophic interaction between a bacterium and partner methanogen; however, the metabolic strategies and behaviour involved are not fully understood. In this study, the first genome analysis of obligately syntrophic propionate degraders (Pelotomaculum schinkii HH and P. propionicicum MGP) and comparison with other syntrophic propionate degrader genomes elucidated novel components of energy metabolism behind Pelotomaculum propionate oxidation. Combined with transcriptomic examination of P. schinkii behaviour in co-culture with Methanospirillum hungatei, we found that formate may be the preferred electron carrier for P. schinkii syntrophy. Propionate-derived menaquinol may be primarily re-oxidized to formate, and energy was conserved during formate generation through newly proposed proton-pumping formate extrusion. P. schinkii did not overexpress conventional energy metabolism associated with a model syntrophic propionate degrader Syntrophobacter fumaroxidans MPOB (i.e., CoA transferase, Fix and Rnf). We also found that P. schinkii and the partner methanogen may also interact through flagellar contact and amino acid and fructose exchange. These findings provide new understanding of syntrophic energy acquisition and interactions.
Collapse
Affiliation(s)
- Catalina A P Hidalgo-Ahumada
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, Wageningen, The Netherlands
| | - Masaru K Nobu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 North Mathews Ave, Urbana, IL, 61801, USA
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, Wageningen, The Netherlands.,Center of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Hiroyuki Imachi
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa, 237-0061, Japan
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, Wageningen, The Netherlands
| |
Collapse
|
44
|
Diender M, Uhl PS, Bitter JH, Stams AJM, Sousa DZ. High Rate Biomethanation of Carbon Monoxide-Rich Gases via a Thermophilic Synthetic Coculture. ACS Sustain Chem Eng 2018; 6:2169-2176. [PMID: 29430341 PMCID: PMC5805405 DOI: 10.1021/acssuschemeng.7b03601] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 11/24/2017] [Indexed: 06/08/2023]
Abstract
Carbon monoxide-fermenting microorganisms can be used for the production of a wide range of commodity chemicals and fuels from syngas (generated by gasification of, e.g., wastes or biomass) or industrial off-gases (e.g., from steel industry). Microorganisms are normally more resistant to contaminants in the gas (e.g., hydrogen sulfide) than chemical catalysts, less expensive and self-regenerating. However, some carboxydotrophs are sensitive to high concentrations of CO, resulting in low growth rates and productivities. We hypothesize that cultivation of synthetic cocultures can be used to improve overall rates of CO bioconversion. As a case study, a thermophilic microbial coculture, consisting of Carboxydothermus hydrogenoformans and Methanothermobacter thermoautotrophicus was constructed to study the effect of cocultivation on conversion of CO-rich gases to methane. In contrast to the methanogenic monoculture, the coculture was able to efficiently utilize CO or mixtures of H2/CO/CO2 to produce methane at high efficiency and high rates. In CSTR-bioreactors operated in continuous mode, the coculture converted artificial syngas (66.6% H2:33.3% CO) to an outflow gas with a methane content of 72%, approaching the 75% theoretical maximum. CO conversion efficiencies of 93% and volumetric production rates of 4 m3methane/m3liquid/day were achieved. This case shows that microbial cocultivation can result in a significant improvement of gas-fermentation of CO-rich gases.
Collapse
Affiliation(s)
- Martijn Diender
- Laboratory
of Microbiology, Wageningen University &
Research, Stippeneng
4, 6708 WE Wageningen, The Netherlands
| | - Philipp S. Uhl
- Laboratory
of Microbiology, Wageningen University &
Research, Stippeneng
4, 6708 WE Wageningen, The Netherlands
| | - Johannes H. Bitter
- Bio-based
Chemistry & Technology, Wageningen University
& Research, Bornse
Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Alfons J. M. Stams
- Laboratory
of Microbiology, Wageningen University &
Research, Stippeneng
4, 6708 WE Wageningen, The Netherlands
- Centre
of Biological Engineering, University of
Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Diana Z. Sousa
- Laboratory
of Microbiology, Wageningen University &
Research, Stippeneng
4, 6708 WE Wageningen, The Netherlands
| |
Collapse
|
45
|
Ziels RM, Sousa DZ, Stensel HD, Beck DAC. DNA-SIP based genome-centric metagenomics identifies key long-chain fatty acid-degrading populations in anaerobic digesters with different feeding frequencies. ISME J 2018; 12:112-123. [PMID: 28895946 PMCID: PMC5737908 DOI: 10.1038/ismej.2017.143] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 06/22/2017] [Accepted: 07/22/2017] [Indexed: 12/14/2022]
Abstract
Fats, oils and greases (FOG) are energy-dense wastes that can be added to anaerobic digesters to substantially increase biomethane recovery via their conversion through long-chain fatty acids (LCFAs). However, a better understanding of the ecophysiology of syntrophic LCFA-degrading microbial communities in anaerobic digesters is needed to develop operating strategies that mitigate inhibitory LCFA accumulation from FOG. In this research, DNA stable isotope probing (SIP) was coupled with metagenomic sequencing for a genome-centric comparison of oleate (C18:1)-degrading populations in two anaerobic codigesters operated with either a pulse feeding or continuous-feeding strategy. The pulse-fed codigester microcosms converted oleate into methane at over 20% higher rates than the continuous-fed codigester microcosms. Differential coverage binning was demonstrated for the first time to recover population genome bins (GBs) from DNA-SIP metagenomes. About 70% of the 13C-enriched GBs were taxonomically assigned to the Syntrophomonas genus, thus substantiating the importance of Syntrophomonas species to LCFA degradation in anaerobic digesters. Phylogenetic comparisons of 13C-enriched GBs showed that phylogenetically distinct Syntrophomonas GBs were unique to each codigester. Overall, these results suggest that syntrophic populations in anaerobic digesters can have different adaptive capacities, and that selection for divergent populations may be achieved by adjusting reactor operating conditions to maximize biomethane recovery.
Collapse
Affiliation(s)
- Ryan M Ziels
- Department of Civil Engineering, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - H David Stensel
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - David A C Beck
- eScience Institute, University of Washington, Seattle, WA, USA
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
| |
Collapse
|
46
|
Arantes AL, Alves JI, Stams AJM, Alves MM, Sousa DZ. Enrichment of syngas-converting communities from a multi-orifice baffled bioreactor. Microb Biotechnol 2017; 11:639-646. [PMID: 29160026 PMCID: PMC6011948 DOI: 10.1111/1751-7915.12864] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 08/31/2017] [Accepted: 09/03/2017] [Indexed: 12/04/2022] Open
Abstract
The substitution of natural gas by renewable biomethane is an interesting option to reduce global carbon footprint. Syngas fermentation has potential in this context, as a diverse range of low‐biodegradable materials that can be used. In this study, anaerobic sludge acclimatized to syngas in a multi‐orifice baffled bioreactor (MOBB) was used to start enrichments with CO. The main goals were to identify the key players in CO conversion and evaluate potential interspecies metabolic interactions conferring robustness to the process. Anaerobic sludge incubated with 0.7 × 105 Pa CO produced methane and acetate. When the antibiotics vancomycin and/or erythromycin were added, no methane was produced, indicating that direct methanogenesis from CO did not occur. Acetobacterium and Sporomusa were the predominant bacterial species in CO‐converting enrichments, together with methanogens from the genera Methanobacterium and Methanospirillum. Subsequently, a highly enriched culture mainly composed of a Sporomusa sp. was obtained that could convert up to 1.7 × 105 Pa CO to hydrogen and acetate. These results attest the role of Sporomusa species in the enrichment as primary CO utilizers and show their importance for methane production as conveyers of hydrogen to methanogens present in the culture.
Collapse
Affiliation(s)
- Ana L Arantes
- Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal.,Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Joana I Alves
- Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
| | - Alfons J M Stams
- Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal.,Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - M Madalena Alves
- Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
| | - Diana Z Sousa
- Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal.,Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| |
Collapse
|
47
|
Paulo LM, Ramiro-Garcia J, van Mourik S, Stams AJM, Sousa DZ. Effect of Nickel and Cobalt on Methanogenic Enrichment Cultures and Role of Biogenic Sulfide in Metal Toxicity Attenuation. Front Microbiol 2017; 8:1341. [PMID: 28769906 PMCID: PMC5513950 DOI: 10.3389/fmicb.2017.01341] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 07/03/2017] [Indexed: 11/13/2022] Open
Abstract
Metals play an important role in microbial metabolism by acting as cofactors for many enzymes. Supplementation of biological processes with metals may result in improved performance, but high metal concentrations are often toxic to microorganisms. In this work, methanogenic enrichment cultures growing on H2/CO2 or acetate were supplemented with trace concentrations of nickel (Ni) and cobalt (Co), but no significant increase in methane production was observed in most of the tested conditions. However, high concentrations of these metals were detrimental to methanogenic activity of the cultures. Cumulative methane production (after 6 days of incubation) from H2/CO2 was 40% lower in the presence of 8 mM of Ni or 30 mM of Co, compared to controls without metal supplementation. When acetate was used as substrate, cumulative methane production was also reduced: by 18% with 8 mM of Ni and by 53% with 30 mM of Co (after 6 days of incubation). Metal precipitation with sulfide was further tested as a possible method to alleviate metal toxicity. Anaerobic sludge was incubated with Co (30 mM) and Ni (8 mM) in the presence of sulfate or sulfide. The addition of sulfide helped to mitigate the toxic effect of the metals. Methane production from H2/CO2 was negatively affected in the presence of sulfate, possibly due to competition of hydrogenotrophic methanogens by sulfate-reducing bacteria. However, in the enrichment cultures growing on acetate, biogenically produced sulfide had a positive effect and more methane was produced in these incubations than in similar assays without sulfate addition. The outcome of competition between methanogens and sulfate-reducing bacteria is a determinant factor for the success of using biogenic sulfide as detoxification method.
Collapse
Affiliation(s)
- Lara M. Paulo
- Laboratory of Microbiology, Wageningen UniversityWageningen, Netherlands
| | | | - Simon van Mourik
- Farm Technology Group, Plant Sciences GroupWageningen, Netherlands
| | - Alfons J. M. Stams
- Laboratory of Microbiology, Wageningen UniversityWageningen, Netherlands
- Centre of Biological Engineering, University of Minho, Campus de GualtarBraga, Portugal
| | - Diana Z. Sousa
- Laboratory of Microbiology, Wageningen UniversityWageningen, Netherlands
| |
Collapse
|
48
|
Badalato N, Guillot A, Sabarly V, Dubois M, Pourette N, Pontoire B, Robert P, Bridier A, Monnet V, Sousa DZ, Durand S, Mazéas L, Buléon A, Bouchez T, Mortha G, Bize A. Whole Proteome Analyses on Ruminiclostridium cellulolyticum Show a Modulation of the Cellulolysis Machinery in Response to Cellulosic Materials with Subtle Differences in Chemical and Structural Properties. PLoS One 2017; 12:e0170524. [PMID: 28114419 PMCID: PMC5256962 DOI: 10.1371/journal.pone.0170524] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 01/05/2017] [Indexed: 11/25/2022] Open
Abstract
Lignocellulosic materials from municipal solid waste emerge as attractive resources for anaerobic digestion biorefinery. To increase the knowledge required for establishing efficient bioprocesses, dynamics of batch fermentation by the cellulolytic bacterium Ruminiclostridium cellulolyticum were compared using three cellulosic materials, paper handkerchief, cotton discs and Whatman filter paper. Fermentation of paper handkerchief occurred the fastest and resulted in a specific metabolic profile: it resulted in the lowest acetate-to-lactate and acetate-to-ethanol ratios. By shotgun proteomic analyses of paper handkerchief and Whatman paper incubations, 151 proteins with significantly different levels were detected, including 20 of the 65 cellulosomal components, 8 non-cellulosomal CAZymes and 44 distinct extracytoplasmic proteins. Consistent with the specific metabolic profile observed, many enzymes from the central carbon catabolic pathways had higher levels in paper handkerchief incubations. Among the quantified CAZymes and cellulosomal components, 10 endoglucanases mainly from the GH9 families and 7 other cellulosomal subunits had lower levels in paper handkerchief incubations. An in-depth characterization of the materials used showed that the lower levels of endoglucanases in paper handkerchief incubations could hypothetically result from its lower crystallinity index (50%) and degree of polymerization (970). By contrast, the higher hemicellulose rate in paper handkerchief (13.87%) did not result in the enhanced expression of enzyme with xylanase as primary activity, including enzymes from the “xyl-doc” cluster. It suggests the absence, in this material, of molecular structures that specifically lead to xylanase induction. The integrated approach developed in this work shows that subtle differences among cellulosic materials regarding chemical and structural characteristics have significant effects on expressed bacterial functions, in particular the cellulolysis machinery, resulting in different metabolic patterns and degradation dynamics.
Collapse
Affiliation(s)
| | - Alain Guillot
- UMR 1319 MICALIS, PAPPSO, INRA, Jouy-en-Josas, France
| | | | | | | | | | | | | | | | - Diana Z. Sousa
- Centre of Biological Engineering, University of Minho, Braga, Portugal
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | | | | | | | | | - Gérard Mortha
- LGP2, UMR CNRS 5518, Grenoble INP-Pagora, Saint Martin d'Hères, France
| | | |
Collapse
|
49
|
Richter H, Molitor B, Diender M, Sousa DZ, Angenent LT. A Narrow pH Range Supports Butanol, Hexanol, and Octanol Production from Syngas in a Continuous Co-culture of Clostridium ljungdahlii and Clostridium kluyveri with In-Line Product Extraction. Front Microbiol 2016; 7:1773. [PMID: 27877166 PMCID: PMC5099930 DOI: 10.3389/fmicb.2016.01773] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 10/21/2016] [Indexed: 12/19/2022] Open
Abstract
Carboxydotrophic bacteria (CTB) have received attention due to their ability to synthesize commodity chemicals from producer gas and synthesis gas (syngas). CTB have an important advantage of a high product selectivity compared to chemical catalysts. However, the product spectrum of wild-type CTB is narrow. Our objective was to investigate whether a strategy of combining two wild-type bacterial strains into a single, continuously fed bioprocessing step would be promising to broaden the product spectrum. Here, we have operated a syngas-fermentation process with Clostridium ljungdahlii and Clostridium kluyveri with in-line product extraction through gas stripping and product condensing within the syngas recirculation line. The main products from C. ljungdahlii fermentation at a pH of 6.0 were ethanol and acetate at net volumetric production rates of 65.5 and 431 mmol C·L−1·d−1, respectively. An estimated 2/3 of total ethanol produced was utilized by C. kluyveri to chain elongate with the reverse β-oxidation pathway, resulting in n-butyrate and n-caproate at net rates of 129 and 70 mmol C·L−1·d−1, respectively. C. ljungdahlii likely reduced the produced carboxylates to their corresponding alcohols with the reductive power from syngas. This resulted in the longer-chain alcohols n-butanol, n-hexanol, and n-octanol at net volumetric production rates of 39.2, 31.7, and 0.045 mmol C·L−1·d−1, respectively. The continuous production of the longer-chain alcohols occurred only within a narrow pH spectrum of 5.7–6.4 due to the pH discrepancy between the two strains. Regardless whether other wild-type strains could overcome this pH discrepancy, the specificity (mol carbon in product per mol carbon in all other liquid products) for each longer-chain alcohol may never be high in a single bioprocessing step. This, because two bioprocesses compete for intermediates (i.e., carboxylates): (1) chain elongation; and (2) biological reduction. This innate competition resulted in a mixture of n-butanol and n-hexanol with traces of n-octanol.
Collapse
Affiliation(s)
- Hanno Richter
- Department for Biological and Environmental Engineering, Cornell University Ithaca, NY, USA
| | - Bastian Molitor
- Department for Biological and Environmental Engineering, Cornell University Ithaca, NY, USA
| | - Martijn Diender
- Laboratory of Microbiology, Wageningen University Wageningen, Netherlands
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University Wageningen, Netherlands
| | - Largus T Angenent
- Department for Biological and Environmental Engineering, Cornell UniversityIthaca, NY, USA; Atkinson Center for a Sustainable Future, Cornell UniversityIthaca, NY, USA
| |
Collapse
|
50
|
Strepis N, Sánchez-Andrea I, van Gelder AH, van Kruistum H, Shapiro N, Kyrpides N, Göker M, Klenk HP, Schaap P, Stams AJM, Sousa DZ. Description of Trichococcus ilyis sp. nov. by combined physiological and in silico genome hybridization analyses. Int J Syst Evol Microbiol 2016; 66:3957-3963. [DOI: 10.1099/ijsem.0.001294] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Nikolaos Strepis
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Laboratory of Systems and Synthetic Biology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Irene Sánchez-Andrea
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Antonie H. van Gelder
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Henri van Kruistum
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Nicole Shapiro
- DOE Joint Genome Institute, 2800 Mitchell Drive 100, Walnut Creek, CA 94598, USA
| | - Nikos Kyrpides
- DOE Joint Genome Institute, 2800 Mitchell Drive 100, Walnut Creek, CA 94598, USA
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
- School of Biology, Newcastle University, Ridley Building 2, Newcastle, NE1 7RU, UK
| | - Peter Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Alfons J. M. Stams
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Diana Z. Sousa
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| |
Collapse
|