The Anaerobic Fungi: Challenges and Opportunities for Industrial Lignocellulosic Biofuel Production

Saye, Luke M. G.; Navaratna, Tejas; Chong, J.; O’Malley, Michelle; Theodorou, Michael K.; Reilly, Matthew

doi:10.3390/microorganisms9040694

Cited by 46 publications

(36 citation statements)

References 182 publications

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“…The hydrogen and formate produced are then exported and available to neighboring methanogens, which assimilate these products and ultimately generate methane [23]. As such, the metabolic exchange between anaerobic fungi and methanogens benefits both microbes, since it is hypothesized that fungal metabolic end products such as H 2 and formate may inhibit fungal growth and function if allowed to accumulate, while the methanogens are provided with their required growth substrates [36].…”

Section: Synthetic Co-cultures Of C Churrovis With Methanogen M Bryantii Produce Methanementioning

confidence: 99%

Co‑cultivation of the anaerobic fungus Caecomyces churrovis with Methanobacterium bryantii enhances transcription of carbohydrate binding modules, dockerins, and pyruvate formate lyases on specific substrates

Brown

Swift

Mondo

et al. 2021

Biotechnol Biofuels

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Anaerobic fungi and methanogenic archaea are two classes of microorganisms found in the rumen microbiome that metabolically interact during lignocellulose breakdown. Here, stable synthetic co-cultures of the anaerobic fungus Caecomyces churrovis and the methanogen Methanobacterium bryantii (not native to the rumen) were formed, demonstrating that microbes from different environments can be paired based on metabolic ties. Transcriptional and metabolic changes induced by methanogen co-culture were evaluated in C. churrovis across a variety of substrates to identify mechanisms that impact biomass breakdown and sugar uptake. A high-quality genome of C. churrovis was obtained and annotated, which is the first sequenced genome of a non-rhizoid-forming anaerobic fungus. C. churrovis possess an abundance of CAZymes and carbohydrate binding modules and, in agreement with previous studies of early-diverging fungal lineages, N6-methyldeoxyadenine (6mA) was associated with transcriptionally active genes. Co-culture with the methanogen increased overall transcription of CAZymes, carbohydrate binding modules, and dockerin domains in co-cultures grown on both lignocellulose and cellulose and caused upregulation of genes coding associated enzymatic machinery including carbohydrate binding modules in family 18 and dockerin domains across multiple growth substrates relative to C. churrovis monoculture. Two other fungal strains grown on a reed canary grass substrate in co-culture with the same methanogen also exhibited high log2-fold change values for upregulation of genes encoding carbohydrate binding modules in families 1 and 18. Transcriptional upregulation indicated that co-culture of the C. churrovis strain with a methanogen may enhance pyruvate formate lyase (PFL) function for growth on xylan and fructose and production of bottleneck enzymes in sugar utilization pathways, further supporting the hypothesis that co-culture with a methanogen may enhance certain fungal metabolic functions. Upregulation of CBM18 may play a role in fungal–methanogen physical associations and fungal cell wall development and remodeling.

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Section: Synthetic Co-cultures Of C Churrovis With Methanogen M Bryantii Produce Methanementioning

confidence: 99%

Co‑cultivation of the anaerobic fungus Caecomyces churrovis with Methanobacterium bryantii enhances transcription of carbohydrate binding modules, dockerins, and pyruvate formate lyases on specific substrates

Brown

Swift

Mondo

et al. 2021

Biotechnol Biofuels

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“…The most likely explanation for these results is that the AF were unable to survive, or at least be active, in the environment provided in this study. Low activity and survival of anaerobic fungi when applied to non-rumen environments has been reported by others [17,18,20]. Anaerobic fungi are known for having a close symbiotic activity and interspecies H 2 transfer with other microbes in the rumen [37,38].…”

Section: Chemical Changes During Hydrolysismentioning

confidence: 80%

“…Recently, studies utilizing AF to improve biogas production and speed up substrate degradation have been reported [17][18][19]. To date, isolates of the genera Anaeromyces, Neocallimastix, and Piromyces have been added to AD systems in an effort to improve lignocellulose degradation and ultimately improve methane yield [18,19].…”

Section: Introductionmentioning

confidence: 99%

Effect of Bioaugmentation with Anaerobic Fungi Isolated from Ruminants on the Hydrolysis of Corn Silage and Phragmites australis

et al. 2021

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Anaerobic fungi produce extracellular hydrolytic enzymes that facilitate degradation of cellulose and hemicellulose in ruminants. The purpose of this work was to study the impact of three different anaerobic fungal species (Anaeromyces mucronatus YE505, Neocallimastix frontalis 27, and Piromyces rhizinflatus YM600) on hydrolysis of two different lignocellulosic substrates, corn (Zea mays L.) silage and reed (Phragmites australis (Cav.) Trin. ex Steud.). Biomass from each plant species was incubated anaerobically for 11 days either in the presence of live fungal inoculum or with heat-inactivated (control) inoculum. Headspace gas composition, dry matter loss, soluble chemical oxygen demand, concentration of volatile fatty acids, and chemical composition were measured before and after hydrolysis. While some microbial activity was observed, inoculation with anaerobic fungi did not result in any significant difference in the degradation of either type of plant biomass tested, likely due to low fungal activity or survival under the experimental conditions tested. While the premise of utilizing the unique biological activities of anaerobic fungi for biotechnology applications remains promising, further research on optimizing culturing and process conditions is necessary.

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“…33 As such, the metabolic exchange between anaerobic fungi and methanogens benefits both microbes, since it is hypothesized that fungal metabolic end products such as H2 and formate may inhibit fungal growth and function if allowed to accumulate, while the methanogens are provided with their required growth substrates. 49 Figure 2A summarizes the design of this experiment. Cumulative pressure was measured daily (as a proxy for microbial growth) in order to determine when mid-log growth phase had been reached, at which time the cultures were harvested for RNA extraction as shown in Figure 2B and C. 8 Gas chromatography was used to determine the concentration of methane and hydrogen in the headspace gas of synthetic cocultures and fungal monocultures on each substrate prior to harvest for RNA extraction at mid-log growth phase.…”

Section: Synthetic Co-cultures Of C Churrovis With Methanogen M Bryantii Produce Methanementioning

confidence: 99%

Co‑cultivation of the anaerobic fungusCaecomyces churroviswithMethanobacterium bryantiienhances transcription of carbohydrate binding modules

Brown

Swift

Mondo³

et al. 2021

Preprint

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Anaerobic fungi and methanogenic archaea are two classes of microorganisms found in the rumen microbiome that metabolically interact during lignocellulose breakdown. Here, stable synthetic co-cultures of the anaerobic fungus Caecomyces churrovis and the methanogen Methanobacterium bryantii (not native to the rumen) were formed, demonstrating that microbes from different environments can be paired based on metabolic ties. Transcriptional and metabolic changes induced by methanogen co-culture were evaluated in C. churrovis across a variety of substrates to identify mechanisms that impact biomass breakdown and sugar uptake. A high-quality genome of C. churrovis was obtained and annotated, which is the first sequenced genome of a non-rhizoid forming anaerobic fungus. C. churrovis possess an abundance of CAZymes and carbohydrate binding modules and, in agreement with previous studies of early-diverging fungal lineages, N6-methyldeoxyadenine (6mA) was associated with transcriptionally active genes. Co-culture with the methanogen increased overall transcription of CAZymes, carbohydrate binding modules, and dockerin domains in co-cultures grown on both lignocellulose and cellulose and caused upregulation of genes coding associated enzymatic machinery including carbohydrate binding modules in family 18 and dockerin domains across multiple growth substrates relative to C. churrovis monoculture. Two other fungal strains grown on a reed canary grass substrate in co-culture with the same methanogen also exhibited high log2fold change values for upregulation of genes encoding carbohydrate binding modules in families 1 and 18. Transcriptional upregulation indicated that co-culture of the C. churrovis strain with a methanogen may enhance pyruvate formate lyase (PFL) function for growth on xylan and fructose and production of bottleneck enzymes in sugar utilization pathways, further supporting the hypothesis that co-culture with a methanogen may enhance certain fungal metabolic functions. Upregulation of CBM18 may play a role in fungal-methanogen physical associations and fungal cell wall development and remodeling.

show abstract

The Anaerobic Fungi: Challenges and Opportunities for Industrial Lignocellulosic Biofuel Production

Cited by 46 publications

References 182 publications

Co‑cultivation of the anaerobic fungus Caecomyces churrovis with Methanobacterium bryantii enhances transcription of carbohydrate binding modules, dockerins, and pyruvate formate lyases on specific substrates

Co‑cultivation of the anaerobic fungus Caecomyces churrovis with Methanobacterium bryantii enhances transcription of carbohydrate binding modules, dockerins, and pyruvate formate lyases on specific substrates

Effect of Bioaugmentation with Anaerobic Fungi Isolated from Ruminants on the Hydrolysis of Corn Silage and Phragmites australis

Co‑cultivation of the anaerobic fungusCaecomyces churroviswithMethanobacterium bryantiienhances transcription of carbohydrate binding modules

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