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Kyawt YY, Aung M, Xu Y, Zhou Y, Li Y, Sun Z, Zhu W, Cheng Y. Methane production and lignocellulosic degradation of wastes from rice, corn and sugarcane by natural anaerobic fungi-methanogens co-culture. World J Microbiol Biotechnol 2024; 40:109. [PMID: 38411737 DOI: 10.1007/s11274-024-03938-8] [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: 09/23/2023] [Accepted: 02/22/2024] [Indexed: 02/28/2024]
Abstract
Biomass from agriculture, forestry, and urban wastes is a potential renewable organic resource for energy generation. Many investigations have demonstrated that anaerobic fungi and methanogens could be co-cultured to degrade lignocellulose for methane generation. Thus, this study aimed to evaluate the effect of natural anaerobic fungi-methanogens co-culture on the methane production and lignocellulosic degradation of wastes from rice, corn and sugarcane. Hu sheep rumen digesta was used to develop a natural anaerobic fungi-methanogen co-culture. The substrates were rice straw (RS), rich husk (RH), corn stover (CS), corn cobs (CC), and sugarcane baggage (SB). Production of total gas and methane, metabolization rate of reducing sugar, glucose, and xylose, digestibility of hemicellulose and cellulose, activity of carboxymethylcellulase and xylanase, and concentrations of total acid and acetate were highest (P < 0.05) in CC, moderate (P < 0.05) in RS and CS, and lowest (P < 0.05) in SB and RH. The pH, lactate and ethanol were lowest (P < 0.05) in CC, moderate (P < 0.05) in RS and CS, and lowest (P < 0.05) SB and RH. Formate was lowest (P < 0.05) in CC, RS and CS, moderate (P < 0.05) in SB, and lowest (P < 0.05) in RH. Therefore, this study indicated that the potential of methane production and lignocellulosic degradation by natural anaerobic fungi-methanogens co-culture were highest in CC, moderate in RS and CS, and lowest in SB and RH.
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Affiliation(s)
- Yin Yin Kyawt
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
- Department of Animal Nutrition, University of Veterinary Science, Nay Pyi Taw, 15013, Myanmar
| | - Min Aung
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
- Department of Animal Nutrition, University of Veterinary Science, Nay Pyi Taw, 15013, Myanmar
| | - Yao Xu
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yaqi Zhou
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuqi Li
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhanying Sun
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanfen Cheng
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China.
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, China.
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Heom KA, Wangsanuwat C, Butkovich LV, Tam SC, Rowe AR, O'Malley MA, Dey SS. Targeted rRNA depletion enables efficient mRNA sequencing in diverse bacterial species and complex co-cultures. mSystems 2023; 8:e0028123. [PMID: 37855606 PMCID: PMC10734481 DOI: 10.1128/msystems.00281-23] [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: 03/23/2023] [Accepted: 09/12/2023] [Indexed: 10/20/2023] Open
Abstract
IMPORTANCE Microbes present one of the most diverse sources of biochemistry in nature, and mRNA sequencing provides a comprehensive view of this biological activity by quantitatively measuring microbial transcriptomes. However, efficient mRNA capture for sequencing presents significant challenges in prokaryotes as mRNAs are not poly-adenylated and typically make up less than 5% of total RNA compared with rRNAs that exceed 80%. Recently developed methods for sequencing bacterial mRNA typically rely on depleting rRNA by tiling large probe sets against rRNAs; however, such approaches are expensive, time-consuming, and challenging to scale to varied bacterial species and complex microbial communities. Therefore, we developed EMBR-seq+, a method that requires fewer than 10 short oligonucleotides per rRNA to achieve up to 99% rRNA depletion in diverse bacterial species. Finally, EMBR-seq+ resulted in a deeper view of the transcriptome, enabling systematic quantification of how microbial interactions result in altering the transcriptional state of bacteria within co-cultures.
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Affiliation(s)
- Kellie A. Heom
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA
- Biological Engineering Program, University of California Santa Barbara, Santa Barbara, California, USA
| | - Chatarin Wangsanuwat
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA
- Biological Engineering Program, University of California Santa Barbara, Santa Barbara, California, USA
| | - Lazarina V. Butkovich
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA
| | - Scott C. Tam
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA
| | - Annette R. Rowe
- Biological Sciences, University of Cincinnati, Cincinnati, Ohio, USA
| | - Michelle A. O'Malley
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA
- Biological Engineering Program, University of California Santa Barbara, Santa Barbara, California, USA
| | - Siddharth S. Dey
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA
- Biological Engineering Program, University of California Santa Barbara, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, California, USA
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3
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Zhang Z, Zhao Z, Huang K, Liang Z. Acid-resistant enzymes: the acquisition strategies and applications. Appl Microbiol Biotechnol 2023; 107:6163-6178. [PMID: 37615723 DOI: 10.1007/s00253-023-12702-1] [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: 06/05/2023] [Revised: 07/18/2023] [Accepted: 07/21/2023] [Indexed: 08/25/2023]
Abstract
Enzymes have promising applications in chemicals, food, pharmaceuticals, and other variety products because of their high efficiency, specificity, and environmentally friendly properties. However, due to the complexity of raw materials, pH, temperature, solvents, etc., the application range of enzymes is greatly limited in the industry. Protein engineering and enzyme immobilization are classical strategies to overcome the limitations of industrial applications. Although the pH tendency of enzymes has been extensively researched, the mechanism underlying enzyme acid resistance is unclear, and a less practical strategy for altering the pH propensity of enzymes has been suggested. This review proposes that the optimum pH of enzyme is determined by the pKa values of active center ionizable amino acid residues. Three levels of acquiring acid-resistant enzymes are summarized: mining from extreme environments and enzyme databases, modification with protein engineering and enzyme microenvironment engineering, and de novo synthesis. The industrial applications of acid-resistant enzymes in chemicals, food, and pharmaceuticals are also summarized. KEY POINTS: • The mechanism of enzyme acid resistance is fundamentally determined. • The three aspects of the method for acquiring acid-resistant enzymes are summarized. • Computer-aided strategies and artificial intelligence are used to obtain acid-resistant enzymes.
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Affiliation(s)
- Zhenzhen Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Zitong Zhao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Kunlun Huang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- The Supervision, Inspection and Testing Center of Genetically Modified Organisms, Ministry of Agriculture, Beijing, China
- Beijing Laboratory for Food Quality and Safety, China Agricultural University, Beijing, China
| | - Zhihong Liang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.
- The Supervision, Inspection and Testing Center of Genetically Modified Organisms, Ministry of Agriculture, Beijing, China.
- Beijing Laboratory for Food Quality and Safety, China Agricultural University, Beijing, China.
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4
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Brown JL, Gierke T, Butkovich LV, Swift CL, Singan V, Daum C, Barry K, Grigoriev IV, O’Malley MA. High-quality RNA extraction and the regulation of genes encoding cellulosomes are correlated with growth stage in anaerobic fungi. FRONTIERS IN FUNGAL BIOLOGY 2023; 4:1171100. [PMID: 37746117 PMCID: PMC10512310 DOI: 10.3389/ffunb.2023.1171100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/02/2023] [Indexed: 09/26/2023]
Abstract
Anaerobic fungi produce biomass-degrading enzymes and natural products that are important to harness for several biotechnology applications. Although progress has been made in the development of methods for extracting nucleic acids for genomic and transcriptomic sequencing of these fungi, most studies are limited in that they do not sample multiple fungal growth phases in batch culture. In this study, we establish a method to harvest RNA from fungal monocultures and fungal-methanogen co-cultures, and also determine an optimal time frame for high-quality RNA extraction from anaerobic fungi. Based on RNA quality and quantity targets, the optimal time frame in which to harvest anaerobic fungal monocultures and fungal-methanogen co-cultures for RNA extraction was 2-5 days of growth post-inoculation. When grown on cellulose, the fungal strain Anaeromyces robustus cocultivated with the methanogen Methanobacterium bryantii upregulated genes encoding fungal carbohydrate-active enzymes and other cellulosome components relative to fungal monocultures during this time frame, but expression patterns changed at 24-hour intervals throughout the fungal growth phase. These results demonstrate the importance of establishing methods to extract high-quality RNA from anaerobic fungi at multiple time points during batch cultivation.
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Affiliation(s)
- Jennifer L. Brown
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Taylor Gierke
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Lazarina V. Butkovich
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Candice L. Swift
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Vasanth Singan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Christopher Daum
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, United States
| | - Michelle A. O’Malley
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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5
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Gharechahi J, Vahidi MF, Sharifi G, Ariaeenejad S, Ding XZ, Han JL, Salekdeh GH. Lignocellulose degradation by rumen bacterial communities: New insights from metagenome analyses. ENVIRONMENTAL RESEARCH 2023; 229:115925. [PMID: 37086884 DOI: 10.1016/j.envres.2023.115925] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/26/2023] [Accepted: 04/15/2023] [Indexed: 05/03/2023]
Abstract
Ruminant animals house a dense and diverse community of microorganisms in their rumen, an enlarged compartment in their stomach, which provides a supportive environment for the storage and microbial fermentation of ingested feeds dominated by plant materials. The rumen microbiota has acquired diverse and functionally overlapped enzymes for the degradation of plant cell wall polysaccharides. In rumen Bacteroidetes, enzymes involved in degradation are clustered into polysaccharide utilization loci to facilitate coordinated expression when target polysaccharides are available. Firmicutes use free enzymes and cellulosomes to degrade the polysaccharides. Fibrobacters either aggregate lignocellulose-degrading enzymes on their cell surface or release them into the extracellular medium in membrane vesicles, a mechanism that has proven extremely effective in the breakdown of recalcitrant cellulose. Based on current metagenomic analyses, rumen Bacteroidetes and Firmicutes are categorized as generalist microbes that can degrade a wide range of polysaccharides, while other members adapted toward specific polysaccharides. Particularly, there is ample evidence that Verrucomicrobia and Spirochaetes have evolved enzyme systems for the breakdown of complex polysaccharides such as xyloglucans, peptidoglycans, and pectin. It is concluded that diversity in degradation mechanisms is required to ensure that every component in feeds is efficiently degraded, which is key to harvesting maximum energy by host animals.
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Affiliation(s)
- Javad Gharechahi
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mohammad Farhad Vahidi
- Animal Science Research Department, Qom Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Qom, Iran
| | - Golandam Sharifi
- Department of Basic Sciences, Encyclopedia Research Center, Institute for Humanities and Cultural Studies, Tehran, Iran
| | - Shohreh Ariaeenejad
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, And Extension Organization, Karaj, Iran
| | - Xue-Zhi Ding
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, 730050, China
| | - Jian-Lin Han
- Livestock Genetics Program, International Livestock Research, Institute (ILRI), 00100, Nairobi, Kenya; CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, And Extension Organization, Karaj, Iran; School of Natural Sciences, Macquarie University, North Ryde, NSW, Australia.
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6
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Lankiewicz TS, Choudhary H, Gao Y, Amer B, Lillington SP, Leggieri PA, Brown JL, Swift CL, Lipzen A, Na H, Amirebrahimi M, Theodorou MK, Baidoo EEK, Barry K, Grigoriev IV, Timokhin VI, Gladden J, Singh S, Mortimer JC, Ralph J, Simmons BA, Singer SW, O'Malley MA. Lignin deconstruction by anaerobic fungi. Nat Microbiol 2023; 8:596-610. [PMID: 36894634 PMCID: PMC10066034 DOI: 10.1038/s41564-023-01336-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 01/31/2023] [Indexed: 03/11/2023]
Abstract
Lignocellulose forms plant cell walls, and its three constituent polymers, cellulose, hemicellulose and lignin, represent the largest renewable organic carbon pool in the terrestrial biosphere. Insights into biological lignocellulose deconstruction inform understandings of global carbon sequestration dynamics and provide inspiration for biotechnologies seeking to address the current climate crisis by producing renewable chemicals from plant biomass. Organisms in diverse environments disassemble lignocellulose, and carbohydrate degradation processes are well defined, but biological lignin deconstruction is described only in aerobic systems. It is currently unclear whether anaerobic lignin deconstruction is impossible because of biochemical constraints or, alternatively, has not yet been measured. We applied whole cell-wall nuclear magnetic resonance, gel-permeation chromatography and transcriptome sequencing to interrogate the apparent paradox that anaerobic fungi (Neocallimastigomycetes), well-documented lignocellulose degradation specialists, are unable to modify lignin. We find that Neocallimastigomycetes anaerobically break chemical bonds in grass and hardwood lignins, and we further associate upregulated gene products with the observed lignocellulose deconstruction. These findings alter perceptions of lignin deconstruction by anaerobes and provide opportunities to advance decarbonization biotechnologies that depend on depolymerizing lignocellulose.
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Affiliation(s)
- Thomas S Lankiewicz
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, USA
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA
- Joint BioEnergy Institute, Emeryville, CA, USA
| | - Hemant Choudhary
- Joint BioEnergy Institute, Emeryville, CA, USA
- Department of Biomaterials and Biomanufacturing, Sandia National Laboratories, Livermore, CA, USA
| | - Yu Gao
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Bashar Amer
- Joint BioEnergy Institute, Emeryville, CA, USA
| | - Stephen P Lillington
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Patrick A Leggieri
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Jennifer L Brown
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Candice L Swift
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, USA
- Department of Environmental Health Sciences, University of South Carolina, Columbia, SC, USA
| | - Anna Lipzen
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hyunsoo Na
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mojgan Amirebrahimi
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michael K Theodorou
- Department of Agriculture and Environment, Harper Adams University, Newport, UK
| | - Edward E K Baidoo
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Igor V Grigoriev
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | | | - John Gladden
- Joint BioEnergy Institute, Emeryville, CA, USA
- Department of Biomaterials and Biomanufacturing, Sandia National Laboratories, Livermore, CA, USA
| | - Seema Singh
- Joint BioEnergy Institute, Emeryville, CA, USA
- Department of Biomaterials and Biomanufacturing, Sandia National Laboratories, Livermore, CA, USA
| | - Jenny C Mortimer
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, South Australia, Australia
| | - John Ralph
- Great Lakes Bioenergy Research Center, Madison, WI, USA
- Department of Biochemistry, University of Wisconsin Madison, Madison, WI, USA
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Steven W Singer
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, USA.
- Joint BioEnergy Institute, Emeryville, CA, USA.
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7
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Chen C, Chen S, Wang B. A glance at the gut microbiota and the functional roles of the microbes based on marmot fecal samples. Front Microbiol 2023; 14:1035944. [PMID: 37125200 PMCID: PMC10140447 DOI: 10.3389/fmicb.2023.1035944] [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: 10/12/2022] [Accepted: 03/13/2023] [Indexed: 05/02/2023] Open
Abstract
Research on the gut microbiota, which involves a large and complex microbial community, is an important part of infectious disease control. In China, few studies have been reported on the diversity of the gut microbiota of wild marmots. To obtain full details of the gut microbiota, including bacteria, fungi, viruses and archaea, in wild marmots, we have sequenced metagenomes from five sample-sites feces on the Hulun Buir Grassland in Inner Mongolia, China. We have created a comprehensive database of bacterial, fungal, viral, and archaeal genomes and aligned metagenomic sequences (determined based on marmot fecal samples) against the database. We delineated the detailed and distinct gut microbiota structures of marmots. A total of 5,891 bacteria, 233 viruses, 236 fungi, and 217 archaea were found. The dominant bacterial phyla were Firmicutes, Proteobacteria, Bacteroidetes, and Actinomycetes. The viral families were Myoviridae, Siphoviridae, Phycodnaviridae, Herpesviridae and Podoviridae. The dominant fungi phyla were Ascomycota, Basidiomycota, and Blastocladiomycota. The dominant archaea were Biobacteria, Omoarchaea, Nanoarchaea, and Microbacteria. Furthermore, the gut microbiota was affected by host species and environment, and environment was the most important factor. There were 36,989 glycoside hydrolase genes in the microbiota, with 365 genes homologous to genes encoding β-glucosidase, cellulase, and cellulose β-1,4-cellobiosidase. Additionally, antibiotic resistance genes such as macB, bcrA, and msbA were abundant. To sum up, the gut microbiota of marmot had population diversity and functional diversity, which provides a basis for further research on the regulatory effects of the gut microbiota on the host. In addition, metagenomics revealed that the gut microbiota of marmots can degrade cellulose and hemicellulose.
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Affiliation(s)
- Chuizhe Chen
- Department of Pathology, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, China
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine and the Second Affiliated Hospital, Hainan Medical University, Haikou, China
| | - Shu Chen
- Medical Laboratory Center, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Bo Wang
- Department of Pathology, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, China
- *Correspondence: Bo Wang,
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8
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Brown JL, Perisin MA, Swift CL, Benyamin M, Liu S, Singan V, Zhang Y, Savage E, Pennacchio C, Grigoriev IV, O'Malley MA. Co‑cultivation of anaerobic fungi with Clostridium acetobutylicum bolsters butyrate and butanol production from cellulose and lignocellulose. J Ind Microbiol Biotechnol 2022; 49:6823545. [PMID: 36367297 PMCID: PMC9923384 DOI: 10.1093/jimb/kuac024] [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: 08/13/2022] [Accepted: 11/09/2022] [Indexed: 11/13/2022]
Abstract
A system for co-cultivation of anaerobic fungi with anaerobic bacteria was established based on lactate cross-feeding to produce butyrate and butanol from plant biomass. Several co-culture formulations were assembled that consisted of anaerobic fungi (Anaeromyces robustus, Neocallimastix californiae, or Caecomyces churrovis) with the bacterium Clostridium acetobutylicum. Co-cultures were grown simultaneously (e.g., 'one pot'), and compared to cultures where bacteria were cultured in fungal hydrolysate sequentially. Fungal hydrolysis of lignocellulose resulted in 7-11 mM amounts of glucose and xylose, as well as acetate, formate, ethanol, and lactate to support clostridial growth. Under these conditions, one-stage simultaneous co-culture of anaerobic fungi with C. acetobutylicum promoted the production of butyrate up to 30 mM. Alternatively, two-stage growth slightly promoted solventogenesis and elevated butanol levels (∼4-9 mM). Transcriptional regulation in the two-stage growth condition indicated that this cultivation method may decrease the time required to reach solventogenesis and induce the expression of cellulose-degrading genes in C. acetobutylicum due to relieved carbon-catabolite repression. Overall, this study demonstrates a proof of concept for biobutanol and bio-butyrate production from lignocellulose using an anaerobic fungal-bacterial co-culture system.
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Affiliation(s)
- Jennifer L Brown
- Department of Chemical Engineering, University of California Santa Barbara, Rm 3357 Engineering II, Santa Barbara, CA 93117, USA
| | - Matthew A Perisin
- Biological and Biotechnology Sciences Division, DEVCOM Army Research Laboratory, 2800 Powder Mill Road, Adelphi, MD 20783, USA
| | - Candice L Swift
- Department of Chemical Engineering, University of California Santa Barbara, Rm 3357 Engineering II, Santa Barbara, CA 93117, USA
| | - Marcus Benyamin
- Biological and Biotechnology Sciences Division, DEVCOM Army Research Laboratory, 2800 Powder Mill Road, Adelphi, MD 20783, USA
| | - Sanchao Liu
- Biological and Biotechnology Sciences Division, DEVCOM Army Research Laboratory, 2800 Powder Mill Road, Adelphi, MD 20783, USA
| | - Vasanth Singan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yu Zhang
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Emily Savage
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Christa Pennacchio
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
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9
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Król B, Słupczyńska M, Wilk M, Asghar M, Cwynar P. Anaerobic rumen fungi and fungal direct-fed microbials
in ruminant feeding. JOURNAL OF ANIMAL AND FEED SCIENCES 2022. [DOI: 10.22358/jafs/153961/2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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10
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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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11
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Suitability of anaerobic fungi culture supernatant or mixed ruminal fluid as novel silage additives. Appl Microbiol Biotechnol 2022; 106:6819-6832. [PMID: 36100752 PMCID: PMC9529681 DOI: 10.1007/s00253-022-12157-w] [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: 06/06/2022] [Revised: 08/12/2022] [Accepted: 08/24/2022] [Indexed: 11/02/2022]
Abstract
Abstract
This study investigated silage quality characteristics and ruminal fiber degradability of grass and straw ensiled with either anaerobic fungi (AF) supernatant with active fungal enzymes or mixed ruminal fluid as novel silage additives. Compared to control silages, AF supernatant improved the quality of grass and straw silages as evidenced by decreased pH, acetic acid concentration, and dry matter losses. Likewise, mixed ruminal fluid enhanced lactic acid fermentation, which further resulted in lower pH of the treated grass silage. The ruminal fiber degradability was determined using in situ incubations and, compared to controls, the cellulose degradability was higher for grass silage with AF supernatant, whereas ruminal degradability of straw silage was reduced by this treatment. In contrast, mixed ruminal fluid did not influence fiber degradability of silages in the rumen. Concluding, both novel additives improved silage quality, whereas only AF supernatant enhanced ruminal fiber degradability of grass silage and therefore may represent an approach for improving forage utilization by ruminants.
Key points
• Enzymes of anaerobic fungi supernatant improve quality of grass and straw silages.
• Mixed ruminal fluid enhances lactic acid fermentation when ensiling grass and straw.
• Enzymes of anaerobic fungi supernatant increase ruminal grass silage degradability.
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12
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YÜCEL H, EKİNCİ K. Carbohydrate active enzyme system in rumen fungi: a review. INTERNATIONAL JOURNAL OF SECONDARY METABOLITE 2022. [DOI: 10.21448/ijsm.1075030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Hydrolysis and dehydration reactions of carbohydrates, which are used as energy raw materials by all living things in nature, are controlled by Carbohydrate Active Enzyme (CAZy) systems. These enzymes are also used in different industrial areas today. There are different types of microorganisms that have the CAZy system and are used in the industrial sector. Apart from current organisms, there are also rumen fungi within the group of candidate microorganisms with the CAZy system. It has been reported that xylanase (EC3.2.1.8 and EC3.2.1.37) enzyme, a member of the glycoside hydrolase enzyme family obtained from Trichoderma sp. and used especially in areas such as bread, paper, and feed industry, is more synthesized in rumen fungi such as Orpinomyces sp. and Neocallimastix sp. Therefore, this study reviews Neocallimastixsp., Orpinomyces sp., Caecomyces sp., Piromyces sp., and Anaeromyces sp., registered in the CAZy and Mycocosm database for rumen fungi to have both CAZy enzyme activity and to be an alternative microorganism in the industry. Furthermore the CAZy enzyme activities of the strains are investigated. The review shows thatNeocallimax sp. and Orpinomyces sp. areconsidered as candidate microorganisms.
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Affiliation(s)
- Halit YÜCEL
- KAHRAMANMARAŞ SÜTÇÜ İMAM ÜNİVERSİTESİ, ZİRAAT FAKÜLTESİ
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13
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Ma J, Zhong P, Li Y, Sun Z, Sun X, Aung M, Hao L, Cheng Y, Zhu W. Hydrogenosome, Pairing Anaerobic Fungi and H2-Utilizing Microorganisms Based on Metabolic Ties to Facilitate Biomass Utilization. J Fungi (Basel) 2022; 8:jof8040338. [PMID: 35448569 PMCID: PMC9026988 DOI: 10.3390/jof8040338] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 02/04/2023] Open
Abstract
Anaerobic fungi, though low in abundance in rumen, play an important role in the degradation of forage for herbivores. When only anaerobic fungi exist in the fermentation system, the continuous accumulation of metabolites (e.g., hydrogen (H2) and formate) generated from their special metabolic organelles—the hydrogenosome—inhibits the enzymatic reactions in the hydrogenosome and reduces the activity of the anaerobic fungi. However, due to interspecific H2 transfer, H2 produced by the hydrogenosome can be used by other microorganisms to form valued bioproducts. This symbiotic interaction between anaerobic fungi and other microorganisms can be used to improve the nutritional value of animal feeds and produce value-added products that are normally in low concentrations in the fermentation system. Because of the important role in the generation and further utilization of H2, the study of the hydrogensome is increasingly becoming an important part of the development of anaerobic fungi as model organisms that can effectively improve the utilization value of roughage. Here, we summarize and discuss the classification and the process of biomass degradation of anaerobic fungi and the metabolism and function of anaerobic fungal hydrogensome, with a focus on the potential role of the hydrogensome in the efficient utilization of biomass.
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Affiliation(s)
- Jing Ma
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (J.M.); (P.Z.); (Y.L.); (Z.S.); (X.S.); (M.A.); (W.Z.)
| | - Pei Zhong
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (J.M.); (P.Z.); (Y.L.); (Z.S.); (X.S.); (M.A.); (W.Z.)
| | - Yuqi Li
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (J.M.); (P.Z.); (Y.L.); (Z.S.); (X.S.); (M.A.); (W.Z.)
| | - Zhanying Sun
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (J.M.); (P.Z.); (Y.L.); (Z.S.); (X.S.); (M.A.); (W.Z.)
| | - Xiaoni Sun
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (J.M.); (P.Z.); (Y.L.); (Z.S.); (X.S.); (M.A.); (W.Z.)
| | - Min Aung
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (J.M.); (P.Z.); (Y.L.); (Z.S.); (X.S.); (M.A.); (W.Z.)
- Department of Animal Nutrition, University of Veterinary Science, Nay Pyi Taw 15013, Myanmar
| | - Lizhuang Hao
- Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Plateau Yak Research Center, Qinghai Academy of Science and Veterinary Medicine of Qinghai University, Xining 810016, China;
| | - Yanfen Cheng
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (J.M.); (P.Z.); (Y.L.); (Z.S.); (X.S.); (M.A.); (W.Z.)
- Correspondence: ; Tel.: +86-25-8439-5523
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (J.M.); (P.Z.); (Y.L.); (Z.S.); (X.S.); (M.A.); (W.Z.)
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14
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Brown JL, Swift CL, Mondo SJ, Seppala S, Salamov A, Singan V, Henrissat B, Drula E, Henske JK, Lee S, LaButti K, He G, Yan M, Barry K, Grigoriev IV, O'Malley MA. 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. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:234. [PMID: 34893091 PMCID: PMC8665504 DOI: 10.1186/s13068-021-02083-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/19/2021] [Indexed: 05/12/2023]
Abstract
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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Affiliation(s)
- Jennifer L Brown
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Candice L Swift
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Stephen J Mondo
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Susanna Seppala
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Vasanth Singan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Bernard Henrissat
- DTU Bioengineering, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Elodie Drula
- Architecture Et Fonction Des Macromolécules Biologiques, CNRS/Aix-Marseille University, Marseille, France
- INRAE USC1408, AFMB, 13009, Marseille, France
| | - John K Henske
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Samantha Lee
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Guifen He
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mi Yan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, 93106, USA.
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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15
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Bouwknegt J, Koster CC, Vos AM, Ortiz-Merino RA, Wassink M, Luttik MAH, van den Broek M, Hagedoorn PL, Pronk JT. Class-II dihydroorotate dehydrogenases from three phylogenetically distant fungi support anaerobic pyrimidine biosynthesis. Fungal Biol Biotechnol 2021; 8:10. [PMID: 34656184 PMCID: PMC8520639 DOI: 10.1186/s40694-021-00117-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/02/2021] [Indexed: 11/10/2022] Open
Abstract
Background In most fungi, quinone-dependent Class-II dihydroorotate dehydrogenases (DHODs) are essential for pyrimidine biosynthesis. Coupling of these Class-II DHODHs to mitochondrial respiration makes their in vivo activity dependent on oxygen availability. Saccharomyces cerevisiae and closely related yeast species harbor a cytosolic Class-I DHOD (Ura1) that uses fumarate as electron acceptor and thereby enables anaerobic pyrimidine synthesis. Here, we investigate DHODs from three fungi (the Neocallimastigomycete Anaeromyces robustus and the yeasts Schizosaccharomyces japonicus and Dekkera bruxellensis) that can grow anaerobically but, based on genome analysis, only harbor a Class-II DHOD. Results Heterologous expression of putative Class-II DHOD-encoding genes from fungi capable of anaerobic, pyrimidine-prototrophic growth (Arura9, SjURA9, DbURA9) in an S. cerevisiae ura1Δ strain supported aerobic as well as anaerobic pyrimidine prototrophy. A strain expressing DbURA9 showed delayed anaerobic growth without pyrimidine supplementation. Adapted faster growing DbURA9-expressing strains showed mutations in FUM1, which encodes fumarase. GFP-tagged SjUra9 and DbUra9 were localized to S. cerevisiae mitochondria, while ArUra9, whose sequence lacked a mitochondrial targeting sequence, was localized to the yeast cytosol. Experiments with cell extracts showed that ArUra9 used free FAD and FMN as electron acceptors. Expression of SjURA9 in S. cerevisiae reproducibly led to loss of respiratory competence and mitochondrial DNA. A cysteine residue (C265 in SjUra9) in the active sites of all three anaerobically active Ura9 orthologs was shown to be essential for anaerobic activity of SjUra9 but not of ArUra9. Conclusions Activity of fungal Class-II DHODs was long thought to be dependent on an active respiratory chain, which in most fungi requires the presence of oxygen. By heterologous expression experiments in S. cerevisiae, this study shows that phylogenetically distant fungi independently evolved Class-II dihydroorotate dehydrogenases that enable anaerobic pyrimidine biosynthesis. Further structure–function studies are required to understand the mechanistic basis for the anaerobic activity of Class-II DHODs and an observed loss of respiratory competence in S. cerevisiae strains expressing an anaerobically active DHOD from Sch. japonicus. Supplementary Information The online version contains supplementary material available at 10.1186/s40694-021-00117-4.
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Affiliation(s)
- Jonna Bouwknegt
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Charlotte C Koster
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Aurin M Vos
- Wageningen Plant Research, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Raúl A Ortiz-Merino
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Mats Wassink
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Marijke A H Luttik
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Marcel van den Broek
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Peter L Hagedoorn
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands.
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16
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Early-diverging fungal phyla: taxonomy, species concept, ecology, distribution, anthropogenic impact, and novel phylogenetic proposals. FUNGAL DIVERS 2021; 109:59-98. [PMID: 34608378 PMCID: PMC8480134 DOI: 10.1007/s13225-021-00480-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 07/19/2021] [Indexed: 01/02/2023]
Abstract
The increasing number of new fungal species described from all over the world along with the use of genetics to define taxa, has dramatically changed the classification system of early-diverging fungi over the past several decades. The number of phyla established for non-Dikarya fungi has increased from 2 to 17. However, to date, both the classification and phylogeny of the basal fungi are still unresolved. In this article, we review the recent taxonomy of the basal fungi and re-evaluate the relationships among early-diverging lineages of fungal phyla. We also provide information on the ecology and distribution in Mucoromycota and highlight the impact of chytrids on amphibian populations. Species concepts in Chytridiomycota, Aphelidiomycota, Rozellomycota, Neocallimastigomycota are discussed in this paper. To preserve the current application of the genus Nephridiophaga (Chytridiomycota: Nephridiophagales), a new type species, Nephridiophaga blattellae, is proposed.
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17
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Kiel Reese B, Sobol MS, Bowles MW, Hinrichs KU. Redefining the Subsurface Biosphere: Characterization of Fungi Isolated From Energy-Limited Marine Deep Subsurface Sediment. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:727543. [PMID: 37744089 PMCID: PMC10512353 DOI: 10.3389/ffunb.2021.727543] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/24/2021] [Indexed: 09/26/2023]
Abstract
The characterization of metabolically active fungal isolates within the deep marine subsurface will alter current ecosystem models and living biomass estimates that are limited to bacterial and archaeal populations. Although marine fungi have been studied for over fifty years, a detailed description of fungal populations within the deep subsurface is lacking. Fungi possess metabolic pathways capable of utilizing previously considered non-bioavailable energy reserves. Therefore, metabolically active fungi would occupy a unique niche within subsurface ecosystems, with the potential to provide an organic carbon source for heterotrophic prokaryotic populations from the transformation of non-bioavailable energy into substrates, as well as from the fungal necromass itself. These organic carbon sources are not currently being considered in subsurface energy budgets. Sediments from South Pacific Gyre subsurface, one of the most energy-limited environments on Earth, were collected during the Integrated Ocean Drilling Program Expedition 329. Anoxic and oxic sediment slurry enrichments using fresh sediment were used to isolate multiple fungal strains in media types that varied in organic carbon substrates and concentration. Metabolically active and dormant fungal populations were also determined from nucleic acids extracted from in situ cryopreserved South Pacific Gyre sediments. For further characterization of physical growth parameters, two isolates were chosen based on their representation of the whole South Pacific Gyre fungal community. Results from this study show that fungi have adapted to be metabolically active and key community members in South Pacific Gyre sediments and potentially within global biogeochemical cycles.
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Affiliation(s)
- Brandi Kiel Reese
- Dauphin Island Sea Lab, Dauphin Island, AL, United States
- School of Marine and Environmental Sciences, University of South Alabama, Mobile, AL, United States
- Hanse-Wissenschaftskolleg Institute for Advanced Study, Delmenhorst, Germany
| | - Morgan S. Sobol
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
- Department of Life Sciences, Texas A&M University, Corpus Christi, TX, United States
| | | | - Kai-Uwe Hinrichs
- MARUM-Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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18
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Swift CL, Malinov NG, Mondo SJ, Salamov A, Grigoriev IV, O'Malley MA. A Genomic Catalog of Stress Response Genes in Anaerobic Fungi for Applications in Bioproduction. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:708358. [PMID: 37744151 PMCID: PMC10512342 DOI: 10.3389/ffunb.2021.708358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/07/2021] [Indexed: 09/26/2023]
Abstract
Anaerobic fungi are a potential biotechnology platform to produce biomass-degrading enzymes. Unlike model fungi such as yeasts, stress responses that are relevant during bioprocessing have not yet been established for anaerobic fungi. In this work, we characterize both the heat shock and unfolded protein responses of four strains of anaerobic fungi (Anaeromyces robustus, Caecomyces churrovis, Neocallimastix californiae, and Piromyces finnis). The inositol-requiring 1 (Ire1) stress sensor, which typically initiates the fungal UPR, was conserved in all four genomes. However, these genomes also encode putative transmembrane kinases with catalytic domains that are similar to the metazoan stress-sensing enzyme PKR-like endoplasmic reticulum kinase (PERK), although whether they function in the UPR of anaerobic fungi remains unclear. Furthermore, we characterized the global transcriptional responses of Anaeromyces robustus and Neocallimastix californiae to a transient heat shock. Both fungi exhibited the hallmarks of ER stress, including upregulation of genes with functions in protein folding, ER-associated degradation, and intracellular protein trafficking. Relative to other fungi, the genomes of Neocallimastigomycetes contained the greatest gene percentage of HSP20 and HSP70 chaperones, which may serve to stabilize their asparagine-rich genomes. Taken together, these results delineate the unique stress response of anaerobic fungi, which is an important step toward their development as a biotechnology platform to produce enzymes and valuable biomolecules.
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Affiliation(s)
- Candice L. Swift
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Nikola G. Malinov
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Stephen J. Mondo
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
| | - Asaf Salamov
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Igor V. Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Michelle A. O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States
- Joint BioEnergy Institute, Emeryville, CA, United States
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19
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Stabel M, Hagemeister J, Heck Z, Aliyu H, Ochsenreither K. Characterization and Phylogenetic Analysis of a Novel GH43 β-Xylosidase From Neocallimastix californiae. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:692804. [PMID: 37744100 PMCID: PMC10512374 DOI: 10.3389/ffunb.2021.692804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 05/26/2021] [Indexed: 09/26/2023]
Abstract
Degradation of lignocellulosic materials to release fermentable mono- and disaccharides is a decisive step toward a sustainable bio-based economy, thereby increasing the demand of robust and highly active lignocellulolytic enzymes. Anaerobic fungi of the phylum Neocallimastigomycota are potent biomass degraders harboring a huge variety of such enzymes. Compared to cellulose, hemicellulose degradation has received much less attention; therefore, the focus of this study has been the enzymatic xylan degradation of anaerobic fungi as these organisms produce some of the most effective known hydrolytic enzymes. We report the heterologous expression of a GH43 xylosidase, Xyl43Nc, and a GH11 endoxylanase, X11Nc, from the anaerobic fungus Neocallimastix californiae in Escherichia coli. The enzymes were identified by screening of the putative proteome. Xyl43Nc was highly active against 4-Nitrophenol-xylopyranosides with a Km of 0.72 mM, a kcat of 29.28 s-1, a temperature optimum of 32°C and a pH optimum of 6. When combined, Xyl43Nc and X11Nc released xylose from beechwood xylan and arabinoxylan from wheat. Phylogenetic analysis revealed that Xyl43Nc shares common ancestry with enzymes from Spirochaetes and groups separately from Ascomycete sequences in our phylogeny, highlighting the importance of horizontal gene transfer in the evolution of the anaerobic fungi.
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Affiliation(s)
- Marcus Stabel
- Process Engineering in Life Sciences 2: Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
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20
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Abstract
Anaerobic fungi (Neocallimastigomycota) isolated from the guts of herbivores are powerful biomass-degrading organisms that enhance their degradative ability through the formation of cellulosomes, multienzyme complexes that synergistically colocalize enzymes to extract sugars from recalcitrant plant matter. However, a functional understanding of how fungal cellulosomes are deployed in vivo to orchestrate plant matter degradation is lacking, as is knowledge of how cellulosome production and function vary throughout the morphologically diverse life cycle of anaerobic fungi. In this work, we generated antibodies against three major fungal cellulosome protein domains, a dockerin, scaffoldin, and glycoside hydrolase (GH) 48 protein, and used them in conjunction with helium ion and immunofluorescence microscopy to characterize cellulosome localization patterns throughout the life cycle of Piromyces finnis when grown on simple sugars and complex cellulosic carbon sources. Our analyses reveal that fungal cellulosomes are cell-localized entities specifically targeted to the rhizoids of mature fungal cells and bodies of zoospores. Examination of cellulosome localization patterns across life stages also revealed that cellulosome production is independent of growth substrate in zoospores but repressed by simple sugars in mature cells. This suggests that further exploration of gene regulation patterns in zoospores is needed and can inform potential strategies for derepressing cellulosome expression and boosting hydrolytic enzyme yields from fungal cultures. Collectively, these findings underscore how life cycle-dependent cell morphology and regulation of cellulosome production impact biomass degradation by anaerobic fungi, insights that will benefit ongoing efforts to develop these organisms and their cellulosomes into platforms for converting waste biomass into valuable bioproducts.
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21
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Renwick S, Ganobis CM, Elder RA, Gianetto-Hill C, Higgins G, Robinson AV, Vancuren SJ, Wilde J, Allen-Vercoe E. Culturing Human Gut Microbiomes in the Laboratory. Annu Rev Microbiol 2021; 75:49-69. [PMID: 34038159 DOI: 10.1146/annurev-micro-031021-084116] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The human gut microbiota is a complex community of prokaryotic and eukaryotic microbes and viral particles that is increasingly associated with many aspects of host physiology and health. However, the classical microbiology approach of axenic culture cannot provide a complete picture of the complex interactions between microbes and their hosts in vivo. As such, recently there has been much interest in the culture of gut microbial ecosystems in the laboratory as a strategy to better understand their compositions and functions. In this review, we discuss the model platforms and methods available in the contemporary microbiology laboratory to study human gut microbiomes, as well as current knowledge surrounding the isolation of human gut microbes for the potential construction of defined communities for use in model systems. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Simone Renwick
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; , , , , , , , ,
| | - Caroline M Ganobis
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; , , , , , , , ,
| | - Riley A Elder
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; , , , , , , , ,
| | - Connor Gianetto-Hill
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; , , , , , , , ,
| | - Gregory Higgins
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; , , , , , , , ,
| | - Avery V Robinson
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; , , , , , , , ,
| | - Sarah J Vancuren
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; , , , , , , , ,
| | - Jacob Wilde
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; , , , , , , , ,
| | - Emma Allen-Vercoe
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; , , , , , , , ,
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22
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Saye LMG, Navaratna TA, Chong JPJ, O’Malley MA, Theodorou MK, Reilly M. The Anaerobic Fungi: Challenges and Opportunities for Industrial Lignocellulosic Biofuel Production. Microorganisms 2021; 9:694. [PMID: 33801700 PMCID: PMC8065543 DOI: 10.3390/microorganisms9040694] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/12/2021] [Accepted: 03/18/2021] [Indexed: 11/17/2022] Open
Abstract
Lignocellulose is a promising feedstock for biofuel production as a renewable, carbohydrate-rich and globally abundant source of biomass. However, challenges faced include environmental and/or financial costs associated with typical lignocellulose pretreatments needed to overcome the natural recalcitrance of the material before conversion to biofuel. Anaerobic fungi are a group of underexplored microorganisms belonging to the early diverging phylum Neocallimastigomycota and are native to the intricately evolved digestive system of mammalian herbivores. Anaerobic fungi have promising potential for application in biofuel production processes due to the combination of their highly effective ability to hydrolyse lignocellulose and capability to convert this substrate to H2 and ethanol. Furthermore, they can produce volatile fatty acid precursors for subsequent biological conversion to H2 or CH4 by other microorganisms. The complex biological characteristics of their natural habitat are described, and these features are contextualised towards the development of suitable industrial systems for in vitro growth. Moreover, progress towards achieving that goal is reviewed in terms of process and genetic engineering. In addition, emerging opportunities are presented for the use of anaerobic fungi for lignocellulose pretreatment; dark fermentation; bioethanol production; and the potential for integration with methanogenesis, microbial electrolysis cells and photofermentation.
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Affiliation(s)
- Luke M. G. Saye
- Department of Biology, University of York, York YO10 5DD, UK; (L.M.G.S.); (J.P.J.C.)
- Department of Agriculture and the Environment, Harper Adams University, Newport TF10 8NB, UK
| | - Tejas A. Navaratna
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA; (T.A.N.); (M.A.O.)
| | - James P. J. Chong
- Department of Biology, University of York, York YO10 5DD, UK; (L.M.G.S.); (J.P.J.C.)
| | - Michelle A. O’Malley
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA; (T.A.N.); (M.A.O.)
| | - Michael K. Theodorou
- Department of Agriculture and the Environment, Harper Adams University, Newport TF10 8NB, UK
| | - Matthew Reilly
- Department of Biology, University of York, York YO10 5DD, UK; (L.M.G.S.); (J.P.J.C.)
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23
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Hartinger T, Zebeli Q. The Present Role and New Potentials of Anaerobic Fungi in Ruminant Nutrition. J Fungi (Basel) 2021; 7:200. [PMID: 33802104 PMCID: PMC8000393 DOI: 10.3390/jof7030200] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/04/2021] [Accepted: 03/05/2021] [Indexed: 01/18/2023] Open
Abstract
The ruminal microbiota allows ruminants to utilize fibrous feeds and is in the limelight of ruminant nutrition research for many years. However, the overwhelming majority of investigations have focused on bacteria, whereas anaerobic fungi (AF) have been widely neglected by ruminant nutritionists. Anaerobic fungi are not only crucial fiber degraders but also important nutrient sources for the host. This review summarizes the current findings on AF and, most importantly, discusses their new application potentials in modern ruminant nutrition. Available data suggest AF can be applied as direct-fed microbials to enhance ruminal fiber degradation, which is indeed of interest for high-yielding dairy cows that often show depressed ruminal fibrolysis in response to high-grain feeding. Moreover, these microorganisms have relevance for the nutrient supply and reduction of methane emissions. However, to reach AF-related improvements in ruminal fiber breakdown and animal performance, obstacles in large-scale AF cultivation and applicable administration options need to be overcome. At feedstuff level, silage production may benefit from the application of fungal enzymes that cleave lignocellulosic structures and consequently enable higher energy exploitation from forages in the rumen. Concluding, AF hold several potentials in improving ruminant feeding and future research efforts are called for to harness these potentials.
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Affiliation(s)
- Thomas Hartinger
- Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, 1210 Vienna, Austria;
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24
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Bandini F, Misci C, Taskin E, Cocconcelli PS, Puglisi E. Biopolymers modulate microbial communities in municipal organic waste digestion. FEMS Microbiol Ecol 2021; 96:5902845. [PMID: 32897356 DOI: 10.1093/femsec/fiaa183] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 09/04/2020] [Indexed: 11/15/2022] Open
Abstract
The development of biopolymers has raised issues about their recalcitrance in the environment. Their disposal is mainly carried out with the organic fraction of municipal solid waste (OFMSW) through thermophilic anaerobic digestion and aerobic composting, bioprocesses aimed at turning organic matter into biogas and compost. However, the effects of biopolymers on OFMSW treatment, on the final compost and on the microbial communities involved are partly unexplored. In this study, the OFMSW treatment was reproduced on a laboratory-scale respecting real plant conditions and testing the impacts of mixing polylactic acid (PLA) and starch-based bioplastic (SBB) separately. The dynamics of bacterial, archaeal and fungal communities during the process was screened by high-throughput sequencing (HTS) of phylogenetic amplicons. Starch-based bioplastic showed a minor and heterogeneous microbial diversity between the anaerobic and aerobic phases. Contrariwise, PLA treatment resulted in wider and more diverse bacterial and fungal communities for the compost and the aerobic biofilm. Since the biodiversity in compost may play a crucial role in its stability and safety, the modulation of environmental microbial communities induced by higher concentrations of PLA in OFMSW treatment can pose relevant issues.
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Affiliation(s)
- Francesca Bandini
- Dipartimento di Scienze e Tecnologie Alimentari per la sostenibilità della filiera agro-alimentare (DISTAS), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122, Piacenza, Italy
| | - Chiara Misci
- Dipartimento di Scienze e Tecnologie Alimentari per la sostenibilità della filiera agro-alimentare (DISTAS), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122, Piacenza, Italy
| | - Eren Taskin
- Dipartimento di Scienze e Tecnologie Alimentari per la sostenibilità della filiera agro-alimentare (DISTAS), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122, Piacenza, Italy
| | - Pier Sandro Cocconcelli
- Dipartimento di Scienze e Tecnologie Alimentari per la sostenibilità della filiera agro-alimentare (DISTAS), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122, Piacenza, Italy
| | - Edoardo Puglisi
- Dipartimento di Scienze e Tecnologie Alimentari per la sostenibilità della filiera agro-alimentare (DISTAS), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122, Piacenza, Italy
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25
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Experimentally Validated Reconstruction and Analysis of a Genome-Scale Metabolic Model of an Anaerobic Neocallimastigomycota Fungus. mSystems 2021; 6:6/1/e00002-21. [PMID: 33594000 PMCID: PMC8561657 DOI: 10.1128/msystems.00002-21] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Anaerobic gut fungi in the phylum Neocallimastigomycota typically inhabit the digestive tracts of large mammalian herbivores, where they play an integral role in the decomposition of raw lignocellulose into its constitutive sugar monomers. However, quantitative tools to study their physiology are lacking, partially due to their complex and unresolved metabolism that includes the largely uncharacterized fungal hydrogenosome. Modern omics approaches combined with metabolic modeling can be used to establish an understanding of gut fungal metabolism and develop targeted engineering strategies to harness their degradation capabilities for lignocellulosic bioprocessing. Here, we introduce a high-quality genome of the anaerobic fungus Neocallimastix lanati from which we constructed the first genome-scale metabolic model of an anaerobic fungus. Relative to its size (200 Mbp, sequenced at 62× depth), it is the least fragmented publicly available gut fungal genome to date. Of the 1,788 lignocellulolytic enzymes annotated in the genome, 585 are associated with the fungal cellulosome, underscoring the powerful lignocellulolytic potential of N. lanati. The genome-scale metabolic model captures the primary metabolism of N. lanati and accurately predicts experimentally validated substrate utilization requirements. Additionally, metabolic flux predictions are verified by 13C metabolic flux analysis, demonstrating that the model faithfully describes the underlying fungal metabolism. Furthermore, the model clarifies key aspects of the hydrogenosomal metabolism and can be used as a platform to quantitatively study these biotechnologically important yet poorly understood early-branching fungi. IMPORTANCE Recent genomic analyses have revealed that anaerobic gut fungi possess both the largest number and highest diversity of lignocellulolytic enzymes of all sequenced fungi, explaining their ability to decompose lignocellulosic substrates, e.g., agricultural waste, into fermentable sugars. Despite their potential, the development of engineering methods for these organisms has been slow due to their complex life cycle, understudied metabolism, and challenging anaerobic culture requirements. Currently, there is no framework that can be used to combine multi-omic data sets to understand their physiology. Here, we introduce a high-quality PacBio-sequenced genome of the anaerobic gut fungus Neocallimastix lanati. Beyond identifying a trove of lignocellulolytic enzymes, we use this genome to construct the first genome-scale metabolic model of an anaerobic gut fungus. The model is experimentally validated and sheds light on unresolved metabolic features common to gut fungi. Model-guided analysis will pave the way for deepening our understanding of anaerobic gut fungi and provides a systematic framework to guide strain engineering efforts of these organisms for biotechnological use.
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26
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Li Y, Meng Z, Xu Y, Shi Q, Ma Y, Aung M, Cheng Y, Zhu W. Interactions between Anaerobic Fungi and Methanogens in the Rumen and Their Biotechnological Potential in Biogas Production from Lignocellulosic Materials. Microorganisms 2021; 9:190. [PMID: 33477342 PMCID: PMC7830786 DOI: 10.3390/microorganisms9010190] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 11/29/2022] Open
Abstract
Anaerobic fungi in the digestive tract of herbivores are one of the critical types of fiber-degrading microorganisms present in the rumen. They degrade lignocellulosic materials using unique rhizoid structures and a diverse range of fiber-degrading enzymes, producing metabolic products such as H2/CO2, formate, lactate, acetate, and ethanol. Methanogens in the rumen utilize some of these products (e.g., H2 and formate) to produce methane. An investigation of the interactions between anaerobic fungi and methanogens is helpful as it provides valuable insight into the microbial interactions within the rumen. During the last few decades, research has demonstrated that anaerobic fungi stimulate the growth of methanogens and maintain methanogenic diversity. Meanwhile, methanogens increase the fiber-degrading capability of anaerobic fungi and stimulate metabolic pathways in the fungal hydrogenosome. The ability of co-cultures of anaerobic fungi and methanogens to degrade fiber and produce methane could potentially be a valuable method for the degradation of lignocellulosic materials and methane production.
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Affiliation(s)
- Yuqi Li
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (Z.M.); (Y.X.); (Q.S.); (Y.M.); (M.A.); (W.Z.)
| | - Zhenxiang Meng
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (Z.M.); (Y.X.); (Q.S.); (Y.M.); (M.A.); (W.Z.)
| | - Yao Xu
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (Z.M.); (Y.X.); (Q.S.); (Y.M.); (M.A.); (W.Z.)
| | - Qicheng Shi
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (Z.M.); (Y.X.); (Q.S.); (Y.M.); (M.A.); (W.Z.)
| | - Yuping Ma
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (Z.M.); (Y.X.); (Q.S.); (Y.M.); (M.A.); (W.Z.)
| | - Min Aung
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (Z.M.); (Y.X.); (Q.S.); (Y.M.); (M.A.); (W.Z.)
- Department of Animal Nutrition, University of Veterinary Science, Nay Pyi Taw 15013, Myanmar
| | - Yanfen Cheng
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (Z.M.); (Y.X.); (Q.S.); (Y.M.); (M.A.); (W.Z.)
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (Z.M.); (Y.X.); (Q.S.); (Y.M.); (M.A.); (W.Z.)
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27
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Peng X, Wilken SE, Lankiewicz TS, Gilmore SP, Brown JL, Henske JK, Swift CL, Salamov A, Barry K, Grigoriev IV, Theodorou MK, Valentine DL, O’Malley MA. Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes. Nat Microbiol 2021; 6:499-511. [PMID: 33526884 PMCID: PMC8007473 DOI: 10.1038/s41564-020-00861-0] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 12/21/2020] [Indexed: 02/06/2023]
Abstract
The herbivore digestive tract is home to a complex community of anaerobic microbes that work together to break down lignocellulose. These microbiota are an untapped resource of strains, pathways and enzymes that could be applied to convert plant waste into sugar substrates for green biotechnology. We carried out more than 400 parallel enrichment experiments from goat faeces to determine how substrate and antibiotic selection influence membership, activity, stability and chemical productivity of herbivore gut communities. We assembled 719 high-quality metagenome-assembled genomes (MAGs) that are unique at the species level. More than 90% of these MAGs are from previously unidentified herbivore gut microorganisms. Microbial consortia dominated by anaerobic fungi outperformed bacterially dominated consortia in terms of both methane production and extent of cellulose degradation, which indicates that fungi have an important role in methane release. Metabolic pathway reconstructions from MAGs of 737 bacteria, archaea and fungi suggest that cross-domain partnerships between fungi and methanogens enabled production of acetate, formate and methane, whereas bacterially dominated consortia mainly produced short-chain fatty acids, including propionate and butyrate. Analyses of carbohydrate-active enzyme domains present in each anaerobic consortium suggest that anaerobic bacteria and fungi employ mostly complementary hydrolytic strategies. The division of labour among herbivore anaerobes to degrade plant biomass could be harnessed for industrial bioprocessing.
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Affiliation(s)
- Xuefeng Peng
- grid.133342.40000 0004 1936 9676Department of Chemical Engineering, University of California, Santa Barbara, CA USA ,grid.133342.40000 0004 1936 9676Marine Science Institute, University of California, Santa Barbara, CA USA
| | - St. Elmo Wilken
- grid.133342.40000 0004 1936 9676Department of Chemical Engineering, University of California, Santa Barbara, CA USA
| | - Thomas S. Lankiewicz
- grid.133342.40000 0004 1936 9676Department of Chemical Engineering, University of California, Santa Barbara, CA USA ,grid.184769.50000 0001 2231 4551Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Sean P. Gilmore
- grid.133342.40000 0004 1936 9676Department of Chemical Engineering, University of California, Santa Barbara, CA USA
| | - Jennifer L. Brown
- grid.133342.40000 0004 1936 9676Department of Chemical Engineering, University of California, Santa Barbara, CA USA
| | - John K. Henske
- grid.133342.40000 0004 1936 9676Department of Chemical Engineering, University of California, Santa Barbara, CA USA
| | - Candice L. Swift
- grid.133342.40000 0004 1936 9676Department of Chemical Engineering, University of California, Santa Barbara, CA USA
| | - Asaf Salamov
- grid.184769.50000 0001 2231 4551Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Kerrie Barry
- grid.184769.50000 0001 2231 4551Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Igor V. Grigoriev
- grid.184769.50000 0001 2231 4551Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Michael K. Theodorou
- grid.417899.a0000 0001 2167 3798Department of Animal Production, Welfare and Veterinary Sciences, Harper Adams University, Newport, UK
| | - David L. Valentine
- grid.133342.40000 0004 1936 9676Department of Earth Science, University of California, Santa Barbara, CA USA
| | - Michelle A. O’Malley
- grid.133342.40000 0004 1936 9676Department of Chemical Engineering, University of California, Santa Barbara, CA USA ,grid.184769.50000 0001 2231 4551Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA USA
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28
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Venice F, Desirò A, Silva G, Salvioli A, Bonfante P. The Mosaic Architecture of NRPS-PKS in the Arbuscular Mycorrhizal Fungus Gigaspora margarita Shows a Domain With Bacterial Signature. Front Microbiol 2020; 11:581313. [PMID: 33329443 PMCID: PMC7732545 DOI: 10.3389/fmicb.2020.581313] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 10/29/2020] [Indexed: 12/31/2022] Open
Abstract
As obligate biotrophic symbionts, arbuscular mycorrhizal fungi (AMF) live in association with most land plants. Among them, Gigaspora margarita has been deeply investigated because of its peculiar features, i.e., the presence of an intracellular microbiota with endobacteria and viruses. The genome sequencing of this fungus revealed the presence of some hybrid non-ribosomal peptide synthases-polyketide synthases (NRPS-PKS) that have been rarely identified in AMF. The aim of this study is to describe the architecture of these NRPS-PKS sequences and to understand whether they are present in other fungal taxa related to G. margarita. A phylogenetic analysis shows that the ketoacyl synthase (KS) domain of one G. margarita NRPS-PKS clusters with prokaryotic sequences. Since horizontal gene transfer (HGT) has often been advocated as a relevant evolutionary mechanism for the spread of secondary metabolite genes, we hypothesized that a similar event could have interested the KS domain of the PKS module. The bacterial endosymbiont of G. margarita, Candidatus Glomeribacter gigasporarum (CaGg), was the first candidate as a donor, since it possesses a large biosynthetic cluster involving an NRPS-PKS. However, bioinformatics analyses do not confirm the hypothesis of a direct HGT from the endobacterium to the fungal host: indeed, endobacterial and fungal sequences show a different evolution and potentially different donors. Lastly, by amplifying a NRPS-PKS conserved fragment and mining the sequenced AMF genomes, we demonstrate that, irrespective of the presence of CaGg, G. margarita, and some other related Gigasporaceae possess such a sequence.
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Affiliation(s)
- Francesco Venice
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy.,Institute for Sustainable Plant Protection (IPSP)-SS Turin-National Research Council (CNR), Turin, Italy
| | - Alessandro Desirò
- Department of Plant, Soil and Microbial Sciences, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, United States
| | - Gladstone Silva
- Department of Mycology, Federal University of Pernambuco, Recife, Brazil
| | - Alessandra Salvioli
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Paola Bonfante
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
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29
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Hassan FU, Arshad MA, Ebeid HM, Rehman MSU, Khan MS, Shahid S, Yang C. Phytogenic Additives Can Modulate Rumen Microbiome to Mediate Fermentation Kinetics and Methanogenesis Through Exploiting Diet-Microbe Interaction. Front Vet Sci 2020; 7:575801. [PMID: 33263013 PMCID: PMC7688522 DOI: 10.3389/fvets.2020.575801] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 10/06/2020] [Indexed: 12/11/2022] Open
Abstract
Ruminants inhabit the consortia of gut microbes that play a critical functional role in their maintenance and nourishment by enabling them to use cellulosic and non-cellulosic feed material. These gut microbes perform major physiological activities, including digestion and metabolism of dietary components, to derive energy to meet major protein (65-85%) and energy (ca 80%) requirements of the host. Owing to their contribution to digestive physiology, rumen microbes are considered one of the crucial factors affecting feed conversion efficiency in ruminants. Any change in the rumen microbiome has an imperative effect on animal physiology. Ruminal microbes are fundamentally anaerobic and produce various compounds during rumen fermentation, which are directly used by the host or other microbes. Methane (CH4) is produced by methanogens through utilizing metabolic hydrogen during rumen fermentation. Maximizing the flow of metabolic hydrogen in the rumen away from CH4 and toward volatile fatty acids (VFA) would increase the efficiency of ruminant production and decrease its environmental impact. Understanding of microbial diversity and rumen dynamics is not only crucial for the optimization of host efficiency but also required to mediate emission of greenhouse gases (GHGs) from ruminants. There are various strategies to modulate the rumen microbiome, mainly including dietary interventions and the use of different feed additives. Phytogenic feed additives, mainly plant secondary compounds, have been shown to modulate rumen microflora and change rumen fermentation dynamics leading to enhanced animal performance. Many in vitro and in vivo studies aimed to evaluate the use of plant secondary metabolites in ruminants have been conducted using different plants or their extract or essential oils. This review specifically aims to provide insights into dietary interactions of rumen microbes and their subsequent consequences on rumen fermentation. Moreover, a comprehensive overview of the modulation of rumen microbiome by using phytogenic compounds (essential oils, saponins, and tannins) for manipulating rumen dynamics to mediate CH4 emanation from livestock is presented. We have also discussed the pros and cons of each strategy along with future prospective of dietary modulation of rumen microbiome to improve the performance of ruminants while decreasing GHG emissions.
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Affiliation(s)
- Faiz-ul Hassan
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, China
- Institute of Animal and Dairy Sciences, Faculty of Animal Husbandry, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Adeel Arshad
- Institute of Animal and Dairy Sciences, Faculty of Animal Husbandry, University of Agriculture, Faisalabad, Pakistan
| | - Hossam M. Ebeid
- Dairy Science Department, National Research Centre, Giza, Egypt
| | - Muhammad Saif-ur Rehman
- Institute of Animal and Dairy Sciences, Faculty of Animal Husbandry, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Sajjad Khan
- Institute of Animal and Dairy Sciences, Faculty of Animal Husbandry, University of Agriculture, Faisalabad, Pakistan
| | - Shehryaar Shahid
- Institute of Animal and Dairy Sciences, Faculty of Animal Husbandry, University of Agriculture, Faisalabad, Pakistan
| | - Chengjian Yang
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, China
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30
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Cut-Lengths of Perennial Ryegrass Leaf-Blades Influences In Vitro Fermentation by the Anaerobic Fungus Neocallimastix frontalis. Microorganisms 2020; 8:microorganisms8111774. [PMID: 33187375 PMCID: PMC7696013 DOI: 10.3390/microorganisms8111774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/31/2020] [Accepted: 11/04/2020] [Indexed: 11/17/2022] Open
Abstract
Anaerobic fungi in the gut of domesticated and wild mammalian herbivores play a key role in the host's ability to utilize plant biomass. Due to their highly effective ability to enzymatically degrade lignocellulose, anaerobic fungi are biotechnologically interesting. Numerous factors have been shown to affect the ability of anaerobic fungi to break down plant biomass. However, methods to reduce the non-productive lag time in batch cultures and the effect of leaf-blade cut-length and condition on the fungal fermentation are not known. Therefore, experimentation using a novel gas production approach with pre-grown, axenic cultures of Neocallimastix frontalis was performed using both fresh and air-dried perennial ryegrass leaf-blades of different cut-lengths. The methodology adopted removed the lag-phase and demonstrated the digestion of un-autoclaved leaf-blades. Fermentation of leaf-blades of 4.0 cm cut-length produced 18.4% more gas yet retained 11.2% more apparent DM relative to 0.5 cm cut-length leaf-blades. Drying did not affect fermentation by N. frontalis, although an interaction between drying and leaf-blade cut-length was noted. Removal of the lag phase and the use of un-autoclaved substrates are important when considering the biotechnological potential of anaerobic fungi. A hypothesis based upon sporulation at cut surfaces is proposed to describe the experimental results.
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Rabee AE, Forster R, Elekwachi C, Sabra E, Lamara M. Comparative analysis of the metabolically active microbial communities in the rumen of dromedary camels under different feeding systems using total rRNA sequencing. PeerJ 2020; 8:e10184. [PMID: 33194403 PMCID: PMC7603790 DOI: 10.7717/peerj.10184] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 09/23/2020] [Indexed: 11/20/2022] Open
Abstract
Breakdown of plant biomass in rumen depends on interactions between bacteria, archaea, fungi, and protozoa; however, the majority of studies of the microbiome of ruminants, including the few studies of the rumen of camels, only studied one of these microbial groups. In this study, we applied total rRNA sequencing to identify active microbial communities in 22 solid and liquid rumen samples from 11 camels. These camels were reared at three stations that use different feeding systems: clover, hay and wheat straw (G1), fresh clover (G2), and wheat straw (G3). Bacteria dominated the libraries of sequence reads generated from all rumen samples, followed by protozoa, archaea, and fungi respectively. Firmicutes, Thermoplasmatales, Diplodinium, and Neocallimastix dominated bacterial, archaeal, protozoal and fungal communities, respectively in all samples. Libraries generated from camels reared at facility G2, where they were fed fresh clover, showed the highest alpha diversity. Principal co-ordinate analysis and linear discriminate analysis showed clusters associated with facility/feed and the relative abundance of microbes varied between liquid and solid fractions. This provides preliminary evidence that bacteria dominate the microbial communities of the camel rumen and these communities differ significantly between populations of domesticated camels.
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Affiliation(s)
- Alaa Emara Rabee
- Animal and Poultry Nutrition Department, Desert Research Center, Cairo, Cairo, Egypt
| | - Robert Forster
- Lethbridge Research and Development Centre, Agriculture and Agrifood Canada, Lethbridge, AB, Canada
| | - Chijioke Elekwachi
- Lethbridge Research and Development Centre, Agriculture and Agrifood Canada, Lethbridge, AB, Canada
| | - Ebrahim Sabra
- Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City, Menoufia, Egypt
| | - Mebarek Lamara
- Institut de Recherche sur les Forêts, Université du Québec en Abitibi-Témiscamingue, Rouyn-Noranda, QC, Canada
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Hess M, Paul SS, Puniya AK, van der Giezen M, Shaw C, Edwards JE, Fliegerová K. Anaerobic Fungi: Past, Present, and Future. Front Microbiol 2020; 11:584893. [PMID: 33193229 PMCID: PMC7609409 DOI: 10.3389/fmicb.2020.584893] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 09/29/2020] [Indexed: 11/13/2022] Open
Abstract
Anaerobic fungi (AF) play an essential role in feed conversion due to their potent fiber degrading enzymes and invasive growth. Much has been learned about this unusual fungal phylum since the paradigm shifting work of Colin Orpin in the 1970s, when he characterized the first AF. Molecular approaches targeting specific phylogenetic marker genes have facilitated taxonomic classification of AF, which had been previously been complicated by the complex life cycles and associated morphologies. Although we now have a much better understanding of their diversity, it is believed that there are still numerous genera of AF that remain to be described in gut ecosystems. Recent marker-gene based studies have shown that fungal diversity in the herbivore gut is much like the bacterial population, driven by host phylogeny, host genetics and diet. Since AF are major contributors to the degradation of plant material ingested by the host animal, it is understandable that there has been great interest in exploring the enzymatic repertoire of these microorganisms in order to establish a better understanding of how AF, and their enzymes, can be used to improve host health and performance, while simultaneously reducing the ecological footprint of the livestock industry. A detailed understanding of AF and their interaction with other gut microbes as well as the host animal is essential, especially when production of affordable high-quality protein and other animal-based products needs to meet the demands of an increasing human population. Such a mechanistic understanding, leading to more sustainable livestock practices, will be possible with recently developed -omics technologies that have already provided first insights into the different contributions of the fungal and bacterial population in the rumen during plant cell wall hydrolysis.
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Affiliation(s)
- Matthias Hess
- Systems Microbiology & Natural Product Discovery Laboratory, Department of Animal Science, University of California, Davis, Davis, CA, United States
| | - Shyam S. Paul
- Gut Microbiome Lab, ICAR-Directorate of Poultry Research, Indian Council of Agricultural Research, Hyderabad, India
| | - Anil K. Puniya
- Anaerobic Microbiology Lab, ICAR-National Dairy Research Institute, Dairy Microbiology Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Mark van der Giezen
- Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, Stavanger, Norway
| | - Claire Shaw
- Systems Microbiology & Natural Product Discovery Laboratory, Department of Animal Science, University of California, Davis, Davis, CA, United States
| | - Joan E. Edwards
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Kateřina Fliegerová
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Prague, Czechia
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An Arduino based automatic pressure evaluation system to quantify growth of non‐model anaerobes in culture. AIChE J 2020. [DOI: 10.1002/aic.16540] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Li Y, Hou Z, Shi Q, Cheng Y, Zhu W. Methane Production From Different Parts of Corn Stover via a Simple Co-culture of an Anaerobic Fungus and Methanogen. Front Bioeng Biotechnol 2020; 8:314. [PMID: 32426337 PMCID: PMC7204275 DOI: 10.3389/fbioe.2020.00314] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 03/23/2020] [Indexed: 12/27/2022] Open
Abstract
To determine ways to improve the utilization of corn stover, this study investigated methane production from different parts of corn stover using a simple co-culture of an anaerobic fungus (Pecoramyces species) and methanogen (Methanobrevibacter species). The simple co-culture was incubated with the stem pith, leaf blade, or stem bark of corn stover (as substrates) at 39°C for 72 h. The results showed that the stem bark had the lowest (P < 0.05) digestibility (38.0 ± 1.36%) and neutral detergent solubles, that is, cell solubles (31.6 ± 0.45%), and the highest (P < 0.05) lignin content (4.8 ± 0.56%). The leaf blade had a significantly higher methane conversion rate (56.6 ± 0.76 mL/g digested substrate) than the stem pith (49.2 ± 1.60 mL/g digested substrate), even though they showed similar levels of methane production (42.4 ± 1.0 mL and 40.9 ± 1.35 mL, respectively). Both the leaf blade and stem pith of corn stover have the potential to produce methane in a simple co-culture of an anaerobic fungus and methanogen.
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Affiliation(s)
- Yuqi Li
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China.,Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agriculture University, Nanjing, China
| | - Zhesheng Hou
- College of Mechanical and Electrical Engineering, Jilin Institute of Chemical Technology, Jilin, China
| | - Qicheng Shi
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China.,Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agriculture University, Nanjing, China
| | - Yanfen Cheng
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China.,Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agriculture University, Nanjing, China
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China.,Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agriculture University, Nanjing, China
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Brethauer S, Shahab RL, Studer MH. Impacts of biofilms on the conversion of cellulose. Appl Microbiol Biotechnol 2020; 104:5201-5212. [PMID: 32337627 PMCID: PMC7275028 DOI: 10.1007/s00253-020-10595-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/24/2020] [Accepted: 03/31/2020] [Indexed: 12/02/2022]
Abstract
Abstract Lignocellulose is a widely available renewable carbon source and a promising feedstock for the production of various chemicals in biorefineries. However, its recalcitrant nature is a major hurdle that must be overcome to enable economic conversion processes. Deconstruction of lignocellulose is part of the global carbon cycle, and efficient microbial degradation systems have evolved that might serve as models to improve commercial conversion processes. Biofilms—matrix encased, spatially organized clusters of microbial cells and the predominating lifestyle in nature—have been recognized for their essential role in the degradation of cellulose in nature, e.g., in soils or in the digestive tracts of ruminant animals. Cellulolytic biofilms allow for a high concentration of enzymes at the boundary layer between the solid substrate and the liquid phase and the more complete capture of hydrolysis products directly at the hydrolysis site, which is energetically favorable. Furthermore, enhanced expression of genes for carbohydrate active enzymes as a response to the attachment on solid substrate has been demonstrated for cellulolytic aerobic fungi and anerobic bacteria. In natural multispecies biofilms, the vicinity of different microbial species allows the creation of efficient food webs and synergistic interactions thereby, e.g., avoiding the accumulation of inhibiting metabolites. In this review, these topics are discussed and attempts to realize the benefits of biofilms in targeted applications such as the consolidated bioprocessing of lignocellulose are highlighted. Key Points Multispecies biofilms enable efficient lignocellulose destruction in the biosphere. Cellulose degradation by anaerobic bacteria often occurs by monolayered biofilms. Fungal biofilms immobilize enzymes and substrates in an external digestion system. Surface attached cultures typically show higher expression of cellulolytic enzymes.
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Affiliation(s)
- Simone Brethauer
- School of Agricultural, Forest and Food Sciences, Laboratory of Biofuels and Biochemicals, Bern University of Applied Sciences (BFH), 3052, Zollikofen, Switzerland
| | - Robert L Shahab
- School of Agricultural, Forest and Food Sciences, Laboratory of Biofuels and Biochemicals, Bern University of Applied Sciences (BFH), 3052, Zollikofen, Switzerland
| | - Michael H Studer
- School of Agricultural, Forest and Food Sciences, Laboratory of Biofuels and Biochemicals, Bern University of Applied Sciences (BFH), 3052, Zollikofen, Switzerland.
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Li Y, Sun M, Li Y, Cheng Y, Zhu W. Co-cultured methanogen improved the metabolism in the hydrogenosome of anaerobic fungus as revealed by gas chromatography-mass spectrometry analysis. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2020; 33:1948-1956. [PMID: 32054157 PMCID: PMC7649409 DOI: 10.5713/ajas.19.0649] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 01/06/2020] [Indexed: 11/27/2022]
Abstract
Objective The purpose of this study was to reveal the metabolic shift in the fungus co-cultured with the methanogen (Methanobrevibacter thaueri). Methods Gas chromatography-mass spectrometry was used to investigate the metabolites in anaerobic fungal (Pecoramyces sp. F1) cells and the supernatant. Results A total of 104 and 102 metabolites were detected in the fungal cells and the supernatant, respectively. The partial least squares-discriminant analysis showed that the metabolite profiles in both the fungal cell and the supernatant were distinctly shifted when co-cultured with methanogen. Statistically, 16 and 30 metabolites were significantly (p<0.05) affected in the fungal cell and the supernatant, respectively by the co-cultured methanogen. Metabolic pathway analysis showed that co-culturing with methanogen reduced the production of lactate from pyruvate in the cytosol and increased metabolism in the hydrogenosomes of the anaerobic fungus. Citrate was accumulated in the cytosol of the fungus co-cultured with the methanogen. Conclusion The co-culture of the anaerobic fungus and the methanogen is a good model for studying the microbial interaction between H2-producing and H2-utilizing microorganisms. However, metabolism in hydrogenosome needs to be further studied to gain better insight in the hydrogen transfer among microorganisms.
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Affiliation(s)
- Yuqi Li
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Meizhou Sun
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuanfei Li
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanfen Cheng
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
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Wang H, Li P, Liu X, Zhang C, Lu Q, Xi D, Yang R, Wang S, Bai W, Yang Z, Zhou R, Cheng X, Leng J. The Composition of Fungal Communities in the Rumen of Gayals ( Bos frontalis), Yaks ( Bos grunniens), and Yunnan and Tibetan Yellow Cattle ( Bos taurs). Pol J Microbiol 2019; 68:505-514. [PMID: 31880894 PMCID: PMC7260705 DOI: 10.33073/pjm-2019-050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 10/17/2019] [Accepted: 10/17/2019] [Indexed: 11/14/2022] Open
Abstract
The rumen is a microbial-rich ecosystem in which rumen fungi play an important role in the feed digestion of ruminants. The composition of rumen fungi in free-range ruminants such as gayals, yaks, Tibetan yellow cattle, and the domesticated Yunnan yellow cattle was investigated by sequencing an internal transcribed spacer region 1 (ITS1) using Illumina MiSeq. A total of 285 092 optimized sequences and 904 operational taxonomic units (OTUs) were obtained from the four cattle breeds. The rumen fungi abundance and Chao and Simpson indexes were all higher in free-range ruminants than in domesticated ruminants. Three fungal phyla were identified by sequence comparison: Neocallimastigomycota, Basidiomycota, and Ascomycota. Basidiomycota and Ascomycota have very low abundance in the rumen of four breeds cattle but anaerobic fungi (AF) Neocallimastigomycota occurred in a high abundance. In Neocallimastigomycota, the dominant genera were Piromyces, Anaeromyces, Cyllamyces, Neocallimastix, and Orpionmyces in four cattle breeds. The composition of the major genera of Neocallimastigaceae varied greatly among the four cattle breeds. The unclassified genera were unequally distributed in gayals, yaks, Tibetan and Yunnan yellow cattle, accounting for 90.63%, 98.52%, 97.79%, and 27.01% respectively. It appears that free-range ruminants have more unknown rumen fungi than domesticated ruminants and the cattle breeds and animal diets had an impact on the diversity of rumen fungi.
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Affiliation(s)
- Houfu Wang
- Key Laboratory of Animal and Feed Science of Yunnan Provincial, Yunnan Agricultural University , Kunming , China
| | - Pengfei Li
- Key Laboratory of Animal and Feed Science of Yunnan Provincial, Yunnan Agricultural University , Kunming , China
| | - Xuchuan Liu
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
| | - Chunyong Zhang
- Key Laboratory of Animal and Feed Science of Yunnan Provincial, Yunnan Agricultural University , Kunming , China ; Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
| | - Qiongfen Lu
- Key Laboratory of Animal and Feed Science of Yunnan Provincial, Yunnan Agricultural University , Kunming , China ; Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
| | - Dongmei Xi
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
| | - Renhui Yang
- Key Laboratory of Animal and Feed Science of Yunnan Provincial, Yunnan Agricultural University , Kunming , China
| | - Shuling Wang
- Key Laboratory of Animal and Feed Science of Yunnan Provincial, Yunnan Agricultural University , Kunming , China
| | - Wenshun Bai
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
| | - Zhen Yang
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
| | - Rongkang Zhou
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
| | - Xiao Cheng
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
| | - Jing Leng
- Key Laboratory of Animal and Feed Science of Yunnan Provincial, Yunnan Agricultural University , Kunming , China ; Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
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Wilken SE, Seppälä S, Lankiewicz TS, Saxena M, Henske JK, Salamov AA, Grigoriev IV, O'Malley MA. Genomic and proteomic biases inform metabolic engineering strategies for anaerobic fungi. Metab Eng Commun 2019; 10:e00107. [PMID: 31799118 PMCID: PMC6883316 DOI: 10.1016/j.mec.2019.e00107] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 10/24/2019] [Accepted: 11/04/2019] [Indexed: 12/22/2022] Open
Abstract
Anaerobic fungi (Neocallimastigomycota) are emerging non-model hosts for biotechnology due to their wealth of biomass-degrading enzymes, yet tools to engineer these fungi have not yet been established. Here, we show that the anaerobic gut fungi have the most GC depleted genomes among 443 sequenced organisms in the fungal kingdom, which has ramifications for heterologous expression of genes as well as for emerging CRISPR-based genome engineering approaches. Comparative genomic analyses suggest that anaerobic fungi may contain cellular machinery to aid in sexual reproduction, yet a complete mating pathway was not identified. Predicted proteomes of the anaerobic fungi also contain an unusually large fraction of proteins with homopolymeric amino acid runs consisting of five or more identical consecutive amino acids. In particular, threonine runs are especially enriched in anaerobic fungal carbohydrate active enzymes (CAZymes) and this, together with a high abundance of predicted N-glycosylation motifs, suggests that gut fungal CAZymes are heavily glycosylated, which may impact heterologous production of these biotechnologically useful enzymes. Finally, we present a codon optimization strategy to aid in the development of genetic engineering tools tailored to these early-branching anaerobic fungi.
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Affiliation(s)
- St Elmo Wilken
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA
| | - Susanna Seppälä
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA
| | - Thomas S Lankiewicz
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA.,Department of Evolution Ecology and Marine Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Mohan Saxena
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA
| | - John K Henske
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA
| | - Asaf A Salamov
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA
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Lillington SP, Leggieri PA, Heom KA, O'Malley MA. Nature's recyclers: anaerobic microbial communities drive crude biomass deconstruction. Curr Opin Biotechnol 2019; 62:38-47. [PMID: 31593910 DOI: 10.1016/j.copbio.2019.08.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/25/2019] [Accepted: 08/29/2019] [Indexed: 12/13/2022]
Abstract
Microbial communities within anaerobic ecosystems have evolved to degrade and recycle carbon throughout the earth. A number of strains have been isolated from anaerobic microbial communities, which are rich in carbohydrate active enzymes (CAZymes) to liberate fermentable sugars from crude plant biomass (lignocellulose). However, natural anaerobic communities host a wealth of microbial diversity that has yet to be harnessed for biotechnological applications to hydrolyze crude biomass into sugars and value-added products. This review highlights recent advances in 'omics' techniques to sequence anaerobic microbial genomes, decipher microbial membership, and characterize CAZyme diversity in anaerobic microbiomes. With a focus on the herbivore rumen, we further discuss methods to discover new CAZymes, including those found within multi-enzyme fungal cellulosomes. Emerging techniques to characterize the interwoven metabolism and spatial interactions between anaerobes are also reviewed, which will prove critical to developing a predictive understanding of anaerobic communities to guide in microbiome engineering.
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Affiliation(s)
- Stephen P Lillington
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, United States
| | - Patrick A Leggieri
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, United States
| | - Kellie A Heom
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, United States
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, United States.
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40
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Wang XW, Benoit I, Groenewald JZ, Houbraken J, Dai X, Peng M, Yang X, Han DY, Gao C, Guo LD. Community dynamics of Neocallimastigomycetes in the rumen of yak feeding on wheat straw revealed by different primer sets. FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2019.03.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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41
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Gilmore SP, Lankiewicz TS, Wilken SE, Brown JL, Sexton JA, Henske JK, Theodorou MK, Valentine DL, O’Malley MA. Top-Down Enrichment Guides in Formation of Synthetic Microbial Consortia for Biomass Degradation. ACS Synth Biol 2019; 8:2174-2185. [PMID: 31461261 DOI: 10.1021/acssynbio.9b00271] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Consortium-based approaches are a promising avenue toward efficient bioprocessing. However, many complex microbial interactions dictate community dynamics and stability that must be replicated in synthetic systems. The rumen and/or hindguts of large mammalian herbivores harbor complex communities of biomass-degrading fungi and bacteria, as well as archaea and protozoa that work collectively to degrade lignocellulose, yet the microbial interactions responsible for stability, resilience, and activity of the community remain largely uncharacterized. In this work, we demonstrate a "top-down" enrichment-based methodology for selecting a minimal but effective lignocellulose-degrading community that produces methane-rich fermentation gas (biogas). The resulting enrichment consortium produced 0.75-1.9-fold more fermentation gas at 1.4-2.1 times the rate compared to a monoculture of fungi from the enrichment. Metagenomic sequencing of the top-down enriched consortium revealed genomes encoding for functional compartmentalization of the community, spread across an anaerobic fungus (Piromyces), a bacterium (Sphaerochaeta), and two methanogenic archaea (Methanosphaera and Methanocorpusculum). Guided by the composition of the top-down enrichment, several synthetic cocultures were formed from the "bottom-up" using previously isolated fungi, Neocallimastix californiae and Anaeromyces robustus paired with the methanogen Methanobacterium bryantii. While cross-feeding occurred in synthetic co-cultures, removal of fungal metabolites by methanogens did not increase the rate of gas production or the rate of substrate deconstruction by the synthetic community relative to fungal monocultures. Metabolomic characterization verified that syntrophy was established within synthetic co-cultures, which generated methane at similar concentrations compared to the enriched consortium but lacked the temporal stability (resilience) seen in the native system. Taken together, deciphering the membership and metabolic potential of an enriched gut consortium enables the design of methanogenic synthetic co-cultures. However, differences in the growth rate and stability of enriched versus synthetic consortia underscore the difficulties in mimicking naturally occurring syntrophy in synthetic systems.
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Affiliation(s)
- Sean P. Gilmore
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Thomas S. Lankiewicz
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - St. Elmo Wilken
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Jennifer L. Brown
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Jessica A. Sexton
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - John K. Henske
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Michael K. Theodorou
- Harper Adams University, Agriculture Centre for Sustainable Energy Systems, Newport, Shropshire TF10 8NB, United Kingdom
| | - David L. Valentine
- Department of Earth Science and Marine Science Institute, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Michelle A. O’Malley
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
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Wang Y, Youssef NH, Couger MB, Hanafy RA, Elshahed MS, Stajich JE. Molecular Dating of the Emergence of Anaerobic Rumen Fungi and the Impact of Laterally Acquired Genes. mSystems 2019; 4:e00247-19. [PMID: 31455637 PMCID: PMC6712302 DOI: 10.1128/msystems.00247-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 08/01/2019] [Indexed: 01/01/2023] Open
Abstract
The anaerobic gut fungi (AGF), or Neocallimastigomycota, inhabit the rumen and alimentary tract of herbivorous mammals, where they play important roles in the degradation of plant fiber. Comparative genomic and phylogenomic analyses of the AGF have long been hampered by their fastidious growth condition, as well as their large (up to 200 Mb) and AT-biased (78 to 84%) genomes. We sequenced 21 AGF transcriptomes and combined them with 5 available AGF genome sequences to explore their evolutionary relationships, time their divergence, and characterize gene gain/loss patterns associated with their evolution. We estimate that the most recent common ancestor of the AGF diverged 66 (±10) million years ago, a time frame that coincides with the evolution of grasses (Poaceae), as well as the mammalian transition from insectivory to herbivory. The concordance of independent estimations suggests that AGF have been important in shaping the success of mammalian herbivory transition by improving the efficiency of energy acquisition from recalcitrant plant materials. Comparative genomics identified multiple lineage-specific genes in the AGF, two of which were acquired from rumen gut bacteria and animal hosts via horizontal gene transfer (HGT). A third AGF domain, plant-like polysaccharide lyase, represents a novel gene in fungi that potentially aids AGF to degrade pectin. Analysis of genomic and transcriptomic sequences confirmed both the presence and expression of these lineage-specific genes in nearly all AGF clades. These genetic elements may contribute to the exceptional abilities of AGF to degrade plant biomass and enable metabolism of the rumen microbes and animal hosts.IMPORTANCE Anaerobic fungi living in the rumen of herbivorous mammals possess an extraordinary ability to degrade plant biomass. We examined the origin and genomic composition of these poorly characterized anaerobic gut fungi using both transcriptome and genomic data. Phylogenomics and molecular dating analyses found remarkable concurrence of the divergence times of the rumen fungi, the forage grasses, and the dietary shift of ancestral mammals from primarily insectivory to herbivory. Comparative genomics identified unique machinery in these fungi to utilize plant polysaccharides. The rumen fungi were also identified with the ability to code for three protein domains with putative functions in plant pectin degradation and microbial defense, which were absent from all other fungal organisms (examined over 1,000 fungal genomes). Two of these domains were likely acquired from rumen gut bacteria and animal hosts separately via horizontal gene transfer. The third one is a plant-like polysaccharide lyase, representing a unique fungal enzyme with potential pectin breakdown abilities.
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Affiliation(s)
- Yan Wang
- Department of Microbiology and Plant Pathology, University of California-Riverside, Riverside, California, USA
- Institute for Integrative Genome Biology, University of California-Riverside, Riverside, California, USA
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Matthew Brian Couger
- High Performance Computing Center, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Radwa A Hanafy
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California-Riverside, Riverside, California, USA
- Institute for Integrative Genome Biology, University of California-Riverside, Riverside, California, USA
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Wang D, Zhao C, Liu S, Zhang T, Yao J, Cao Y. Effects of Piromyces sp. CN6 CGMCC 14449 on fermentation quality, nutrient composition and the in vitro degradation rate of whole crop maize silage. AMB Express 2019; 9:121. [PMID: 31359220 PMCID: PMC6663944 DOI: 10.1186/s13568-019-0846-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 07/23/2019] [Indexed: 11/28/2022] Open
Abstract
This study investigated the effects of the rumen fungus Piromyces sp. CN6 CGMCC 14449 as a silage additive on the fermentation quality, nutrient composition and in vitro digestibility of whole crop maize silage. Whole crop maize served as the silage material and was vacuum packed in polyethylene bags. Three ensiling treatments were applied: a control (CK), addition of a fungus (FU) at 105 thallus-forming units per gram, and addition of compound enzyme (EN) at 0.033 mg/g (containing cellulase and xylanase at activities of 90 filter paper units and 6000 IU per gram, respectively). Compared with the CK, the FU and EN treatments decreased the pH after 30 days fermentation (P <0.05). Both FU and EN treatments increased the lactate, crude protein, and water-soluble carbohydrate contents (P <0.05), whereas reduced the acetate, ADF and NDF contents as well as the ammonia nitrogen to total nitrogen ratio in silage after 30 days of ensilaging (P <0.05), compared with those for the CK, while no changes were found in the dry matter and dry matter recovery (P > 0.05). The fungal inoculant increased the in vitro digestibility of dry matter, NDF and ADF in silage after 30 days fermentation (P <0.05). In conclusion, the rumen fungus Piromyces sp. CN6 CGMCC 14449 can improve the quality and nutrient composition of whole crop maize silage and increase the crude fibre digestibility.
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Champreda V, Mhuantong W, Lekakarn H, Bunterngsook B, Kanokratana P, Zhao XQ, Zhang F, Inoue H, Fujii T, Eurwilaichitr L. Designing cellulolytic enzyme systems for biorefinery: From nature to application. J Biosci Bioeng 2019; 128:637-654. [PMID: 31204199 DOI: 10.1016/j.jbiosc.2019.05.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 05/06/2019] [Accepted: 05/11/2019] [Indexed: 12/14/2022]
Abstract
Cellulolytic enzymes play a key role on conversion of lignocellulosic plant biomass to biofuels and biochemicals in sugar platform biorefineries. In this review, we survey composite carbohydrate-active enzymes (CAZymes) among groups of cellulolytic fungi and bacteria that exist under aerobic and anaerobic conditions. Recent advances in designing effective cellulase mixtures are described, starting from the most complex microbial consortium-based enzyme preparations, to single-origin enzymes derived from intensively studied cellulase producers such as Trichoderma reesei, Talaromyces cellulolyticus, and Penicellium funiculosum, and the simplest minimal enzyme systems comprising selected sets of mono-component enzymes tailor-made for specific lignocellulosic substrates. We provide a comprehensive update on studies in developing high-performance cellulases for biorefineries.
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Affiliation(s)
- Verawat Champreda
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand.
| | - Wuttichai Mhuantong
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Hataikarn Lekakarn
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University, Rangsit Campus, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Benjarat Bunterngsook
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Pattanop Kanokratana
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fei Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hiroyuki Inoue
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology, 3-11-32 Kagamiyama, Hiroshima 739-0046, Japan
| | - Tatsuya Fujii
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology, 3-11-32 Kagamiyama, Hiroshima 739-0046, Japan
| | - Lily Eurwilaichitr
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand
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Co-cultivation of the anaerobic fungus Anaeromyces robustus with Methanobacterium bryantii enhances transcription of carbohydrate active enzymes. J Ind Microbiol Biotechnol 2019; 46:1427-1433. [PMID: 31089985 DOI: 10.1007/s10295-019-02188-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 05/07/2019] [Indexed: 12/18/2022]
Abstract
Anaerobic gut fungi are biomass degraders that form syntrophic associations with other microbes in their native rumen environment. Here, RNA-Seq was used to track and quantify carbohydrate active enzyme (CAZyme) transcription in a synthetic consortium composed of the anaerobic fungus Anaeromyces robustus with methanogen Methanobacterium bryantii. Approximately 5% of total A. robustus genes were differentially regulated in co-culture with M. bryantii relative to cultivation of A. robustus alone. We found that 105 CAZymes (12% of the total predicted CAZymes of A. robustus) were upregulated while 29 were downregulated. Upregulated genes encode putative proteins with a wide array of cellulolytic, xylanolytic, and carbohydrate transport activities; 75% were fused to fungal dockerin domains, associated with a carbohydrate binding module, or both. Collectively, this analysis suggests that co-culture of A. robustus with M. bryantii remodels the transcriptional landscape of CAZymes and associated metabolic pathways in the fungus to aid in lignocellulose breakdown.
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Nagler M, Kozjek K, Etemadi M, Insam H, Podmirseg SM. Simple yet effective: Microbial and biotechnological benefits of rumen liquid addition to lignocellulose-degrading biogas plants. J Biotechnol 2019; 300:1-10. [PMID: 31082412 DOI: 10.1016/j.jbiotec.2019.05.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 05/07/2019] [Accepted: 05/09/2019] [Indexed: 01/30/2023]
Abstract
In biogas plants, lignocellulose-rich biomass (LCB) is particularly slowly degraded, causing high hydraulic retention times. This fact lowers the interests for such substrates. To enhance LCB-degradation, cattle rumen fluid, a highly active microbial resource accruing in the growing meat industry, might be used as a potential source for bioaugmentation. This study compares 0%, 20% and 40% rumen liquid in a batch anaerobic digestion approach. Moreover, it determines the biogas- and methane-potentials as well as degradation-speeds of corn straw, co-digested with cattle manure. It inspects microbial communities via marker-gene sequencing, qPCR and RNA-DGGE and draws attention on possible beneficial effects of rumen addition on the biogas-producing community. Bioaugmentation with 20% and 40% v/v rumen liquid accelerated methane yields by 5 and 6 days, respectively (i.e. reaching 90% of total methane production). It also enhanced LCB- as well as (hemi)cellulose- and volatile fatty acid degradation. These results are supported by increased abundances of bacteria, methanogens and anaerobic fungi in treatments with rumen liquid amendment, and point towards the persistence of specific rumen-borne microorganisms especially during the first phase of the experiment. The results suggest that rumen liquid addition is a promising strategy for enhanced and accelerated exploitation of LCB for biomethanisation.
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Affiliation(s)
- Magdalena Nagler
- Institute of Microbiology, Universität Innsbruck, Technikerstraße 25d, 6020 Innsbruck, Austria; ACIB Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria.
| | - Katja Kozjek
- Institute of Microbiology, Universität Innsbruck, Technikerstraße 25d, 6020 Innsbruck, Austria; ACIB Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
| | - Mohammad Etemadi
- Institute of Microbiology, Universität Innsbruck, Technikerstraße 25d, 6020 Innsbruck, Austria
| | - Heribert Insam
- Institute of Microbiology, Universität Innsbruck, Technikerstraße 25d, 6020 Innsbruck, Austria
| | - Sabine Marie Podmirseg
- Institute of Microbiology, Universität Innsbruck, Technikerstraße 25d, 6020 Innsbruck, Austria; ACIB Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
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Seppälä S, Yoo JI, Yur D, O'Malley MA. Heterologous transporters from anaerobic fungi bolster fluoride tolerance in Saccharomyces cerevisiae. Metab Eng Commun 2019; 9:e00091. [PMID: 31016136 PMCID: PMC6475669 DOI: 10.1016/j.mec.2019.e00091] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 03/22/2019] [Accepted: 04/09/2019] [Indexed: 12/21/2022] Open
Abstract
Membrane-embedded transporters are crucial for the stability and performance of microbial production strains. Apart from engineering known transporters derived from model systems, it is equally important to identify transporters from nonconventional organisms that confer advantageous traits for biotechnological applications. Here, we transferred genes encoding fluoride exporter (FEX) proteins from three strains of early-branching anaerobic fungi (Neocallimastigomycota) to Saccharomyces cerevisiae. The heterologous transporters are localized to the plasma membrane and complement a fluoride-sensitive yeast strain that is lacking endogenous fluoride transporters up to 10.24 mM fluoride. Furthermore, we show that fusing an amino-terminal leader sequence to FEX proteins in yeast elevates protein yields, yet inadvertently causes a loss of transporter function. Adaptive laboratory evolution of FEX proteins restores fluoride tolerance of these strains, in one case exceeding the solute tolerance observed in wild type S. cerevisiae; however, the underlying molecular mechanisms and cause for the increased tolerance in the evolved strains remain elusive. Our results suggest that microbial cultures can achieve solvent tolerance through different adaptive trajectories, and the study is a promising step towards the identification, production, and biotechnological application of membrane proteins from nonconventional fungi. First report describing the heterologous production of functional ion transport proteins sourced from anaerobic gut fungi. Codon-optimization enables production of functional, gut fungal membrane proteins in S. cerevisiae but not in E. coli. Addition of an N-terminal leader peptide elevates membrane protein yields yet diminishes cellular activity. Adaptive laboratory evolution restores cellular fluoride export activity in yeast to levels exceeding native tolerance.
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Affiliation(s)
- Susanna Seppälä
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA
| | - Justin I. Yoo
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA
| | - Daniel Yur
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA
| | - Michelle A. O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA
- Corresponding author.
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Podolsky IA, Seppälä S, Lankiewicz TS, Brown JL, Swift CL, O'Malley MA. Harnessing Nature's Anaerobes for Biotechnology and Bioprocessing. Annu Rev Chem Biomol Eng 2019; 10:105-128. [PMID: 30883214 DOI: 10.1146/annurev-chembioeng-060718-030340] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Industrial biotechnology has the potential to decrease our reliance on petroleum for fuel and bio-based chemical production and also enable valorization of waste streams. Anaerobic microorganisms thrive in resource-limited environments and offer an array of novel bioactivities in this regard that could revolutionize biomanufacturing. However, they have not been adopted for widespread industrial use owing to their strict growth requirements, limited number of available strains, difficulty in scale-up, and genetic intractability. This review provides an overview of current and future uses for anaerobes in biotechnology and bioprocessing in the postgenomic era. We focus on the recently characterized anaerobic fungi (Neocallimastigomycota) native to the digestive tract of large herbivores, which possess a trove of enzymes, pathways, transporters, and other biomolecules that can be harnessed for numerous biotechnological applications. Resolving current genetic intractability, scale-up, and cultivation challenges will unlock the potential of these lignocellulolytic fungi and other nonmodel micro-organisms to accelerate bio-based production.
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Affiliation(s)
- Igor A Podolsky
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA; , , , , ,
| | - Susanna Seppälä
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA; , , , , ,
| | - Thomas S Lankiewicz
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA; , , , , ,
| | - Jennifer L Brown
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA; , , , , ,
| | - Candice L Swift
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA; , , , , ,
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA; , , , , ,
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Mura E, Edwards J, Kittelmann S, Kaerger K, Voigt K, Mrázek J, Moniello G, Fliegerova K. Anaerobic fungal communities differ along the horse digestive tract. Fungal Biol 2018; 123:240-246. [PMID: 30798879 DOI: 10.1016/j.funbio.2018.12.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 11/23/2018] [Accepted: 12/19/2018] [Indexed: 10/27/2022]
Abstract
Anaerobic fungi are potent fibre degrading microbes in the equine hindgut, yet our understanding of their diversity and community structure is limited to date. In this preliminary work, using a clone library approach we studied the diversity of anaerobic fungi along six segments of the horse hindgut: caecum, right ventral colon (RVC), left ventral colon (LVC), left dorsal colon (LDC), right dorsal colon (RDC) and rectum. Of the 647 ITS1 clones, 61.7 % were assigned to genus level groups that are so far without any cultured representatives, and 38.0 % were assigned to the cultivated genera Neocallimastix (35.1 %), Orpinomyces (2.3 %), and Anaeromyces (0.6 %). AL1 dominated the group of uncultured anaerobic fungi, particularly in the RVC (88 %) and LDC (97 %). Sequences from the LSU clone library analysis of the LDC, however, split into two distinct phylogenetic clusters with low sequence identity to Caecomyces sp. (94-96 %) and Liebetanzomyces sp. (92 %) respectively. Sequences belonging to cultured Neocallimastix spp. dominated in LVC (81 %) and rectum (75.5 %). Quantification of anaerobic fungi showed significantly higher concentrations in RVC and RDC compared to other segments, which influenced the interpretation of the changes in anaerobic fungal diversity along the horse hindgut. These preliminary findings require further investigation.
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Affiliation(s)
- Erica Mura
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100 Sassari, Italy
| | - Joan Edwards
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, 6708 WE, the Netherlands
| | - Sandra Kittelmann
- Wilmar International Ltd., Wil@NUS Corporate Lab, National University of Singapore, Singapore 117599, Singapore
| | - Kerstin Kaerger
- Institute of Microbiology, University of Jena, Neugasse 25, 07743 Jena, Germany; Leibniz Institute for Natural Product Research and Infection Biology, Jena Microbial Resource Collection, Adolf-Reichwein-Str. 23, 07745 Jena, Germany
| | - Kerstin Voigt
- Institute of Microbiology, University of Jena, Neugasse 25, 07743 Jena, Germany; Leibniz Institute for Natural Product Research and Infection Biology, Jena Microbial Resource Collection, Adolf-Reichwein-Str. 23, 07745 Jena, Germany
| | - Jakub Mrázek
- Institute of Animal Physiology and Genetics, CAS, Vídeňská 1083, Prague 14220, Czech Republic
| | - Giuseppe Moniello
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100 Sassari, Italy
| | - Katerina Fliegerova
- Institute of Animal Physiology and Genetics, CAS, Vídeňská 1083, Prague 14220, Czech Republic.
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Mbareche H, Veillette M, Dubuis MÈ, Bakhiyi B, Marchand G, Zayed J, Lavoie J, Bilodeau GJ, Duchaine C. Fungal bioaerosols in biomethanization facilities. JOURNAL OF THE AIR & WASTE MANAGEMENT ASSOCIATION (1995) 2018; 68:1198-1210. [PMID: 29939829 DOI: 10.1080/10962247.2018.1492472] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/25/2018] [Accepted: 06/20/2018] [Indexed: 06/08/2023]
Abstract
Biomethanization is a new technology used for green-waste valorization where organic waste is biodegraded by microbial communities under anaerobic conditions. The main product of this type of anaerobic digestion is a biogas used as an energy source. Moving and handling organic waste may lead to the emission of high concentrations of bioaerosols. High exposure levels are associated with adverse health effects amongst green environment workers. Fungal spores are suspected to play a role in many respiratory illnesses. There is a paucity of information related to the detailed fungal diversity in biomethanization facilities. The aim of this study was to provide an in-depth description of fungal bioaerosols in biomethanization work environments using a next-generation sequencing approach combined with real-time polymerase chain reaction (PCR). Two biomethanization facilities treating different wastes were visited during the sampling campaign (n = 16). Quantification of Penicillium/Aspergillus and Aspergillus fumigatus revealed a greater exposure risk during summer for both facilities visited. Concentrations of Penicillium and Aspergillus were similar in all work areas in both biomethanization facilities. Taxonomy analyses showed that the type of waste treated affects the fungal diversity of aerosols emitted. Although eight classes were evenly distributed in all samples, Eurotiomycetes were more dominant in the first facility and Agaricomycetes were dominant in the second one. A large diversity profile was observed in bioaerosols from both facilities showing the presence of pathogenic fungi. The following fungi detected are known allergens and/or are opportunistic pathogens: Aspergillus, Malassezia, Emericella, Fusarium, Acremonium, and Candida. Daily exposure to these fungi may put workers at risk. The information from this study can be used as a reference for minimizing occupational exposure in future biomethanization facilities. Implications: Biomethanization is a new technology used for green-waste valorization where organic waste is biodegraded by microbial communities. Effective waste management is increasingly recognized as a strategic approach for achieving newly created regulations concerning the disposal of organic residues; therefore, an expansion of facilities is expected. Workers' exposure to diverse fungal communities is certain, as fungi are ubiquitous and necessary in organic matter decomposition. Monitoring this occupational exposure is important in order to prevent workers' health problems.
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Affiliation(s)
- Hamza Mbareche
- a Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec (CRIUCPQ) , Quebec City , Quebec , Canada
- c Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie , Laval University , Quebec City , Quebec , Canada
| | - Marc Veillette
- a Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec (CRIUCPQ) , Quebec City , Quebec , Canada
| | - Marie-Ève Dubuis
- a Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec (CRIUCPQ) , Quebec City , Quebec , Canada
- c Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie , Laval University , Quebec City , Quebec , Canada
| | - Bouchra Bakhiyi
- b Institut de Recherche Robert-Sauvé en Santé et en Sécurité du Travail (IRSST) , Montreal , Quebec , Canada
- d Department of Environmental and Occupational Health , School of Public Health, University of Montreal , Montreal , Quebec , Canada
| | - Geneviève Marchand
- b Institut de Recherche Robert-Sauvé en Santé et en Sécurité du Travail (IRSST) , Montreal , Quebec , Canada
- d Department of Environmental and Occupational Health , School of Public Health, University of Montreal , Montreal , Quebec , Canada
| | - Joseph Zayed
- b Institut de Recherche Robert-Sauvé en Santé et en Sécurité du Travail (IRSST) , Montreal , Quebec , Canada
- d Department of Environmental and Occupational Health , School of Public Health, University of Montreal , Montreal , Quebec , Canada
| | - Jacques Lavoie
- b Institut de Recherche Robert-Sauvé en Santé et en Sécurité du Travail (IRSST) , Montreal , Quebec , Canada
- d Department of Environmental and Occupational Health , School of Public Health, University of Montreal , Montreal , Quebec , Canada
| | - Guillaume J Bilodeau
- e Pathogen Identification Research Laboratory , Canadian Food Inspection Agency (CFIA) , Ottawa , Ontario , Canada
| | - Caroline Duchaine
- a Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec (CRIUCPQ) , Quebec City , Quebec , Canada
- c Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie , Laval University , Quebec City , Quebec , Canada
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