1
|
Hoque E, Fritscher J. Are anaerobic fungi crucial hidden players of microbiomes in anoxic environment? Crit Rev Microbiol 2023:1-24. [PMID: 37452612 DOI: 10.1080/1040841x.2023.2224425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 11/20/2022] [Accepted: 11/25/2022] [Indexed: 07/18/2023]
Abstract
Anaerobic fungi are known to migrate and establish a 3D network of biofilms (microbiomes) and live invisible in the rumen and terrestrial subsurface, deep-sea - marine, and anoxic environment. They deserve our attention to understand anoxic fungal ecology and functions and develop new products and solutions. Such fungi activate unique genes to produce various polysaccharidases deemed essential for degrading plants' lignocellulosic materials. Nutrient release, recycling, and physical support by anaerobic fungi are crucial for microbiome formation. Multiple reports point to the ability of strictly anaerobic and facultative fungi to adapt and live in anoxic subsurface. Deep-sea sediments and natural anoxic methane-emitting salty waters of sulfidic springs offer suitable habitats for developing prokaryotic-fungal microbiomes. Researchers found a billion-year-old fossil of the fungus-prokaryotic sulfate-reducing consortium buried in deep-sea biospheres. Fungal spores' ability to migrate, even after germination, through sandy layers demonstrates their potential to move up and down porous geological layers or rock fissures. Selective fungal affinity to specific wood in wood chip arrays might help differentiate viable anaerobic fungi from an anoxic environment for their rapid collection and investigation. New collection methods, cultivation, gene expression, and drug and enzyme activity analyses can boost anaerobic fungal research.
Collapse
Affiliation(s)
- Enamul Hoque
- Department of Biotechnology, University of Science and Technology, Foy's Lake, Chittagong, Bangladesh
- International Virtual Institute for Advanced Science and Technology (IVAST), Section Microbial Technology, Munich, Germany
- Department of Environmental Science, Helmholtz Zentrum München GmbH - German Research Center for Environmental Health, Neuherberg, Germany
| | - Johannes Fritscher
- Department of Biotechnology, University of Science and Technology, Foy's Lake, Chittagong, Bangladesh
- International Virtual Institute for Advanced Science and Technology (IVAST), Section Microbial Technology, Munich, Germany
- Department of Environmental Science, Helmholtz Zentrum München GmbH - German Research Center for Environmental Health, Neuherberg, Germany
| |
Collapse
|
2
|
Lange L, Barrett K, Pilgaard B, Gleason F, Tsang A. Enzymes of early-diverging, zoosporic fungi. Appl Microbiol Biotechnol 2019; 103:6885-6902. [PMID: 31309267 PMCID: PMC6690862 DOI: 10.1007/s00253-019-09983-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 06/12/2019] [Accepted: 06/13/2019] [Indexed: 11/26/2022]
Abstract
The secretome, the complement of extracellular proteins, is a reflection of the interaction of an organism with its host or substrate, thus a determining factor for the organism’s fitness and competitiveness. Hence, the secretome impacts speciation and organismal evolution. The zoosporic Chytridiomycota, Blastocladiomycota, Neocallimastigomycota, and Cryptomycota represent the earliest diverging lineages of the Fungal Kingdom. The review describes the enzyme compositions of these zoosporic fungi, underscoring the enzymes involved in biomass degradation. The review connects the lifestyle and substrate affinities of the zoosporic fungi to the secretome composition by examining both classical phenotypic investigations and molecular/genomic-based studies. The carbohydrate-active enzyme profiles of 19 genome-sequenced species are summarized. Emphasis is given to recent advances in understanding the functional role of rumen fungi, the basis for the devastating chytridiomycosis, and the structure of fungal cellulosome. The approach taken by the review enables comparison of the secretome enzyme composition of anaerobic versus aerobic early-diverging fungi and comparison of enzyme portfolio of specialized parasites, pathogens, and saprotrophs. Early-diverging fungi digest most major types of biopolymers: cellulose, hemicellulose, pectin, chitin, and keratin. It is thus to be expected that early-diverging fungi in its entirety represents a rich and diverse pool of secreted, metabolic enzymes. The review presents the methods used for enzyme discovery, the diversity of enzymes found, the status and outlook for recombinant production, and the potential for applications. Comparative studies on the composition of secretome enzymes of early-diverging fungi would contribute to unraveling the basal lineages of fungi.
Collapse
Affiliation(s)
- Lene Lange
- Bioeconomy, Research & Advisory, Karensgade 5, Valby, DK-2500, Copenhagen, Denmark.
| | - Kristian Barrett
- Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, DK-2800, Kgs. Lyngby, Denmark
| | - Bo Pilgaard
- Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, DK-2800, Kgs. Lyngby, Denmark
| | - Frank Gleason
- School of Life and Environmental Sciences, University of Sydney, Sydney, 2006, Australia
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, H4B1R6, Canada
| |
Collapse
|
3
|
The biotechnological potential of anaerobic fungi on fiber degradation and methane production. World J Microbiol Biotechnol 2018; 34:155. [PMID: 30276481 DOI: 10.1007/s11274-018-2539-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 09/26/2018] [Indexed: 01/16/2023]
Abstract
Anaerobic fungi (phylum Neocallimastigomycota), an early branching family of fungi, are commonly encountered in the digestive tract of mammalian herbivores. To date, isolates from ten described genera have been reported, and several novel taxonomic groupings are detected using culture-independent molecular methods. Anaerobic fungi are recognized as playing key roles in the decomposition of lignocellulose (up to 50% of the ingested and untreated lignocellulose), with their physical penetration and extracellular enzymatical secretion of an unbiased diverse repertoire of cell-wall-degrading enzymes. The secreted cell-wall-degrading enzymes of anaerobic fungi include both free enzymes and extracellular multi-enzyme complexes called cellulosomes, both of which have potential as fiber degraders in industries. In addition, anaerobic fungi can provide large amounts of substrates such as hydrogen, formate, and acetate for their co-cultured methanogens. Consequently, large amounts of methane can be produced. And thus, it is promising to use the co-culture of anaerobic fungi and methanogens in the biogas process to intensify the biogas yield owing to the efficient and robust degradation of recalcitrant biomass by anaerobic fungi and improved methane production from co-cultures of anaerobic fungi and methanogens.
Collapse
|
4
|
Dollhofer V, Callaghan TM, Griffith GW, Lebuhn M, Bauer J. Presence and transcriptional activity of anaerobic fungi in agricultural biogas plants. BIORESOURCE TECHNOLOGY 2017; 235:131-139. [PMID: 28365340 DOI: 10.1016/j.biortech.2017.03.116] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 03/19/2017] [Accepted: 03/20/2017] [Indexed: 06/07/2023]
Abstract
Bioaugmentation with anaerobic fungi (AF) is promising for improved biogas generation from lignocelluloses-rich substrates. However, before implementing AF into biogas processes it is necessary to investigate their natural occurrence, community structure and transcriptional activity in agricultural biogas plants. Thus, AF were detected with three specific PCR based methods: (i) Copies of their 18S genes were found in 7 of 10 biogas plants. (ii) Transcripts of a GH5 endoglucanase gene were present at low level in two digesters, indicating transcriptional cellulolytic activity of AF. (iii) Phylogeny of the AF-community was inferred with the 28S gene. A new Piromyces species was isolated from a PCR-positive digester. Evidence for AF was only found in biogas plants operated with high proportions of animal feces. Thus, AF were most likely transferred into digesters with animal derived substrates. Additionally, high process temperatures in combination with long retention times seemed to impede AF survival and activity.
Collapse
Affiliation(s)
- Veronika Dollhofer
- Department for Quality Assurance and Analytics, Bavarian State Research Center for Agriculture, Lange Point 6, 85354 Freising, Germany(1).
| | - Tony M Callaghan
- Institute of Biological Sciences, University of Wales, Aberystwyth, UK.
| | - Gareth W Griffith
- Institute of Biological Sciences, University of Wales, Aberystwyth, UK.
| | - Michael Lebuhn
- Department for Quality Assurance and Analytics, Bavarian State Research Center for Agriculture, Lange Point 6, 85354 Freising, Germany(1).
| | - Johann Bauer
- Chair of Animal Hygiene, WZW, TUM, Weihenstephaner Berg 3, 85354 Freising, Germany.
| |
Collapse
|
5
|
Henske JK, Gilmore SP, Knop D, Cunningham FJ, Sexton JA, Smallwood CR, Shutthanandan V, Evans JE, Theodorou MK, O’Malley MA. Transcriptomic characterization of Caecomyces churrovis: a novel, non-rhizoid-forming lignocellulolytic anaerobic fungus. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:305. [PMID: 29270219 PMCID: PMC5737911 DOI: 10.1186/s13068-017-0997-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 12/12/2017] [Indexed: 05/19/2023]
Abstract
Anaerobic gut fungi are the primary colonizers of plant material in the rumen microbiome, but are poorly studied due to a lack of characterized isolates. While most genera of gut fungi form extensive rhizoidal networks, which likely participate in mechanical disruption of plant cell walls, fungi within the Caecomyces genus do not possess these rhizoids. Here, we describe a novel fungal isolate, Caecomyces churrovis, which forms spherical sporangia with a limited rhizoidal network yet secretes a diverse set of carbohydrate active enzymes (CAZymes) for plant cell wall hydrolysis. Despite lacking an extensive rhizoidal system, C. churrovis is capable of growth on fibrous substrates like switchgrass, reed canary grass, and corn stover, although faster growth is observed on soluble sugars. Gut fungi have been shown to use enzyme complexes (fungal cellulosomes) in which CAZymes bind to non-catalytic scaffoldins to improve biomass degradation efficiency. However, transcriptomic analysis and enzyme activity assays reveal that C. churrovis relies more on free enzymes compared to other gut fungal isolates. Only 15% of CAZyme transcripts contain non-catalytic dockerin domains in C. churrovis, compared to 30% in rhizoid-forming fungi. Furthermore, C. churrovis is enriched in GH43 enzymes that provide complementary hemicellulose degrading activities, suggesting that a wider variety of these activities are required to degrade plant biomass in the absence of an extensive fungal rhizoid network. Overall, molecular characterization of a non-rhizoid-forming anaerobic fungus fills a gap in understanding the roles of CAZyme abundance and associated degradation mechanisms during lignocellulose breakdown within the rumen microbiome.
Collapse
Affiliation(s)
- John K. Henske
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106 USA
| | - Sean P. Gilmore
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106 USA
| | - Doriv Knop
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106 USA
| | - Francis J. Cunningham
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106 USA
| | - Jessica A. Sexton
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106 USA
| | - Chuck R. Smallwood
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354 USA
| | | | - James E. Evans
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354 USA
| | - Michael K. Theodorou
- Agriculture Centre for Sustainable Energy Systems (ACSES), Animal Production, Welfare and Veterinary Sciences, Harper Adams University, Newport, Shropshire TF10 8NB UK
| | - Michelle A. O’Malley
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106 USA
| |
Collapse
|
6
|
Isolation, characterization and fibre degradation potential of anaerobic rumen fungi from cattle. ANN MICROBIOL 2012. [DOI: 10.1007/s13213-012-0577-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
|
7
|
Yang H, Yue Q. The modification of glucose levels and N source in the Hungate's medium to stimulate the production of fibrolytic enzymes of Anaeromyces sp. YQ3 grown on corn stalks. Anim Feed Sci Technol 2012. [DOI: 10.1016/j.anifeedsci.2011.10.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
8
|
Yang HJ, Yue Q. Effect of glucose addition and N sources in defined media on fibrolytic activity profiles ofNeocallimastix sp. YQ1 grown on corn stover. J Anim Physiol Anim Nutr (Berl) 2011; 96:554-62. [DOI: 10.1111/j.1439-0396.2011.01177.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
9
|
Comlekcioglu U, Ozkose E, Yazdic FC, Akyol I, Ekinci MS. Polysaccharidase and glycosidase production of avicel grown rumen fungus Orpinomyces sp. GMLF5. ACTA BIOLOGICA HUNGARICA 2010; 61:333-43. [PMID: 20724279 DOI: 10.1556/abiol.61.2010.3.9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Extracellular and cell-associated enzyme preparations were obtained from ruminal anaerobic fungi Orpinomyces sp. GMLF5 grown in culture containing microcrystalline cellulose (avicel) as sole energy source and degradation capacities of the preparations towards several polysaccharides and glycosides were studied. Fungus showed substantial increases in xylanase, carboxymethyl cellulase (CMCase), lichenase, amylase, beta-xylosidase, beta-glucosidase and alpha-L-arabinofuranosidase activities between 72 and 168 hours. High amounts of cell associated beta-xylosidase were noted in 4 and 5 days old cultures. Optimum temperature and pH of the polysaccharidases were found at 50 degrees C and 6.0-6.5, respectively. Xylanase was found to be virtually stable at 50 degrees C, CMCase and lichenase were stable at 40 degrees C for 200 min, however amylase was found more sensitive to heat treatment. The fibrolytic enzymes of the isolate GMLF5 were observed to be capable of hydrolyze the avicel.
Collapse
Affiliation(s)
- U Comlekcioglu
- Animal Science Department, Agriculture Faculty, Kahramanmaras Sutcu Imam University, Kahramanmaras, Turkey.
| | | | | | | | | |
Collapse
|
10
|
Yang H, Yue Q, Cao Y, Zhang D, Wang J. Effects of crude feruloyl and acetyl esterase solutions of Neocallimastix sp. YQ1 and Anaeromyces sp. YQ3 isolated from Holstein steers on hydrolysis of Chinese wildrye grass hay, wheat bran, maize bran, wheat straw and corn stalks. Anim Feed Sci Technol 2009. [DOI: 10.1016/j.anifeedsci.2009.09.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
11
|
Yue Q, Yang H, Cao Y, Zhang D, Jiang Y, Wang J. Feruloyl and acetyl esterase production of an anaerobic rumen fungus Neocallimastix sp. YQ2 effected by glucose and soluble nitrogen supplementations and its potential in the hydrolysis of fibrous feedstuffs. Anim Feed Sci Technol 2009. [DOI: 10.1016/j.anifeedsci.2009.06.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
12
|
Diversity of anaerobic fungal populations in cattle revealed by selective enrichment culture using different carbon sources. FUNGAL ECOL 2009. [DOI: 10.1016/j.funeco.2009.01.005] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
13
|
Matsui H, Ban-Tokuda T. Studies on carboxymethyl cellulase and xylanase activities of anaerobic fungal isolate CR4 from the bovine rumen. Curr Microbiol 2008; 57:615-9. [PMID: 18791765 DOI: 10.1007/s00284-008-9252-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2008] [Revised: 04/12/2008] [Accepted: 07/28/2008] [Indexed: 11/24/2022]
Abstract
An anaerobic fungal isolate, CR4, was isolated from the bovine rumen. The DNA sequence of internal transcribed spacer region 1 showed that CR4 belonged to the genus Caecocmyces. The dry matter digestibility of timothy hay by anaerobic fungal isolate CR4 was determined. The effects of carbohydrate growth substrates on carboxymethyl cellulase (CMCase) and xylanase activities also were examined. The extent of dry matter digestibility of timothy hay was 31% at 6 days' incubation. The highest specific activity of CMCase in the culture supernatant (SN) fraction was observed in xylose culture. The activity of CMCase was not detected in the SN fraction of cellobiose and xylan or in the cell-bound fraction of all growth substrates. The highest specific activity of xylanase in the SN fraction was observed in glucose culture. These results suggest that fiber-degrading enzyme activities were affected by growth substrates and that CR4 is xylanolytic. Zymogram analysis showed that CR4 produces three CMCases of molecular mass (95, 89, and 64 kDa) and three xylanases of molecular mass (82, 73, and 66 kDa). This is the first demonstration showing the molecular mass of fiber-degrading enzymes of Caecomyces.
Collapse
Affiliation(s)
- Hiroki Matsui
- Graduate School of Bioresources, Mie University, Mie, Japan.
| | | |
Collapse
|
14
|
Graminha E, Gonçalves A, Pirota R, Balsalobre M, Da Silva R, Gomes E. Enzyme production by solid-state fermentation: Application to animal nutrition. Anim Feed Sci Technol 2008. [DOI: 10.1016/j.anifeedsci.2007.09.029] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
15
|
Fliegerová K, Hodrová B, Voigt K. Classical and molecular approaches as a powerful tool for the characterization of rumen polycentric fungi. Folia Microbiol (Praha) 2005; 49:157-64. [PMID: 15227788 DOI: 10.1007/bf02931392] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Ribosomal ITS1 and ITS2 fragments from 8 isolates of polycentric rumen anaerobic fungi were PCR-amplified and sequenced; the sequences obtained were aligned with published data and phylogenetic analyses were performed. Analysis of the ITS1 fragment clearly differentiated between the two polycentric genera Orpinomyces and Anaeromyces and this classification is supported by morphological observation. A multi-order phylogram based on ITS2 sequences proved that anaerobic rumen fungi are separated from aerobic chytrids, which form a well-supported monophylum with the highest possible bootstrap proportion values of 100%. Sequence analysis of ITS regions is a powerful tool for classification of anaerobic fungi but morphological description of strains is still necessary because some genera of rumen fungi display a high genetic heterogeneity.
Collapse
Affiliation(s)
- K Fliegerová
- Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Prague, Czechia.
| | | | | |
Collapse
|