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Seid N, Ochsenreither K, Neumann A. Caproate production from Enset fiber in one-pot two-step fermentation using anaerobic fungi (Neocallimastix cameroonii strain G341) and Clostridium kluyveri DSM 555. Microb Cell Fact 2023; 22:216. [PMID: 37864174 PMCID: PMC10588050 DOI: 10.1186/s12934-023-02224-w] [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: 08/10/2023] [Accepted: 10/06/2023] [Indexed: 10/22/2023] Open
Abstract
BACKGROUND Lignocellulosic biomass plays a crucial role in creating a circular bioeconomy and minimizing environmental impact. Enset biomass is a byproduct of traditional Ethiopian Enset food processing that is thrown away in huge quantities. This study aimed to produce caproate from Enset fiber using Neocallimastix cameroonii strain G341 and Clostridium kluyveri DSM 555 in one-pot two-step fermentation. RESULTS The process started by growing N. cameroonii on Enset fiber as a carbon source for 7 days. Subsequently, the fungal culture was inoculated with active C. kluyveri preculture and further incubated. The results showed that N. cameroonii grew on 0.25 g untreated Enset fiber as the sole carbon source and produced 1.16 mmol acetate, 0.51 mmol hydrogen, and 1.34 mmol formate. In addition, lactate, succinate, and ethanol were detected in small amounts, 0.17 mmol, 0.08 mmol, and 0.7 mmol, respectively. After inoculating with C. kluyveri, 0.3 mmol of caproate and 0.48 mmol of butyrate were produced, and hydrogen production also increased to 0.95 mmol compared to sole N. cameroonii fermentation. Moreover, after the culture was supplemented with 2.18 mmol of ethanol during C. kluyveri inoculation, caproate, and hydrogen production was further increased to 1.2 and 1.36 mmol, respectively, and the consumption of acetate also increased. CONCLUSION A novel microbial cell factory was developed to convert untreated lignocellulosic Enset fiber into the medium chain carboxylic acid caproate and H2 by a co-culture of the anaerobic fungi N. cameroonii and C. kluyveri. This opens a new value chain for Enset farmers, as the process requires only locally available raw materials and low-price fermenters. As the caproate production was mainly limited by the available ethanol, the addition of locally produced ethanol-containing fermentation broth ("beer") would further increase the titer.
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Affiliation(s)
- Nebyat Seid
- Electrobiotechnology, Institute of Process Engineering in Life Science 2, Karlsruhe Institute of Technology (KIT), 76131, Karlsruhe, Germany.
- School of Chemical and Bio Engineering, Addis Ababa Institute of Technology, Addis Ababa University, P.O.B: 1176, Addis Ababa, Ethiopia.
| | - Katrin Ochsenreither
- Department of Chemical and Process Engineering, Karlsruhe Institute of Technology (KIT), 76131, Karlsruhe, Germany
| | - Anke Neumann
- Electrobiotechnology, Institute of Process Engineering in Life Science 2, Karlsruhe Institute of Technology (KIT), 76131, Karlsruhe, Germany.
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Lebuhn M, Podmirseg SM, Baier U. Editorial for Special Issue "Unleashing the Hidden Potential of Anaerobic Fungi". Microorganisms 2023; 11:652. [PMID: 36985225 PMCID: PMC10059939 DOI: 10.3390/microorganisms11030652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 02/24/2023] [Indexed: 03/06/2023] Open
Abstract
Anaerobic fungi (AF) of the phylum Neocallimastigomycota are a very peculiar group of microorganisms [...].
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Affiliation(s)
- Michael Lebuhn
- Department for Quality Assurance and Analytics, Bavarian State Research Center for Agriculture, 85354 Freising, Germany
| | | | - Urs Baier
- Institute of Chemistry and Biotechnology (ICBT), Zurich University of Applied Sciences (ZHAW), 8820 Wädenswil, Switzerland
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Hanafy RA, Wang Y, Stajich JE, Pratt CJ, Youssef NH, Elshahed MS. Phylogenomic analysis of the Neocallimastigomycota: proposal of Caecomycetaceae fam. nov., Piromycetaceae fam. nov., and emended description of the families Neocallimastigaceae and Anaeromycetaceae. Int J Syst Evol Microbiol 2023; 73. [PMID: 36827202 DOI: 10.1099/ijsem.0.005735] [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: 02/25/2023] Open
Abstract
The anaerobic gut fungi (AGF) represent a coherent phylogenetic clade within the Mycota. Twenty genera have been described so far. Currently, the phylogenetic and evolutionary relationships between AGF genera remain poorly understood. Here, we utilized 52 transcriptomic datasets from 14 genera to resolve AGF inter-genus relationships using phylogenomics, and to provide a quantitative estimate (amino acid identity, AAI) for intermediate rank assignments. We identify four distinct supra-genus clades, encompassing all genera producing polyflagellated zoospores, bulbous rhizoids, the broadly circumscribed genus Piromyces, and the Anaeromyces and affiliated genera. We also identify the genus Khoyollomyces as the earliest evolving AGF genus. Concordance between phylogenomic outputs and RPB1 and D1/D2 LSU, but not RPB2, MCM7, EF1α or ITS1, phylogenies was observed. We combine phylogenomic analysis and AAI outputs with informative phenotypic traits to propose accommodating 14/20 AGF genera into four families: Caecomycetaceae fam. nov. (encompassing the genera Caecomyces and Cyllamyces), Piromycetaceae fam. nov. (encompassing the genus Piromyces), emend the description of the family Neocallimastigaceae to encompass the genera Neocallimastix, Orpinomyces, Pecoramyces, Feramyces, Ghazallomyces, Aestipascuomyces and Paucimyces, as well as the family Anaeromycetaceae to include the genera Oontomyces, Liebetanzomyces and Capellomyces in addition to Anaeromyces. We refrain from proposing families for the deeply branching genus Khoyollomyces and for genera with uncertain position (Buwchfawromyces, Joblinomyces, Tahromyces, Agriosomyces and Aklioshbomyces) pending availability of additional isolates and sequence data; and these genera are designated as 'genera incertae sedis' in the order Neocallimastigales. Our results establish an evolutionary-grounded Linnaean taxonomic framework for the AGF, provide quantitative estimates for rank assignments, and demonstrate the utility of RPB1 as an additional informative marker in Neocallimastigomycota taxonomy.
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Affiliation(s)
- Radwa A Hanafy
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA.,Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, DE, USA
| | - Yan Wang
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada.,Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA
| | - Carrie J Pratt
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
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Joshi A, Young D, Huang L, Mosberger L, Munk B, Vinzelj J, Flad V, Sczyrba A, Griffith GW, Podmirseg SM, Warthmann R, Lebuhn M, Insam H. Effect of Growth Media on the Diversity of Neocallimastigomycetes from Non-Rumen Habitats. Microorganisms 2022; 10:1972. [PMID: 36296248 PMCID: PMC9612151 DOI: 10.3390/microorganisms10101972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/25/2022] [Accepted: 10/01/2022] [Indexed: 12/02/2022] Open
Abstract
Anaerobic fungi (AF), belonging to the phylum Neocallimastigomycota, are a pivotal component of the digestive tract microbiome of various herbivorous animals. In the last decade, the diversity of AF has rapidly expanded due to the exploration of numerous (novel) habitats. Studies aiming at understanding the role of AF require robust and reliable isolation and cultivation techniques, many of which remained unchanged for decades. Using amplicon sequencing, we compared three different media: medium with rumen fluid (RF), depleted rumen fluid (DRF), and no rumen fluid (NRF) to enrich the AF from the feces of yak, as a rumen control; and Przewalski's horse, llama, guanaco, and elephant, as a non-rumen habitats. The results revealed the selective enrichment of Piromyces and Neocallimastix from the feces of elephant and llama, respectively, in the RF medium. Similarly, the enrichment culture in DRF medium explicitly manifested Piromyces-related sequences from elephant feces. Five new clades (MM1-5) were defined from llama, guanaco, yak, and elephant feces that could as well be enriched from llama and elephant samples using non-conventional DRF and NRF media. This study presents evidence for the selective enrichment of certain genera in medium with RF and DRF from rumen as well as from non-rumen samples. NRF medium is suggested for the isolation of AF from non-rumen environments.
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Affiliation(s)
- Akshay Joshi
- Biocatalysis, Environment and Process Technology Unit, Life Science and Facility Management, Zurich University of Applied Sciences (ZHAW), 8820 Wadenswil, Switzerland
- Department of Microbiology, University of Innsbruck, Technikerstrasse 25d, A-6020 Innsbruck, Austria
| | - Diana Young
- Central Department for Quality Assurance and Analytics, Micro- and Molecular Biology, Bavarian State Research Center for Agriculture, Lange Point 6, 85354 Freising, Germany
| | - Liren Huang
- Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
| | - Lona Mosberger
- Biocatalysis, Environment and Process Technology Unit, Life Science and Facility Management, Zurich University of Applied Sciences (ZHAW), 8820 Wadenswil, Switzerland
| | - Bernhard Munk
- Chair of Urban Water Systems Engineering, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Julia Vinzelj
- Department of Microbiology, University of Innsbruck, Technikerstrasse 25d, A-6020 Innsbruck, Austria
| | - Veronika Flad
- Central Department for Quality Assurance and Analytics, Micro- and Molecular Biology, Bavarian State Research Center for Agriculture, Lange Point 6, 85354 Freising, Germany
| | - Alexander Sczyrba
- Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
| | - Gareth W. Griffith
- Department of Life Sciences, Cledwyn Building, Aberystwyth University, Aberystwyth SY23 3DD, UK
| | - Sabine Marie Podmirseg
- Department of Microbiology, University of Innsbruck, Technikerstrasse 25d, A-6020 Innsbruck, Austria
| | - Rolf Warthmann
- Biocatalysis, Environment and Process Technology Unit, Life Science and Facility Management, Zurich University of Applied Sciences (ZHAW), 8820 Wadenswil, Switzerland
| | - Michael Lebuhn
- Central Department for Quality Assurance and Analytics, Micro- and Molecular Biology, Bavarian State Research Center for Agriculture, Lange Point 6, 85354 Freising, Germany
| | - Heribert Insam
- Department of Microbiology, University of Innsbruck, Technikerstrasse 25d, A-6020 Innsbruck, Austria
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Vinzelj J, Joshi A, Young D, Begovic L, Peer N, Mosberger L, Luedi KCS, Insam H, Flad V, Nagler M, Podmirseg SM. No time to die: Comparative study on preservation protocols for anaerobic fungi. Front Microbiol 2022; 13:978028. [PMID: 36225373 PMCID: PMC9549207 DOI: 10.3389/fmicb.2022.978028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 08/24/2022] [Indexed: 11/13/2022] Open
Abstract
Anaerobic fungi (AF, phylum Neocallimastigomycota) are best known for their ability to anaerobically degrade recalcitrant lignocellulosic biomass through mechanic and enzymatic means. While their biotechnological potential is well-recognized, applied research on AF is still hampered by the time-consuming and cost-intensive laboratory routines required to isolate, maintain, and preserve AF cultures. Reliable long-term preservation of specific AF strains would aid basic as well as applied research, but commonly used laboratory protocols for AF preservation can show erratic survival rates and usually exhibit only moderate resuscitation success for up to one or two years after preservation. To address both, the variability, and the preservation issues, we have set up a cross-laboratory, year-long study. We tested five different protocols for the preservation of AF. The experiments were performed at three different laboratories (Austria, Germany, Switzerland) with the same three morphologically distinct AF isolates (Anaeromyces mucronatus, Caeocmyces sp., and Neocallimastix cameroonii) living in stable co-culture with their naturally occurring, syntrophic methanogens. We could show that handling greatly contributes to the variability of results, especially in Anaeromyces mucronatus. Cryopreservation of (mature) biomass in liquid nitrogen had the highest overall survival rates (85-100%, depending on the strain and laboratory). Additionally, preservation on agar at 39°C had surprisingly high survival rates for up to 9 months, if pieces of agar containing mature AF thalli were resuscitated. This low-cost, low-effort method could replace consecutive batch cultivation for periods of up to 6 months, while long-term preservation is best done by cryopreservation in liquid nitrogen. Regardless of the method, however, preserving several replicates (>three) of the same strain is highly advisable.
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Affiliation(s)
- Julia Vinzelj
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Akshay Joshi
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
- Institute of Chemistry and Biotechnology, Biocatalysis and Process Technology Unit, Zurich University of Applied Sciences, Wäedenswil, Switzerland
| | - Diana Young
- Micro- and Molecular Biology, Central Department for Quality Assurance and Analytics, Bavarian State Research Center for Agriculture, Freising, Germany
| | - Ljubica Begovic
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Nico Peer
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Lona Mosberger
- Institute of Chemistry and Biotechnology, Biocatalysis and Process Technology Unit, Zurich University of Applied Sciences, Wäedenswil, Switzerland
| | - Katharina Cécile Schmid Luedi
- Institute of Chemistry and Biotechnology, Biocatalysis and Process Technology Unit, Zurich University of Applied Sciences, Wäedenswil, Switzerland
| | - Heribert Insam
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Veronika Flad
- Micro- and Molecular Biology, Central Department for Quality Assurance and Analytics, Bavarian State Research Center for Agriculture, Freising, Germany
| | - Magdalena Nagler
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
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Stabel M, Haack K, Lübbert H, Greif M, Gorenflo P, Aliyu H, Ochsenreither K. Metabolic shift towards increased biohydrogen production during dark fermentation in the anaerobic fungus Neocallimastix cameroonii G341. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:96. [PMID: 36117170 PMCID: PMC9484062 DOI: 10.1186/s13068-022-02193-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 08/31/2022] [Indexed: 11/25/2022]
Abstract
Background Anaerobic fungi of the phylum Neocallimastigomycota have a high biotechnological potential due to their robust lignocellulose degrading capabilities and the production of several valuable metabolites like hydrogen, acetate, formate, lactate, and ethanol. The metabolism of these fungi, however, remains poorly understood due to limitations of the current cultivation strategies in still-standing bottles, thereby restricting the comprehensive evaluation of cultivation conditions. Results We describe the analysis of growth conditions and their influence on the metabolism of the previously isolated fungus Neocallimastix cameroonii G341. We established a bioreactor process in a stirred tank, enabling cultivation under defined conditions. The optimal growth temperature for the fungus was between 38.5 °C and 41.5 °C, while the optimal pH was 6.6–6.8. Like other dark fermentation systems, hydrogen production is dependent on the hydrogen partial pressure and pH. Shaking the bottles or stirring the fermenters led to an increase in hydrogen and a decrease in lactate and ethanol production. Regulation of the pH to 6.8 in the fermenter nearly doubled the amount of produced hydrogen. Conclusions Novel insights into the metabolism of Neocallimastix cameroonii were gained, with hydrogen being the preferred way of electron disposal over lactate and ethanol. In addition, our study highlights the potential application of the fungus for hydrogen production from un-pretreated biomass. Finally, we established the first cultivation of an anaerobic fungus in a stirred tank reactor system. Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02193-z.
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Hanafy RA, Dagar SS, Griffith GW, Pratt CJ, Youssef NH, Elshahed MS. Taxonomy of the anaerobic gut fungi ( Neocallimastigomycota): a review of classification criteria and description of current taxa. Int J Syst Evol Microbiol 2022; 72. [PMID: 35776761 DOI: 10.1099/ijsem.0.005322] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Members of the anaerobic gut fungi (Neocallimastigomycota) reside in the rumen and alimentary tract of larger mammalian and some reptilian, marsupial and avian herbivores. The recent decade has witnessed a significant expansion in the number of described Neocallimastigomycota genera and species. However, the difficulties associated with the isolation and maintenance of Neocallimastigomycota strains has greatly complicated comparative studies to resolve inter- and intra-genus relationships. Here, we provide an updated outline of Neocallimastigomycota taxonomy. We critically evaluate various morphological, microscopic and phylogenetic traits previously and currently utilized in Neocallimastigomycota taxonomy, and provide an updated key for quick characterization of all genera. We then synthesize data from taxa description manuscripts, prior comparative efforts and molecular sequence data to present an updated list of Neocallimastigomycota genera and species, with an emphasis on resolving relationships and identifying synonymy between recent and historic strains. We supplement data from published manuscripts with information and illustrations from strains in the authors' collections. Twenty genera and 36 species are recognized, but the status of 10 species in the genera Caecomyces, Piromyces, Anaeromyces and Cyllamyces remains uncertain due to the unavailability of culture and conferre (cf.) strains, lack of sequence data, and/or inadequacy of available microscopic and phenotypic data. Six cases of synonymy are identified in the genera Neocallimastix and Caecomyces, and two names in the genus Piromyces are rejected based on apparent misclassification.
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Affiliation(s)
- Radwa A Hanafy
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Sumit S Dagar
- Bioenergy Group, Agharkar Research Institute, Pune, India
| | - Gareth W Griffith
- Institute of Biological, Environmental, and Rural Sciences (IBERS) Aberystwyth University, Aberystwyth, Wales, UK
| | - Carrie J Pratt
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
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Seid N, Griesheimer P, Neumann A. Investigating the Processing Potential of Ethiopian Agricultural Residue Enset/Ensete ventricosum for Biobutanol Production. Bioengineering (Basel) 2022; 9:bioengineering9040133. [PMID: 35447693 PMCID: PMC9025969 DOI: 10.3390/bioengineering9040133] [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] [Received: 02/21/2022] [Revised: 03/17/2022] [Accepted: 03/21/2022] [Indexed: 12/05/2022] Open
Abstract
The Enset plant is a potential food source for about 20 million Ethiopians. A massive amount of residual byproduct is discarded from traditional Ethiopian Enset food processing. This study shows a compositional analysis of Enset biomass and its use for biobutanol production. The Enset biomass was pretreated with 2% (w/v) NaOH or 2% (v/v) H2SO4 and subjected to enzymatic hydrolysis. The enzymatic hydrolysates were then fermented anaerobically by C. saccharoperbutylacetonicum DSM 14923. The majority of Enset biomass waste samples contained 36–67% cellulose, 16–20% hemicelluloses, and less than 6.8% lignin. In all alkali-pretreated Enset biomass samples, the enzyme converted 80–90% of the biomass to glucose within 24 h, while it took 60 h to convert 48–80% of the acid-pretreated Enset biomass. In addition, the alkali pretreatment method released more glucose than the acid pretreatment in all Enset biomass samples. After 72 h of ABE fermentation, 2.8 g/L acetone, 9.9 g/L butanol, and 1.6 g/L ethanol were produced from mixed Enset waste hydrolysate pretreated with alkali, achieving an ABE yield of 0.32 g/g and productivity of 0.2 g × L−1 × h−1, showing the first value of butanol produced from Enset biomass in the literature.
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Affiliation(s)
- Nebyat Seid
- Technical Biology, Institute of Process Engineering in Life Science 2, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany;
| | - Pia Griesheimer
- Institute of Catalysis Research and Technology, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany;
| | - Anke Neumann
- Technical Biology, Institute of Process Engineering in Life Science 2, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany;
- Correspondence:
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