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Wu L, Ngo HH, Wang C, Hou Y, Chen X, Guo W, Duan H, Ni BJ, Wei W. Lactobacillus inoculation mediated carboxylates and alcohols production from waste activated sludge fermentation system: Insight into process outcomes and metabolic network. BIORESOURCE TECHNOLOGY 2024:131191. [PMID: 39094964 DOI: 10.1016/j.biortech.2024.131191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 07/28/2024] [Accepted: 07/30/2024] [Indexed: 08/04/2024]
Abstract
Producing medium chain fatty acids (MCFAs) from waste activated sludge (WAS) is crucial for sustainable chemical industries. This study addressed the electron donor requirement for MCFAs production by inoculating Lactobacillus at varying concentrations (7.94 × 1010, 3.18 × 1011, and 6.35 × 1011 cell/L) to supply lactate internally. Interestingly, the highest MCFAs yield (∼2000 mg COD/L) occurred at the lowest Lactobacillus inoculation. Higher inoculation concentrations redirected more carbon from WAS towards alcohols production rather than MCFAs generation, with up to 2852 mg COD/L alcohols obtained under 6.35 × 1011 cell/L inoculation. Clostridium dominance and increased genes abundance for substrate hydrolysis, lactate conversion, and MCFAs/alcohol production collectively enhanced WAS-derived MCFAs and alcohols synthesis after Lactobacillus inoculation. Overall, the strategy of Lactobacillus inoculation regulated fermentation outcomes and subsequent carbon recovery in WAS, presenting a sustainable technology to achieve liquid bio-energy production from underutilized wet wastes.
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Affiliation(s)
- Lan Wu
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Huu Hao Ngo
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Chen Wang
- School of Civil and Environmental Engineering, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Yanan Hou
- School of Civil and Environmental Engineering, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Xueming Chen
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou 350116, China
| | - Wenshan Guo
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Haoran Duan
- School of Civil and Environmental Engineering, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Bing-Jie Ni
- School of Civil and Environmental Engineering, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Wei Wei
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia.
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2
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Silverio MP, Neumann T, Schaubruch K, Heermann R, Pérez-García P, Chow J, Streit WR. Metagenome-derived SusD-homologs affiliated with Bacteroidota bind to synthetic polymers. Appl Environ Microbiol 2024; 90:e0093324. [PMID: 38953372 PMCID: PMC11267923 DOI: 10.1128/aem.00933-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Accepted: 06/04/2024] [Indexed: 07/04/2024] Open
Abstract
Starch utilization system (Sus)D-homologs are well known for their carbohydrate-binding capabilities and are part of the sus operon in microorganisms affiliated with the phylum Bacteroidota. Until now, SusD-like proteins have been characterized regarding their affinity toward natural polymers. In this study, three metagenomic SusD homologs (designated SusD1, SusD38489, and SusD70111) were identified and tested with respect to binding to natural and non-natural polymers. SusD1 and SusD38489 are cellulose-binding modules, while SusD70111 preferentially binds chitin. Employing translational fusion proteins with superfolder GFP (sfGFP), pull-down assays, and surface plasmon resonance (SPR) has provided evidence for binding to polyethylene terephthalate (PET) and other synthetic polymers. Structural analysis suggested that a Trp triad might be involved in protein adsorption. Mutation of these residues to Ala resulted in an impaired adsorption to microcrystalline cellulose (MC), but not so to PET and other synthetic polymers. We believe that the characterized SusDs, alongside the methods and considerations presented in this work, will aid further research regarding bioremediation of plastics. IMPORTANCE SusD1 and SusD38489 can be considered for further applications regarding their putative adsorption toward fossil-fuel based polymers. This is the first time that SusD homologs from the polysaccharide utilization loci (PUL), largely described for the phylum Bacteroidota, are characterized as synthetic polymer-binding proteins.
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Affiliation(s)
| | - Tabea Neumann
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Kirsten Schaubruch
- Institute of Molecular Physiology, Johannes-Gutenberg University of Mainz, Mainz, Germany
| | - Ralf Heermann
- Institute of Molecular Physiology, Johannes-Gutenberg University of Mainz, Mainz, Germany
| | - Pablo Pérez-García
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Jennifer Chow
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Wolfgang R. Streit
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
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3
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Walters KA, Myers KS, Donohue TJ, Noguera DR. Metagenome-assembled genomes from microbiomes fermenting dairy coproducts. Microbiol Resour Announc 2024; 13:e0017324. [PMID: 38819152 PMCID: PMC11256825 DOI: 10.1128/mra.00173-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 05/01/2024] [Indexed: 06/01/2024] Open
Abstract
To advance knowledge of microbial communities capable of fermenting agro-industrial residues into value-added products, we report metagenomes of microbial communities from six anaerobic bioreactors that were fed a mixture of ultra-filtered milk permeate and cottage cheese acid whey. These metagenomes produced 122 metagenome-assembled genomes that represent 34 distinct taxa.
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Affiliation(s)
- Kevin A. Walters
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kevin S. Myers
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Timothy J. Donohue
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Daniel R. Noguera
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
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4
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Gallipoli A, Angelini F, Angelini S, Braguglia CM, Montecchio D, Tonanzi B, Gianico A. Thermally enhanced solid-liquid separation process in food waste biorefinery: modelling the anaerobic digestion of solid residues. Front Bioeng Biotechnol 2024; 12:1343396. [PMID: 38371422 PMCID: PMC10869513 DOI: 10.3389/fbioe.2024.1343396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 01/18/2024] [Indexed: 02/20/2024] Open
Abstract
The biochemical valorization potential of food waste (FW) could be exploited by extracting decreasing added-value bio-based products and converting the final residues into energy. In this context, multi-purpose and versatile schemes integrating thermal and biochemical conversion processes will play a key role. An upstream thermal pretreatment + solid-liquid separation unit was here proposed to optimize the conversion of the liquid fraction of FW into valuable chemicals through semi-continuous fermentation process, and the conversion of the residual solid fraction into biomethane through anaerobic digestion. The solid residues obtained after thermal pretreatment presented a higher soluble COD fraction, which resulted in higher methane production with respect to the raw residues (0.33 vs. 0.29 Nm3CH4 kg-1VSfed) and higher risk of acidification and failure of methanogenesis when operating at lower HRT (20d). On the contrary, at HRT = 40 d, the pretreatment did not affect the methane conversion rates and both tests evidenced similar methane productions of 0.33 Nm3CH4 kg-1VSfed. In the reactor fed with pretreated residue, the association of hydrogenotrophic methanogens with syntrophic bacteria prevented the acidification of the system. Modelling proved the eligibility of the FW solid residues as substrates for anaerobic digestion, given their small inert fractions that ranged between 0% and 30% of the total COD content.
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Affiliation(s)
| | | | | | | | | | | | - Andrea Gianico
- National Research Council of Italy, Water Research Institute, CNR-IRSA, Rome, Italy
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5
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Yang L, Chen L, Zhao C, Li H, Cai J, Deng Z, Liu M. Biogas slurry recirculation regulates food waste fermentation: Effects and mechanisms. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 347:119101. [PMID: 37748298 DOI: 10.1016/j.jenvman.2023.119101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/09/2023] [Accepted: 09/19/2023] [Indexed: 09/27/2023]
Abstract
Regularly adding biogas slurry into fermentation reactors is an effective way to enhance hydrogen or methane production. However, how this method affects the production of valuable organic acids and alcohols is still being determined. This study investigated the effects of different addition ratios on semi-continuous fermentation reactors using food waste as a substrate. The results showed that an addition ratio of 0.2 increased lactic acid production by 30% with a yield of 0.38 ± 0.01 g/g VS, while a ratio of 0.4 resulted in mixed acid fermentation dominated by n-butyric acid (0.07 ± 0.01 g/g VS) and n-caproic acid (0.06 ± 0.00 g/g VS). The introduction of Bifidobacteriaceae by biogas slurry played a crucial role in increasing lactic acid production. In contrast, exclusive medium-chain fatty acid producers enhanced the synthesis of caproic acid and heptanoic acid via the reverse β-oxidation pathway. Mechanism analyses suggested that microbial community structure and activity, substrate hydrolysis, and cell membrane transport system and structure changed to varying degrees after adding biogas slurry.
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Affiliation(s)
- Luxin Yang
- Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Liang Chen
- Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Chuyun Zhao
- Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Huan Li
- Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China.
| | - Jiabai Cai
- Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China; Department of Environmental Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Katsura C-1-3, 615-8540, Kyoto, Japan
| | - Zhou Deng
- Shenzhen Lisai Environmental Technology Co. Ltm., Shenzhen, 518055, China
| | - Mengqian Liu
- Shenzhen Originwater Ecological Investment Construction Co., LTD, China
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6
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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: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [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.
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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
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7
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Tucci M, Fernández-Verdejo D, Resitano M, Ciacia P, Guisasola A, Blánquez P, Marco-Urrea E, Cruz Viggi C, Matturro B, Crognale S, Aulenta F. Toluene-driven anaerobic biodegradation of chloroform in a continuous-flow bioelectrochemical reactor. CHEMOSPHERE 2023; 338:139467. [PMID: 37437617 DOI: 10.1016/j.chemosphere.2023.139467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/12/2023] [Accepted: 07/09/2023] [Indexed: 07/14/2023]
Abstract
Subsurface co-contamination by multiple pollutants can be challenging for the design of bioremediation strategies since it may require promoting different and often antagonistic degradation pathways. Here, we investigated the simultaneous degradation of toluene and chloroform (CF) in a continuous-flow anaerobic bioelectrochemical reactor. As a result, 47 μmol L-1 d-1 of toluene and 60 μmol L-1 d-1 of CF were concurrently removed, when the anode was polarized at +0.4 V vs. Standard Hydrogen Electrode (SHE). Analysis of the microbial community structure and key functional genes allowed to identify the involved degradation pathways. Interestingly, when acetate was supplied along with toluene, to simulate the impact of a readily biodegradable substrate on process performance, toluene degradation was adversely affected, likely due to competitive inhibition effects. Overall, this study proved the efficacy of the developed bioelectrochemical system in simultaneously treating multiple groundwater contaminants, paving the way for the application in real-world scenarios.
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Affiliation(s)
- Matteo Tucci
- Water Research Institute (IRSA), National Research Council (CNR), Via Salaria km 29.300, 00015, Monterotondo, RM, Italy
| | - David Fernández-Verdejo
- Biorem UAB, Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Marco Resitano
- Water Research Institute (IRSA), National Research Council (CNR), Via Salaria km 29.300, 00015, Monterotondo, RM, Italy
| | - Pamela Ciacia
- Water Research Institute (IRSA), National Research Council (CNR), Via Salaria km 29.300, 00015, Monterotondo, RM, Italy
| | - Albert Guisasola
- GENOCOV, Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Paqui Blánquez
- Biorem UAB, Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Ernest Marco-Urrea
- Biorem UAB, Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Carolina Cruz Viggi
- Water Research Institute (IRSA), National Research Council (CNR), Via Salaria km 29.300, 00015, Monterotondo, RM, Italy
| | - Bruna Matturro
- Water Research Institute (IRSA), National Research Council (CNR), Via Salaria km 29.300, 00015, Monterotondo, RM, Italy; National Biodiversity Future Center (NBFC), Palermo, Italy
| | - Simona Crognale
- Water Research Institute (IRSA), National Research Council (CNR), Via Salaria km 29.300, 00015, Monterotondo, RM, Italy; National Biodiversity Future Center (NBFC), Palermo, Italy
| | - Federico Aulenta
- Water Research Institute (IRSA), National Research Council (CNR), Via Salaria km 29.300, 00015, Monterotondo, RM, Italy; National Biodiversity Future Center (NBFC), Palermo, Italy.
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8
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Ma J, Tan L, Xie S, Feng Y, Shi Z, Ke S, He Q, Ke Q, Zhao Q. The role of hydrochloric acid pretreated activated carbon in chain elongation of D-lactate to caproate: Adsorption and facilitation. ENVIRONMENTAL RESEARCH 2023; 233:116387. [PMID: 37302743 DOI: 10.1016/j.envres.2023.116387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/03/2023] [Accepted: 06/09/2023] [Indexed: 06/13/2023]
Abstract
Medium chain fatty acids (MCFA) generation is attracting growing interest due to fossil fuel depletion. To promote the production of MCFA, especially caproate, hydrochloric acid pretreated activated carbon (AC) was introduced into chain elongation fermentation. In this study, the role of pretreated AC on caproate production was investigated using lactate and butyrate as electron donor and electron acceptor, respectively. The results showed that AC did not improve the chain elongation reaction at beginning but promoted the caproate production at later stage. The addition of 15 g/L AC facilitated reactor reaching the peak of caproate concentration (78.92 mM), caproate electron efficiency (63.13%), and butyrate utilization rate (51.88%). The adsorption experiment revealed a positive correlation between the adsorption capacity of pretreated AC and the concentration as well as the carbon chain length of carboxylic acids. Moreover, the adsorption of undissociated caproate by pretreated AC contributed to a mitigated toxicity towards microorganisms, thereby facilitating the production of MCFA. Microbial community analysis revealed an increasing enrichment of key functional chain elongation bacteria, including Eubacterium, Megasphaera, Caproiciproducens, and Pseudoramibacter, but a suppression on acrylate pathway microorganism Veillonella, as the dosage of pretreated AC increasing. The findings of this study demonstrated the substantial impact of the adsorption effect of acid-pretreated AC on promoting caproate production, which would aid to the development of more efficient caproate production process.
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Affiliation(s)
- Jingwei Ma
- Hunan Engineering Research Center of Water Security Technology and Application, College of Civil Engineering, Hunan University, Changsha, 410082, PR China; Key Laboratory of Building Safety and Energy Efficiency, Ministry of Education, Hunan University, Changsha, 410082, PR China
| | - Liyi Tan
- Hunan Engineering Research Center of Water Security Technology and Application, College of Civil Engineering, Hunan University, Changsha, 410082, PR China; Key Laboratory of Building Safety and Energy Efficiency, Ministry of Education, Hunan University, Changsha, 410082, PR China
| | - Shanbiao Xie
- Hunan Engineering Research Center of Water Security Technology and Application, College of Civil Engineering, Hunan University, Changsha, 410082, PR China; Key Laboratory of Building Safety and Energy Efficiency, Ministry of Education, Hunan University, Changsha, 410082, PR China
| | - Yingxin Feng
- Hunan Engineering Research Center of Water Security Technology and Application, College of Civil Engineering, Hunan University, Changsha, 410082, PR China; Key Laboratory of Building Safety and Energy Efficiency, Ministry of Education, Hunan University, Changsha, 410082, PR China
| | - Zhou Shi
- Hunan Engineering Research Center of Water Security Technology and Application, College of Civil Engineering, Hunan University, Changsha, 410082, PR China; Key Laboratory of Building Safety and Energy Efficiency, Ministry of Education, Hunan University, Changsha, 410082, PR China
| | - Shuizhou Ke
- Hunan Engineering Research Center of Water Security Technology and Application, College of Civil Engineering, Hunan University, Changsha, 410082, PR China; Key Laboratory of Building Safety and Energy Efficiency, Ministry of Education, Hunan University, Changsha, 410082, PR China
| | - Qiulai He
- Hunan Engineering Research Center of Water Security Technology and Application, College of Civil Engineering, Hunan University, Changsha, 410082, PR China; Key Laboratory of Building Safety and Energy Efficiency, Ministry of Education, Hunan University, Changsha, 410082, PR China.
| | - Qiang Ke
- National and Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, Wenzhou University, Wenzhou, 325035, PR China.
| | - Quanbao Zhao
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, PR China
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9
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Sabbe K, D'Haen L, Boon N, Ganigué R. Predicting the performance of chain elongating microbiomes through flow cytometric fingerprinting. WATER RESEARCH 2023; 243:120323. [PMID: 37459796 DOI: 10.1016/j.watres.2023.120323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/29/2023] [Accepted: 07/06/2023] [Indexed: 09/07/2023]
Abstract
As part of the circular bio-economy paradigm shift, waste management and valorisation practices have moved away from sanitation and towards the production of added-value compounds. Recently, the development of mixed culture bioprocess for the conversion of waste(water) to platform chemicals, such as medium chain carboxylic acids, has attracted significant interest. Often, the microbiology of these novel bioprocesses is less diverse and more prone to disturbances, which can lead to process failure. This issue can be tackled by implementing an advanced monitoring strategy based on the microbiology of the process. In this study, flow cytometry was used to monitor the microbiology of lactic acid chain elongation for the production of caproic acid, and assess its performance both qualitatively and quantitatively. Two continuous stirred tank reactors for chain elongation were monitored flow cytometrically for over 336 days. Through community typing, four specific community types could be identified and correlated to both a specific functionality and genotypic diversity. Additionally, the machine-learning algorithms trained in this study demonstrated the ability to predict production rates of, amongst others, caproic acid with high accuracy in the present (R² > 0.87) and intermediate accuracy in the near future (R² > 0.63). The identification of specific community types and the development of predictive algorithms form the basis of advanced bioprocess monitoring based on flow cytometry, and have the potential to improve bioprocess control and optimization, leading to better product quality and yields.
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Affiliation(s)
- Kevin Sabbe
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium; Center for Advanced Process Technology for Urban Resource Recovery (CAPTURE), Frieda Saeysstraat 1, 9052 Ghent, Belgium
| | - Liese D'Haen
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium; Center for Advanced Process Technology for Urban Resource Recovery (CAPTURE), Frieda Saeysstraat 1, 9052 Ghent, Belgium
| | - Ramon Ganigué
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium; Center for Advanced Process Technology for Urban Resource Recovery (CAPTURE), Frieda Saeysstraat 1, 9052 Ghent, Belgium.
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10
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Walters KA, Mohan G, Myers KS, Ingle AT, Donohue TJ, Noguera DR. A metagenome-level analysis of a microbial community fermenting ultra-filtered milk permeate. Front Bioeng Biotechnol 2023; 11:1173656. [PMID: 37324413 PMCID: PMC10263058 DOI: 10.3389/fbioe.2023.1173656] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 05/03/2023] [Indexed: 06/17/2023] Open
Abstract
Fermentative microbial communities have the potential to serve as biocatalysts for the conversion of low-value dairy coproducts into renewable chemicals, contributing to a more sustainable global economy. To develop predictive tools for the design and operation of industrially relevant strategies that utilize fermentative microbial communities, there is a need to determine the genomic features of community members that are characteristic to the accumulation of different products. To address this knowledge gap, we performed a 282-day bioreactor experiment with a microbial community that was fed ultra-filtered milk permeate, a low-value coproduct from the dairy industry. The bioreactor was inoculated with a microbial community from an acid-phase digester. A metagenomic analysis was used to assess microbial community dynamics, construct metagenome-assembled genomes (MAGs), and evaluate the potential for lactose utilization and fermentation product synthesis of community members represented by the assembled MAGs. This analysis led us to propose that, in this reactor, members of the Actinobacteriota phylum are important in the degradation of lactose, via the Leloir pathway and the bifid shunt, and the production of acetic, lactic, and succinic acids. In addition, members of the Firmicutes phylum contribute to the chain-elongation-mediated production of butyric, hexanoic, and octanoic acids, with different microbes using either lactose, ethanol, or lactic acid as the growth substrate. We conclude that genes encoding carbohydrate utilization pathways, and genes encoding lactic acid transport into the cell, electron confurcating lactate dehydrogenase, and its associated electron transfer flavoproteins, are genomic features whose presence in Firmicutes needs to be established to infer the growth substrate used for chain elongation.
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Affiliation(s)
- Kevin A. Walters
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, United States
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Geethaanjali Mohan
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, United States
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Kevin S. Myers
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, United States
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Abel T. Ingle
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, United States
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, United States
| | - Timothy J. Donohue
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, United States
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Daniel R. Noguera
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, United States
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, United States
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11
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Myers KS, Ingle AT, Walters KA, Fortney NW, Scarborough MJ, Donohue TJ, Noguera DR. Comparison of metagenomes from fermentation of various agroindustrial residues suggests a common model of community organization. Front Bioeng Biotechnol 2023; 11:1197175. [PMID: 37260833 PMCID: PMC10228549 DOI: 10.3389/fbioe.2023.1197175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 04/27/2023] [Indexed: 06/02/2023] Open
Abstract
The liquid residue resulting from various agroindustrial processes is both rich in organic material and an attractive source to produce a variety of chemicals. Using microbial communities to produce chemicals from these liquid residues is an active area of research, but it is unclear how to deploy microbial communities to produce specific products from the different agroindustrial residues. To address this, we fed anaerobic bioreactors one of several agroindustrial residues (carbohydrate-rich lignocellulosic fermentation conversion residue, xylose, dairy manure hydrolysate, ultra-filtered milk permeate, and thin stillage from a starch bioethanol plant) and inoculated them with a microbial community from an acid-phase digester operated at the wastewater treatment plant in Madison, WI, United States. The bioreactors were monitored over a period of months and sampled to assess microbial community composition and extracellular fermentation products. We obtained metagenome assembled genomes (MAGs) from the microbial communities in each bioreactor and performed comparative genomic analyses to identify common microorganisms, as well as any community members that were unique to each reactor. Collectively, we obtained a dataset of 217 non-redundant MAGs from these bioreactors. This metagenome assembled genome dataset was used to evaluate whether a specific microbial ecology model in which medium chain fatty acids (MCFAs) are simultaneously produced from intermediate products (e.g., lactic acid) and carbohydrates could be applicable to all fermentation systems, regardless of the feedstock. MAGs were classified using a multiclass classification machine learning algorithm into three groups, organisms fermenting the carbohydrates to intermediate products, organisms utilizing the intermediate products to produce MCFAs, and organisms producing MCFAs directly from carbohydrates. This analysis revealed common biological functions among the microbial communities in different bioreactors, and although different microorganisms were enriched depending on the agroindustrial residue tested, the results supported the conclusion that the microbial ecology model tested was appropriate to explain the MCFA production potential from all agricultural residues.
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Affiliation(s)
- Kevin S. Myers
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, United States
| | - Abel T. Ingle
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, United States
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, United States
| | - Kevin A. Walters
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, United States
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - Nathaniel W. Fortney
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, United States
| | - Matthew J. Scarborough
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, United States
| | - Timothy J. Donohue
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, United States
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - Daniel R. Noguera
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, United States
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, United States
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12
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Cruz Viggi C, Tucci M, Resitano M, Palushi V, Crognale S, Matturro B, Petrangeli Papini M, Rossetti S, Aulenta F. Enhancing the Anaerobic Biodegradation of Petroleum Hydrocarbons in Soils with Electrically Conductive Materials. Bioengineering (Basel) 2023; 10:bioengineering10040441. [PMID: 37106628 PMCID: PMC10135592 DOI: 10.3390/bioengineering10040441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/24/2023] [Accepted: 03/29/2023] [Indexed: 04/05/2023] Open
Abstract
Anaerobic bioremediation is a relevant process in the management of sites contaminated by petroleum hydrocarbons. Recently, interspecies electron transfer processes mediated by conductive minerals or particles have been proposed as mechanisms through which microbial species within a community share reducing equivalents to drive the syntrophic degradation of organic substrates, including hydrocarbons. Here, a microcosm study was set up to investigate the effect of different electrically conductive materials (ECMs) in enhancing the anaerobic biodegradation of hydrocarbons in historically contaminated soil. The results of a comprehensive suite of chemical and microbiological analyses evidenced that supplementing the soil with (5% w/w) magnetite nanoparticles or biochar particles is an effective strategy to accelerate the removal of selected hydrocarbons. In particular, in microcosms supplemented with ECMs, the removal of total petroleum hydrocarbons was enhanced by up to 50% relative to unamended controls. However, chemical analyses suggested that only a partial bioconversion of contaminants occurred and that longer treatment times would have probably been required to drive the biodegradation process to completion. On the other hand, biomolecular analyses confirmed the presence of several microorganisms and functional genes likely involved in hydrocarbon degradation. Furthermore, the selective enrichment of known electroactive bacteria (i.e., Geobacter and Geothrix) in microcosms amended with ECMs, clearly pointed to a possible role of DIET (Diet Interspecies Electron Transfer) processes in the observed removal of contaminants.
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Affiliation(s)
- Carolina Cruz Viggi
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy
| | - Matteo Tucci
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy
| | - Marco Resitano
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy
| | - Valentina Palushi
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy
| | - Simona Crognale
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy
- National Biodiversity Future Center, 90133 Palermo, Italy
| | - Bruna Matturro
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy
- National Biodiversity Future Center, 90133 Palermo, Italy
| | | | - Simona Rossetti
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy
| | - Federico Aulenta
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy
- National Biodiversity Future Center, 90133 Palermo, Italy
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13
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Crognale S, Massimi A, Sbicego M, Braguglia CM, Gallipoli A, Gazzola G, Gianico A, Tonanzi B, Di Pippo F, Rossetti S. Ecology of food waste chain-elongating microbiome. Front Bioeng Biotechnol 2023; 11:1157243. [PMID: 37113665 PMCID: PMC10126515 DOI: 10.3389/fbioe.2023.1157243] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 03/31/2023] [Indexed: 04/29/2023] Open
Abstract
Microbial chain elongation has emerged as a valuable bioprocess for obtaining marketable products, such as medium chain fatty acids usable in several industrial applications, from organic waste. The understanding of the microbiology and microbial ecology in these systems is crucial to apply these microbiomes in reliable production processes controlling microbial pathways to promote favourable metabolic processes, which will in turn increase product specificity and yields. In this research, the dynamics, cooperation/competition and potentialities of bacterial communities involved in the long-term lactate-based chain elongation process from food waste extract were evaluated under different operating conditions by DNA/RNA amplicon sequencing and functional profile prediction. The feeding strategies and the applied organic loading rates strongly affected the microbial community composition. The use of food waste extract promoted the selection of primary fermenters (i.e., Olsenella, Lactobacillus) responsible for the in situ production of electron donors (i.e., lactate). The discontinuous feeding and the organic loading rate 15 gCOD L-1 d-1 selected the best performing microbiome in which microbes coexist and cooperate to complete the chain elongation process. Both at DNA and RNA level, this microbiome was composed by the lactate producer Olsenella, the short chain fatty acids producers Anaerostipes, Clostridium sensu stricto 7, C. sensu stricto 12, Corynebacterium, Erysipelotrichaceae UCG-004, F0332, Leuconostoc, and the chain elongator Caproiciproducens. This microbiome also showed the highest predicted abundance of short-chain acyl-CoA dehydrogenase, the functional enzyme responsible for the chain elongation process. The combined approach herein used allowed to study the microbial ecology of chain elongation process from food waste by identifying the main functional groups, establishing the presence of potential biotic interactions within the microbiomes, and predicting metabolic potentialities. This study provided pivotal indications for the selection of high-performance microbiome involved in caproate production from food waste that can serve as a basis for further improving system performance and engineering the process scale-up.
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14
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Tucci M, Viggi CC, Crognale S, Matturro B, Rossetti S, Capriotti AL, Cavaliere C, Cerrato A, Montone CM, Harnisch F, Aulenta F. Insights into the syntrophic microbial electrochemical oxidation of toluene: a combined chemical, electrochemical, taxonomical, functional gene-based, and metaproteomic approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 850:157919. [PMID: 35964739 DOI: 10.1016/j.scitotenv.2022.157919] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 08/04/2022] [Accepted: 08/04/2022] [Indexed: 06/15/2023]
Abstract
Biodegradation of aromatic hydrocarbons in anoxic contaminated environments is typically limited by the lack of bioavailable electron acceptors. Microbial electrochemical technologies (METs) are able to provide a virtually inexhaustible electron acceptor in the form of a solid electrode. Recently, we provided first experimental evidence for the syntrophic degradation of toluene in a continuous-flow bioelectrochemical reactor known as the "bioelectric well". Herein, we further analyzed the structure and function of the electroactive toluene-degrading microbiome using a suite of chemical, electrochemical, phylogenetic, proteomic, and functional gene-based analyses. The bioelectric well removed 83 ± 7 % of the toluene from the influent with a coulombic efficiency of 84 %. Cyclic voltammetry allowed to identify the formal potentials of four putative electron transfer sites, which ranged from -0.2 V to +0.1 V vs. SHE, consistent with outer membrane c-type cytochromes and pili of electroactive Geobacter species. The biofilm colonizing the surface of the anode was indeed highly enriched in Geobacter species. On the other hand, the planktonic communities thriving in the bulk of the reactor harbored aromatic hydrocarbons degraders and fermentative propionate-producing microorganisms, as revealed by phylogenetic and proteomic analyses. Most likely, propionate, acetate or other VFAs produced in the bulk liquid from the degradation of toluene were utilized as substrates by the electroactive biofilm. Interestingly, key-functional genes related to the degradation of toluene were found both in the biofilm and in the planktonic communities. Taken as a whole, the herein reported results highlight the importance of applying a comprehensive suite of techniques to unravel the complex cooperative metabolisms occurring in METs.
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Affiliation(s)
- Matteo Tucci
- Water Research Institute (IRSA), National Research Council (CNR), Monterotondo, RM, Italy
| | - Carolina Cruz Viggi
- Water Research Institute (IRSA), National Research Council (CNR), Monterotondo, RM, Italy
| | - Simona Crognale
- Water Research Institute (IRSA), National Research Council (CNR), Monterotondo, RM, Italy
| | - Bruna Matturro
- Water Research Institute (IRSA), National Research Council (CNR), Monterotondo, RM, Italy
| | - Simona Rossetti
- Water Research Institute (IRSA), National Research Council (CNR), Monterotondo, RM, Italy
| | | | - Chiara Cavaliere
- Department of Chemistry, Sapienza - University of Rome, Rome, Italy
| | - Andrea Cerrato
- Department of Chemistry, Sapienza - University of Rome, Rome, Italy
| | | | - Falk Harnisch
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Federico Aulenta
- Water Research Institute (IRSA), National Research Council (CNR), Monterotondo, RM, Italy.
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15
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Zhu X, Huang H, He Y, Wang X, Jia J, Feng X, Li D, Li H. A preliminary study on the feasibility of industrialization for n-caproic acid recovery from food wastewater: From lab to pilot. BIORESOURCE TECHNOLOGY 2022; 366:128154. [PMID: 36270389 DOI: 10.1016/j.biortech.2022.128154] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/12/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
Abstract
Food wastewater is associated with greenhouse gas emission and has a significant water footprint. Here, the platform chemical n-caproate was recovered from liquor brewing wastewater at maximum and mean concentrations of 26.4 g/L and 17.0 ± 4.3 g/L, respectively, after 377 d operation. Laboratory-scale lactate-driven chain elongation (CE) process was implemented first. Taxonomic composition and metagenomic data analyses revealed that Caproiciproducens (e.g., Ruminococcaceae bacterium CPB6) and bacteria affiliated with Lachnospiraceae transformed lactate to n-caproate by reverse β-oxidation and/or fatty acid biosynthesis. The lactate-driven CE process was then scaled up from 2.5 L to 500 L and achieved a n-caproate production of 14.5 ± 0.6 g/L within 96 h. n-Caproic acid was extracted at a concentration and purity of 815.9 ± 8.3 g/L and 88.6 ± 8.9 %, respectively. The present study demonstrated a commercially viable strategy for resource recovery and carbon fixation from food waste streams.
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Affiliation(s)
- Xiaoyu Zhu
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China; University of Chinese Academy of Sciences, Beijing 100864, PR China.
| | - Huanhuan Huang
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China; University of Chinese Academy of Sciences, Beijing 100864, PR China
| | - Yong He
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China; University of Chinese Academy of Sciences, Beijing 100864, PR China
| | - Xinyu Wang
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China; University of Chinese Academy of Sciences, Beijing 100864, PR China; Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, Guilin 541004, PR China
| | - Jia Jia
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China; University of Chinese Academy of Sciences, Beijing 100864, PR China
| | - Xin Feng
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China; University of Chinese Academy of Sciences, Beijing 100864, PR China
| | - Dong Li
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China; University of Chinese Academy of Sciences, Beijing 100864, PR China
| | - Haixiang Li
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, Guilin 541004, PR China
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16
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Baleeiro FCF, Raab J, Kleinsteuber S, Neumann A, Sträuber H. Mixotrophic chain elongation with syngas and lactate as electron donors. Microb Biotechnol 2022; 16:322-336. [PMID: 36378491 PMCID: PMC9871530 DOI: 10.1111/1751-7915.14163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 11/16/2022] Open
Abstract
Feeding microbial communities with both organic and inorganic substrates can improve sustainability and feasibility of chain elongation processes. Sustainably produced H2 , CO2 , and CO can be co-fed to microorganisms as a source for acetyl-CoA, while a small amount of an ATP-generating organic substrate helps overcome the kinetic hindrances associated with autotrophic carboxylate production. Here, we operated two semi-continuous bioreactor systems with continuous recirculation of H2 , CO2 , and CO while co-feeding an organic model feedstock (lactate and acetate) to understand how a mixotrophic community is shaped during carboxylate production. Contrary to the assumption that H2 , CO2 , and CO support chain elongation via ethanol production in open cultures, significant correlations (p < 0.01) indicated that relatives of Clostridium luticellarii and Eubacterium aggregans produced carboxylates (acetate to n-caproate) while consuming H2 , CO2 , CO, and lactate themselves. After 100 days, the enriched community was dominated by these two bacteria coexisting in cyclic dynamics shaped by the CO partial pressure. Homoacetogenesis was strongest when the acetate concentration was low (3.2 g L-1 ), while heterotrophs had the following roles: Pseudoramibacter, Oscillibacter, and Colidextribacter contributed to n-caproate production and Clostridium tyrobutyricum and Acidipropionibacterium spp. grew opportunistically producing n-butyrate and propionate, respectively. The mixotrophic chain elongation community was more efficient in carboxylate production compared with the heterotrophic one and maintained average carbon fixation rates between 0.088 and 1.4 g CO2 equivalents L-1 days-1 . The extra H2 and CO consumed routed 82% more electrons to carboxylates and 50% more electrons to carboxylates longer than acetate. This study shows for the first time long-term, stable production of short- and medium-chain carboxylates with a mixotrophic community.
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Affiliation(s)
- Flávio C. F. Baleeiro
- Department of Environmental MicrobiologyHelmholtz Centre for Environmental Research – UFZLeipzigGermany,Technical Biology, Institute of Process Engineering in Life ScienceKarlsruhe Institute of Technology – KITKarlsruheGermany
| | - Jana Raab
- Department of Environmental MicrobiologyHelmholtz Centre for Environmental Research – UFZLeipzigGermany
| | - Sabine Kleinsteuber
- Department of Environmental MicrobiologyHelmholtz Centre for Environmental Research – UFZLeipzigGermany
| | - Anke Neumann
- Technical Biology, Institute of Process Engineering in Life ScienceKarlsruhe Institute of Technology – KITKarlsruheGermany
| | - Heike Sträuber
- Department of Environmental MicrobiologyHelmholtz Centre for Environmental Research – UFZLeipzigGermany
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17
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Viggi CC, Tucci M, Resitano M, Matturro B, Crognale S, Feigl V, Molnár M, Rossetti S, Aulenta F. Passive electrobioremediation approaches for enhancing hydrocarbons biodegradation in contaminated soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 845:157325. [PMID: 35839884 DOI: 10.1016/j.scitotenv.2022.157325] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/10/2022] [Accepted: 07/09/2022] [Indexed: 06/15/2023]
Abstract
Electrobioremediation technologies hold considerable potential for the treatment of soils contaminated by petroleum hydrocarbons (PH), since they allow stimulating biodegradation processes with no need for subsurface chemicals injection and with little to no energy consumption. Here, a microbial electrochemical snorkel (MES) was applied for the treatment of a soil contaminated by hydrocarbons. The MES consists of direct coupling of a microbial anode with a cathode, being a single conductive, non-polarized material positioned suitably to create an electrochemical connection between the anoxic zone (the contaminated soil) and the oxic zone (the overlying oxygenated water). Soil was also supplemented with electrically conductive particles of biochar as a strategy to construct a conductive network with microbes in the soil matrix, thus extending the radius of influence of the snorkel. The results of a comprehensive suite of chemical, microbiological and ecotoxicological analyses evidenced that biochar addition, rather than the presence of a snorkel, was the determining factor in accelerating PH removal from contaminated soils, possibly accelerating syntrophic and/or cooperative metabolisms involved in the degradation of PH. The enhancement of biodegradation was mirrored by an increased abundance of anaerobic and aerobic microorganisms known to be involved in the degradation of PH and related functional genes. Plant ecotoxicity assays confirmed a reduction of soils toxicity in treatments receiving electrically conductive biochar.
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Affiliation(s)
- Carolina Cruz Viggi
- Water Research Institute (IRSA), National Research Council (CNR), Montelibretti (RM) 00010, Italy.
| | - Matteo Tucci
- Water Research Institute (IRSA), National Research Council (CNR), Montelibretti (RM) 00010, Italy
| | - Marco Resitano
- Water Research Institute (IRSA), National Research Council (CNR), Montelibretti (RM) 00010, Italy
| | - Bruna Matturro
- Water Research Institute (IRSA), National Research Council (CNR), Montelibretti (RM) 00010, Italy
| | - Simona Crognale
- Water Research Institute (IRSA), National Research Council (CNR), Montelibretti (RM) 00010, Italy
| | - Viktória Feigl
- Department of Applied Biotechnology and Food Science, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, H-1111 Budapest, Hungary
| | - Mónika Molnár
- Department of Applied Biotechnology and Food Science, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, H-1111 Budapest, Hungary
| | - Simona Rossetti
- Water Research Institute (IRSA), National Research Council (CNR), Montelibretti (RM) 00010, Italy
| | - Federico Aulenta
- Water Research Institute (IRSA), National Research Council (CNR), Montelibretti (RM) 00010, Italy
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18
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Srinivas M, O’Sullivan O, Cotter PD, van Sinderen D, Kenny JG. The Application of Metagenomics to Study Microbial Communities and Develop Desirable Traits in Fermented Foods. Foods 2022; 11:3297. [PMCID: PMC9601669 DOI: 10.3390/foods11203297] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The microbial communities present within fermented foods are diverse and dynamic, producing a variety of metabolites responsible for the fermentation processes, imparting characteristic organoleptic qualities and health-promoting traits, and maintaining microbiological safety of fermented foods. In this context, it is crucial to study these microbial communities to characterise fermented foods and the production processes involved. High Throughput Sequencing (HTS)-based methods such as metagenomics enable microbial community studies through amplicon and shotgun sequencing approaches. As the field constantly develops, sequencing technologies are becoming more accessible, affordable and accurate with a further shift from short read to long read sequencing being observed. Metagenomics is enjoying wide-spread application in fermented food studies and in recent years is also being employed in concert with synthetic biology techniques to help tackle problems with the large amounts of waste generated in the food sector. This review presents an introduction to current sequencing technologies and the benefits of their application in fermented foods.
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Affiliation(s)
- Meghana Srinivas
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, P61 C996 Cork, Ireland
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland
- School of Microbiology, University College Cork, T12 CY82 Cork, Ireland
| | - Orla O’Sullivan
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, P61 C996 Cork, Ireland
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland
- VistaMilk SFI Research Centre, Fermoy, P61 C996 Cork, Ireland
| | - Paul D. Cotter
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, P61 C996 Cork, Ireland
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland
- VistaMilk SFI Research Centre, Fermoy, P61 C996 Cork, Ireland
| | - Douwe van Sinderen
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland
- School of Microbiology, University College Cork, T12 CY82 Cork, Ireland
| | - John G. Kenny
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, P61 C996 Cork, Ireland
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland
- VistaMilk SFI Research Centre, Fermoy, P61 C996 Cork, Ireland
- Correspondence:
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19
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Wu L, Wei W, Liu X, Wang D, Ni BJ. Potentiality of recovering bioresource from food waste through multi-stage Co-digestion with enzymatic pretreatment. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 319:115777. [PMID: 35982572 DOI: 10.1016/j.jenvman.2022.115777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 07/15/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
Food waste (FW) is not only a major social, nutritional and environmental issue, but also an underutilized resource with significant energy, which has not been fully explored currently. Considering co-digestion can adjust carbon to nitrogen ratio (C/N) of the feedstock and improve the synergetic interactions among microorganisms, anaerobic co-digestion (AnCoD) is then becoming an emerging approach to achieve higher energy recovery from FW while ensuring the stability of the system. To obtain higher economic gain from such biodegradable wastes, increasing attention has been paid on optimizing the system configuration or applying enzymatic hydrolysis before digesting FW. A better understanding on the potentiality of correlating enzymatic pretreatment and AnCoD operated in various system configuration would enhance the bioresource recovery from FW and increase revenue through treating this organic waste. Specifically, the biobased chemicals outputs from FW-related co-digestion system with different configuration were firstly compared in this review. A deep discussion concerning the challenges for achieving bioresources recovery from FW co-digestion systems with enzymatic pretreatment was then given. Recommendations for future studies regarding FW co-digestion were then proposed at last.
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Affiliation(s)
- Lan Wu
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Wei Wei
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Xuran Liu
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Dongbo Wang
- Key Laboratory of Environmental Biology and Pollution Control, College of Environmental Science and Engineering, Hunan University, Changsha, 410082, China.
| | - Bing-Jie Ni
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW, 2007, Australia.
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20
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Di Pippo F, Crognale S, Levantesi C, Vitanza L, Sighicelli M, Pietrelli L, Di Vito S, Amalfitano S, Rossetti S. Plastisphere in lake waters: Microbial diversity, biofilm structure, and potential implications for freshwater ecosystems. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 310:119876. [PMID: 35934149 DOI: 10.1016/j.envpol.2022.119876] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 07/26/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Once dispersed in water, microplastic (MP) particles are rapidly colonised by aquatic microbes, which can adhere and grow onto solid surfaces in the form of biofilms. This study provides new insights on microbial diversity and biofilm structure of plastisphere in lake waters. By combining Fourier Confocal Laser Scanning Microscopy (CLSM), Transform Infrared Spectroscopy (FT-IR) and high-throughput DNA sequencing, we investigated the microbial colonization patterns on floating MPs and, for the first time, the occurrence of eukaryotic core members and their possible relations with biofilm-forming bacterial taxa within the plastisphere of four different lakes. Through PCR-based methods (qPCR, LAMP-PCR), we also evaluated the role of lake plastisphere as long-term dispersal vectors of potentially harmful organisms (including pathogens) and antibiotic resistance genes (ARGs) in freshwater ecosystems. Consistent variation patterns of the microbial community composition occurred between water and among the plastisphere samples of the different lakes. The eukaryotic core microbiome was mainly composed by typical freshwater biofilm colonizers, such as diatoms (Pennales, Bacillariophyceaea) and green algae (Chlorophyceae), which interact with eukaryotic and prokaryotic microbes of different trophic levels. Results also showed that MPs are suitable vectors of biofilm-forming opportunistic pathogens and a hotspot for horizontal gene transfer, likely facilitating antibiotic resistance spread in the environments.
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Affiliation(s)
- Francesca Di Pippo
- Water Research Institute, CNR-IRSA, National Research Council, Rome, Italy.
| | - Simona Crognale
- Water Research Institute, CNR-IRSA, National Research Council, Rome, Italy
| | - Caterina Levantesi
- Water Research Institute, CNR-IRSA, National Research Council, Rome, Italy
| | - Luca Vitanza
- Water Research Institute, CNR-IRSA, National Research Council, Rome, Italy
| | - Maria Sighicelli
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA) CR Casaccia, Rome, Italy
| | - Loris Pietrelli
- Department of Chemistry, Sapienza University of Rome, Rome, Italy
| | | | - Stefano Amalfitano
- Water Research Institute, CNR-IRSA, National Research Council, Rome, Italy
| | - Simona Rossetti
- Water Research Institute, CNR-IRSA, National Research Council, Rome, Italy
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21
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Metagenomes and Metagenome-Assembled Genomes from Microbiomes Metabolizing Thin Stillage from an Ethanol Biorefinery. Microbiol Resour Announc 2022; 11:e0029022. [PMID: 35862918 PMCID: PMC9387277 DOI: 10.1128/mra.00290-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we report the metagenomes from five anaerobic bioreactors, operated under different conditions, that were fed carbohydrate-rich thin stillage from a corn starch ethanol plant. The putative functions of the abundant taxa identified here will inform future studies of microbial communities involved in valorizing this and other low-value agroindustrial residues.
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22
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Gazzola G, Maria Braguglia C, Crognale S, Gallipoli A, Mininni G, Piemonte V, Rossetti S, Tonanzi B, Gianico A. Biorefining food waste through the anaerobic conversion of endogenous lactate into caproate: A fragile balance between microbial substrate utilization and product inhibition. WASTE MANAGEMENT (NEW YORK, N.Y.) 2022; 150:328-338. [PMID: 35907330 DOI: 10.1016/j.wasman.2022.07.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/27/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
New technologies development and renewable source exploitation are key tools to realize the European Green Deal and to boost the bio-based economy. In this context, fermentation of organic residues as food waste is an efficient method to obtain marketable products such as carboxylic acids widely applied in industrial production. Under favourable thermodynamic conditions, short chain fatty acids deriving from primary fermentation could be biologically converted into medium-chain fatty acids as caproate via chain elongation (CE) process, by using ethanol or lactate as electron donors. This study evaluates the effectivity of producing caproate from Food Waste extract rich in organics with in situ electron donor production. The test carried out at OLR 15 gCOD L-1d-1 showed high Volatile Fatty Acids (from acetic to caproic acid) yields (0.37 g g-1CODfed), with a maximum caproate concentration of 8 g L-1. The associated microbiome was composed by lactate-producing bacteria (Corynebacterium, Lactobacillus, and Olsenella) and by chain elongators (Clostridiaceae and Caproiciproducens). By stressing the system with OLR increase up to 20 gCOD L-1d-1, the CE process was inhibited by the high concentration of caproate (low occurrence of Clostridiaceae and Caproiciproducens). Nevertheless, after few days of stop-feeding regime imposed to the system, the microbiome restored its capability to proceed with lactate-based CE pathways. Different batch tests carried out with the inhibited biomass at increasing initial caproate concentration confirmed its impact on lactate utilization kinetics.
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Affiliation(s)
- Giulio Gazzola
- Water Research Institute, National Research Council of Italy, CNR-IRSA, Area della Ricerca RM1, Via Salaria km 29.300, 00015 Monterotondo, Roma, Italy
| | - Camilla Maria Braguglia
- Water Research Institute, National Research Council of Italy, CNR-IRSA, Area della Ricerca RM1, Via Salaria km 29.300, 00015 Monterotondo, Roma, Italy
| | - Simona Crognale
- Water Research Institute, National Research Council of Italy, CNR-IRSA, Area della Ricerca RM1, Via Salaria km 29.300, 00015 Monterotondo, Roma, Italy
| | - Agata Gallipoli
- Water Research Institute, National Research Council of Italy, CNR-IRSA, Area della Ricerca RM1, Via Salaria km 29.300, 00015 Monterotondo, Roma, Italy
| | - Giuseppe Mininni
- Water Research Institute, National Research Council of Italy, CNR-IRSA, Area della Ricerca RM1, Via Salaria km 29.300, 00015 Monterotondo, Roma, Italy
| | - Vincenzo Piemonte
- Faculty of Engineering, University Campus Bio-Medico, Via Alvaro del Portillo, 21, 00128 Roma, Italy
| | - Simona Rossetti
- Water Research Institute, National Research Council of Italy, CNR-IRSA, Area della Ricerca RM1, Via Salaria km 29.300, 00015 Monterotondo, Roma, Italy
| | - Barbara Tonanzi
- Water Research Institute, National Research Council of Italy, CNR-IRSA, Area della Ricerca RM1, Via Salaria km 29.300, 00015 Monterotondo, Roma, Italy
| | - Andrea Gianico
- Water Research Institute, National Research Council of Italy, CNR-IRSA, Area della Ricerca RM1, Via Salaria km 29.300, 00015 Monterotondo, Roma, Italy.
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23
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Editorial for Special Issue "Microorganisms and Organic Waste Valorisation". Microorganisms 2022; 10:microorganisms10081493. [PMID: 35893551 PMCID: PMC9331733 DOI: 10.3390/microorganisms10081493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 11/17/2022] Open
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24
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Metagenomes and Metagenome-Assembled Genomes from Microbial Communities Fermenting Ultrafiltered Milk Permeate. Microbiol Resour Announc 2022; 11:e0029322. [PMID: 35770995 PMCID: PMC9302107 DOI: 10.1128/mra.00293-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fermentative microbial communities can be utilized for the conversion of various agroindustrial residues into valuable chemicals. Here, we report 34 metagenomes from anaerobic bioreactors fed lactose-rich ultrafiltered milk permeate and 278 metagenome-assembled genomes (MAGs). These MAGs can inform future studies aimed at generating renewable chemicals from dairy and other agroindustrial residues.
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25
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Cruz Viggi C, Tucci M, Resitano M, Crognale S, Di Franca ML, Rossetti S, Aulenta F. Coupling of bioelectrochemical toluene oxidation and trichloroethene reductive dechlorination for single-stage treatment of groundwater containing multiple contaminants. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2022; 11:100171. [PMID: 36158759 PMCID: PMC9488093 DOI: 10.1016/j.ese.2022.100171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/29/2022] [Accepted: 03/29/2022] [Indexed: 05/12/2023]
Abstract
Bioremediation of groundwater contaminated by a mixture of aromatic hydrocarbons and chlorinated solvents is typically challenged because these contaminants are degraded via distinctive oxidative and reductive pathways, thus requiring different amendments and redox conditions. Here, we provided the proof-of-concept of a single-stage treatment of synthetic groundwater containing toluene and trichloroethene (TCE) in a tubular bioelectrochemical reactor, known as a "bioelectric well". Toluene was degraded by a microbial bioanode (up to 150 μmol L-1 d-1) with a polarized graphite anode (+0.2 V vs. SHE) serving as the terminal electron acceptor. The electric current deriving from microbially-driven toluene oxidation resulted in (abiotic) hydrogen production (at a stainless-steel cathode), which sustained the reductive dechlorination of TCE to less-chlorinated intermediates (i.e., cis-DCE, VC, and ETH), at a maximum rate of 500 μeq L-1 d-1, in the bulk of the reactor. A phylogenetic and functional gene-based analysis of the "bioelectric well" confirmed the establishment of a microbiome harboring the metabolic potential for anaerobic toluene oxidation and TCE reductive dechlorination. However, Toluene degradation and current generation were found to be rate-limited by external mass transport phenomena, thus indicating the existing potential for further process optimization.
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26
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Kumar R, Kumar R, Brar SK, Kaur G. Next-generation -omics approaches to drive carboxylate production by acidogenic fermentation of food waste: a review. Bioengineered 2022; 13:14987-15002. [PMID: 37105768 DOI: 10.1080/21655979.2023.2180583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023] Open
Abstract
Acidogenic fermentation of food waste using mixed microbial cultures can produce carboxylates [or volatile fatty acids (VFA)] as high-valued bioproducts via a complex interplay of microorganisms during different stages of this process. However, the present fermentation systems are incapable of reaching the industrially relevant VFA production yields of ≥50 g/L primarly due to the complex process operation, competitive metabolic pathways, and limited understanding of microbial interplays. Recent reports have demonstrated the significant roles played by microbial communities from different phyla, which work together to control the process kinetics of various stages underlying acidogenic fermentation. In order to fully delineate the abundance, structure, and functionality of these microbial communities, next-generation high-throughput meta-omics technologies are required. In this article, we review the potential of metagenomics and metatranscriptomics approaches to enable microbial community engineering. Specifically, a deeper analysis of taxonomic relationships, shifts in microbial communities, and differences in the genetic expression of key pathway enzymes under varying operational and environmental parameters of acidogenic fermentation could lead to the identification of species-level functionalities for both cultivable and non-cultivable microbial fractions. Furthermore, it could also be used for successful gene sequence-guided microbial isolation and consortium development for bioaugmentation to allow VFA production with high concentrations and purity. Such highly controlled and engineered microbial systems could pave the way for tailored and high-yielding VFA synthesis, thereby creating a petrochemically competitive waste-to-value chain and promoting the circular bioeconomy.Research HighlightsMixed microbial mediated acidogenic fermentation of food waste.Metagenomics and metatranscriptomics based microbial community analysis.Omics derived function-associated microbial isolation and consortium engineering.High-valued sustainable carboxylate bio-products, i.e. volatile fatty acids.
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Affiliation(s)
- Reema Kumar
- Department of Civil Engineering, Lassonde School of Engineering, York University, Toronto, Ontario, Canada
| | - Rajat Kumar
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - Satinder K Brar
- Department of Civil Engineering, Lassonde School of Engineering, York University, Toronto, Ontario, Canada
| | - Guneet Kaur
- Department of Civil Engineering, Lassonde School of Engineering, York University, Toronto, Ontario, Canada
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27
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Trachsel JM, Bearson BL, Kerr BJ, Shippy DC, Byrne KA, Loving CL, Bearson SMD. Short Chain Fatty Acids and Bacterial Taxa Associated with Reduced Salmonella enterica serovar I 4,[5],12:i:- Shedding in Swine Fed a Diet Supplemented with Resistant Potato Starch. Microbiol Spectr 2022; 10:e0220221. [PMID: 35532355 PMCID: PMC9241843 DOI: 10.1128/spectrum.02202-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 04/17/2022] [Indexed: 12/03/2022] Open
Abstract
Salmonella enterica serovar I 4,[5],12:i:- is a foodborne pathogen of concern because many isolates are multidrug-resistant (resistant to ≥3 antimicrobial classes) and metal tolerant. In this study, three in-feed additives were individually tested for their ability to reduce Salmonella I 4,[5],12:i:- shedding in swine: resistant potato starch (RPS), high amylose corn starch, and a fatty acid blend, compared with a standard control diet over 21 days. Only RPS-fed pigs exhibited a reduction in Salmonella fecal shedding, different bacterial community compositions, and different cecal short chain fatty acid (SCFA) profiles relative to control animals. Within the RPS treatment group, pigs shedding the least Salmonella tended to have greater cecal concentrations of butyrate, valerate, caproate, and succinate. Additionally, among RPS-fed pigs, several bacterial taxa (Prevotella_7, Olsenella, and Bifidobacterium, and others) exhibited negative relationships between their abundances of and the amount of Salmonella in the feces of their hosts. Many of these same taxa also had significant positive associations with cecal concentrations of butyrate, valerate, caproate, even though they are not known to produce these SCFAs. Together, these data suggest the RPS-associated reduction in Salmonella shedding may be dependent on the establishment of bacterial cross feeding interactions that result in the production of certain SCFAs. However, directly feeding a fatty acid mix did not replicate the effect. RPS supplementation could be an effective means to reduce multidrug-resistant (MDR) S. enterica serovar I 4,[5],12:i:- in swine, provided appropriate bacterial communities are present in the gut. IMPORTANCE Prebiotics, such as resistant potato starch (RPS), are types of food that help to support beneficial bacteria and their activities in the intestines. Salmonella enterica serovar I 4,[5],12:i:- is a foodborne pathogen that commonly resides in the intestines of pigs without disease, but can make humans sick if unintentionally consumed. Here we show that in Salmonella inoculated pigs, feeding them a diet containing RPS altered the colonization and activity of certain beneficial bacteria in a way that reduced the amount of Salmonella in their feces. Additionally, within those fed RPS, swine with higher abundance of these types of beneficial bacteria had less Salmonella I 4,[5],12:i:- in their feces. This work illustrates likely synergy between the prebiotic RPS and the presence of certain gut microorganisms to reduce the amount of Salmonella in the feces of pigs and therefore reduce the risk that humans will become ill with MDR Salmonella serovar I 4,[5],12:i:-.
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Affiliation(s)
- Julian M. Trachsel
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, USDA, ARS, Ames, Iowa, USA
| | - Bradley L. Bearson
- Agroecosystems Management Research Unit, National Laboratory for Agriculture and the Environment, USDA, ARS, Ames, Iowa, USA
| | - Brian J. Kerr
- Agroecosystems Management Research Unit, National Laboratory for Agriculture and the Environment, USDA, ARS, Ames, Iowa, USA
| | - Daniel C. Shippy
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, USDA, ARS, Ames, Iowa, USA
| | - Kristen A. Byrne
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, USDA, ARS, Ames, Iowa, USA
| | - Crystal L. Loving
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, USDA, ARS, Ames, Iowa, USA
| | - Shawn M. D. Bearson
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, USDA, ARS, Ames, Iowa, USA
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28
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Gianico A, Gallipoli A, Gazzola G, Pastore C, Tonanzi B, Braguglia CM. A novel cascade biorefinery approach to transform food waste into valuable chemicals and biogas through thermal pretreatment integration. BIORESOURCE TECHNOLOGY 2021; 338:125517. [PMID: 34273629 DOI: 10.1016/j.biortech.2021.125517] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/02/2021] [Accepted: 07/04/2021] [Indexed: 06/13/2023]
Abstract
A novel biorefinery platform integrating thermal pretreatment and solid-liquid separation unit is here proposed to fully exploit food waste (FW) potential for production of valuable chemicals and energy through semi-continuous anaerobic bioconversion. The liquid fraction deriving from raw or pretreated FW, was fermented into volatile fatty acids (VFAs, from acetic to caproic acid) while the residual fraction was converted into biomethane. Thermal pretreatment effectively extracted a portion of the macromolecular organics, especially starch, to the liquid phase, promoting acidogenic fermentation and chain elongation pathways (0.43 gVFA g-1VSfed and 0.58 gVFA g-1VSfed with raw and pretreated extract, respectively). In parallel, anaerobic digestion of solid residue in 10 L reactors showed process stability and higher conversion rate for the pretreated residue (0.31 against 0.26 Nm3CH4 kg-1VSfed). The mass-transfer balance coupled with the economic assessment, calculated in terms of direct gross added value, indicated promising revenues by integrating the thermal upstream treatment.
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Affiliation(s)
- Andrea Gianico
- National Research Council of Italy, Water Research Institute, CNR-IRSA, Area della Ricerca RM1, Via Salaria km 29.300, Monterotondo, Rome 00015, Italy
| | - Agata Gallipoli
- National Research Council of Italy, Water Research Institute, CNR-IRSA, Area della Ricerca RM1, Via Salaria km 29.300, Monterotondo, Rome 00015, Italy.
| | - Giulio Gazzola
- National Research Council of Italy, Water Research Institute, CNR-IRSA, Area della Ricerca RM1, Via Salaria km 29.300, Monterotondo, Rome 00015, Italy
| | - Carlo Pastore
- National Research Council of Italy, Water Research Institute, CNR-IRSA, Via F. de Blasio 5, Bari 70132, Italy
| | - Barbara Tonanzi
- National Research Council of Italy, Water Research Institute, CNR-IRSA, Area della Ricerca RM1, Via Salaria km 29.300, Monterotondo, Rome 00015, Italy
| | - Camilla M Braguglia
- National Research Council of Italy, Water Research Institute, CNR-IRSA, Area della Ricerca RM1, Via Salaria km 29.300, Monterotondo, Rome 00015, Italy
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29
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Simultaneous removal of hydrocarbons and sulfate from groundwater using a “bioelectric well”. Electrochim Acta 2021. [DOI: 10.1016/j.electacta.2021.138636] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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30
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Guadamuro L, Azcárate-Peril MA, Tojo R, Mayo B, Delgado S. Impact of Dietary Isoflavone Supplementation on the Fecal Microbiota and Its Metabolites in Postmenopausal Women. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18157939. [PMID: 34360231 PMCID: PMC8345437 DOI: 10.3390/ijerph18157939] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 07/20/2021] [Accepted: 07/22/2021] [Indexed: 12/23/2022]
Abstract
Isoflavones are metabolized by components of the gut microbiota and can also modulate their composition and/or activity. This study aimed to analyze the modifications of the fecal microbial populations and their metabolites in menopausal women under dietary treatment with soy isoflavones for one month. Based on the level of urinary equol, the women had been stratified previously as equol-producers (n = 3) or as equol non-producers (n = 5). The composition of the fecal microbiota was assessed by high-throughput sequencing of 16S rRNA gene amplicons and the changes in fatty acid excretion in feces were analyzed by gas chromatography. A greater proportion of sequence reads of the genus Slackia was detected after isoflavone supplementation. Sequences of members of the family Lachnospiraceae and the genus Pseudoflavonifractor were significantly increased in samples from equol-producing women. Multivariable analysis showed that, after isoflavone treatment, the fecal microbial communities of equol producers were more like each other. Isoflavone supplementation increased the production of caproic acid, suggesting differential microbial activity, leading to a high fecal excretion of this compound. However, differences between equol producers and non-producers were not scored. These results may contribute to characterizing the modulating effect of isoflavones on the gut microbiota, which could lead to unravelling of their beneficial health effects.
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Affiliation(s)
- Lucía Guadamuro
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Departament of Microbiology and Biochemistry of Dairy Products, Paseo Río Linares s/n, 33300 Villaviciosa, Spain; (L.G.); (B.M.)
| | - M. Andrea Azcárate-Peril
- Division of Gastroenterology and Hepatology, and Microbiome Core, School of Medicine, Department of Medicine, University of North Carolina (UNC), Chapel Hill, NC 2759, USA;
| | - Rafael Tojo
- Gastroenterology Department, Cabueñes University Hospital, 33203 Gijón, Spain;
| | - Baltasar Mayo
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Departament of Microbiology and Biochemistry of Dairy Products, Paseo Río Linares s/n, 33300 Villaviciosa, Spain; (L.G.); (B.M.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Avenida de Roma s/n, 33011 Oviedo, Spain
| | - Susana Delgado
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Departament of Microbiology and Biochemistry of Dairy Products, Paseo Río Linares s/n, 33300 Villaviciosa, Spain; (L.G.); (B.M.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Avenida de Roma s/n, 33011 Oviedo, Spain
- Correspondence:
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31
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Wei Y, Ren B, Zheng S, Feng X, He Y, Zhu X, Zhou L, Li D. Effect of high concentration of ammonium on production of n-caproate: Recovery of a high-value biochemical from food waste via lactate-driven chain elongation. WASTE MANAGEMENT (NEW YORK, N.Y.) 2021; 128:25-35. [PMID: 33957431 DOI: 10.1016/j.wasman.2021.04.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 03/08/2021] [Accepted: 04/05/2021] [Indexed: 06/12/2023]
Abstract
Ammonium accumulation is inevitable during the fermentation of food waste (FW), challenging the application of chain elongation process upgrading FW into the high-value biochemical n-caproate, which is a medium chain carboxylate. This study is the first to investigate ammonium inhibition of lactate-driven chain elongation process. The short-term exposure of a Clostridium IV-dominated chain elongating reactor microbiome at an ammonium concentration of 1-4 g L-1 linearly decreased n-caproate production by 25-80%. High levels of ammonium (≥5 g L-1) could cause failure of chain elongation, shifting the product from n-caproate to propionate. The involved mechanisms revealed that ammonium reshaped the microbial community from Clostridium IV domination to Clostridium IV and Propionibacterium co-domination (based on 16S rRNA sequencing) and reduced the activities of key enzymes involved in the reversed β-oxidization pathway. We propose an effective strategy from our study, which is the first one to do in our knowledge, to upgrade raw FW without dilution to n-caproate: lowering the ammonium accumulation to 1.0 g L-1 at the setup phase for adaptation and prolonging the hydraulic retention time (10 days) during the operation phase for the colonization of chain-elongation bacteria. These findings lay a foundation for the implementation of the LCE process on FW, providing an alternative way to alleviate the global FW crisis.
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Affiliation(s)
- Yong Wei
- School of Environmental and Safety Engineering, Changzhou University, Changzhou 213000, PR China
| | - Bing Ren
- School of Environmental and Safety Engineering, Changzhou University, Changzhou 213000, PR China; Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province; Chengdu Institute of Biology, Chinese Academy of Sciences. Chengdu, 610041, PR China; University of Chinese Academy of Sciences, Beijing 100864, PR China
| | - Shaorui Zheng
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province; Chengdu Institute of Biology, Chinese Academy of Sciences. Chengdu, 610041, PR China; University of Chinese Academy of Sciences, Beijing 100864, PR China; Department of Environmental Engineering, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210014, PR China
| | - Xin Feng
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province; Chengdu Institute of Biology, Chinese Academy of Sciences. Chengdu, 610041, PR China; University of Chinese Academy of Sciences, Beijing 100864, PR China
| | - Yong He
- School of Environmental and Safety Engineering, Changzhou University, Changzhou 213000, PR China; Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province; Chengdu Institute of Biology, Chinese Academy of Sciences. Chengdu, 610041, PR China; University of Chinese Academy of Sciences, Beijing 100864, PR China
| | - Xiaoyu Zhu
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province; Chengdu Institute of Biology, Chinese Academy of Sciences. Chengdu, 610041, PR China; University of Chinese Academy of Sciences, Beijing 100864, PR China.
| | - Lixiang Zhou
- Department of Environmental Engineering, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210014, PR China
| | - Dong Li
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province; Chengdu Institute of Biology, Chinese Academy of Sciences. Chengdu, 610041, PR China; University of Chinese Academy of Sciences, Beijing 100864, PR China
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