1887

Abstract

Establishing a solid taxonomic framework is crucial for enabling discovery and documentation efforts. This ensures effective communication between scientists as well as reproducibility of results between laboratories, and facilitates the exchange and preservation of biological material. Such framework can only be achieved by establishing clear criteria for taxa characterization and rank assignment. Within the anaerobic fungi (phylum Neocallimastigomycota), the need for such criteria is especially vital. Difficulties associated with their isolation, maintenance and long-term storage often result in limited availability and loss of previously described taxa. To this end, we provide here a list of morphological, microscopic, phylogenetic and phenotypic criteria for assessment and documentation when characterizing newly obtained Neocallimastigomycota isolates. We also recommend a polyphasic rank-assignment scheme for novel genus-, species- and strain-level designations for newly obtained Neocallimastigomycota isolates.

  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005449
2022-07-19
2024-04-27
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/72/7/ijsem005449.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.005449&mimeType=html&fmt=ahah

References

  1. Hawkswirth DL, Lücking R. Fungal diversity revisited: 2.2 to 3.8 million species. Microbiol Spectr 2017; 5:0052
    [Google Scholar]
  2. May TW, Redhead SA, Bensch K, Hawksworth DL, Lendemer J et al. Chapter F of the international code of nomenclature for algae, fungi, and plants as approved by the 11th International Mycological Congress, San Juan, Puerto Rico, July 2018. IMA Fungus 2019; 10:1–14 [View Article] [PubMed]
    [Google Scholar]
  3. Aime MC, Miller AN, Aoki T, Bensch K, Cai L et al. How to publish a new fungal species, or name, version 3.0. IMA Fungus 2021; 12:11 [View Article] [PubMed]
    [Google Scholar]
  4. Callaghan TM, Podmirseg SM, Hohlweck D, Edwards JE, Puniya AK et al. Buwchfawromyces eastonii gen. nov., sp. nov.: a new anaerobic fungus (Neocallimastigomycota) isolated from buffalo faeces. MC 2015; 9:11–28 [View Article]
    [Google Scholar]
  5. Dagar SS, Kumar S, Griffith GW, Edwards JE, Callaghan TM et al. A new anaerobic fungus (Oontomyces anksri gen. nov., sp. nov.) from the digestive tract of the Indian camel (Camelus dromedarius). Fungal Biol 2015; 119:731–737 [View Article]
    [Google Scholar]
  6. Hanafy RA, Elshahed MS, Liggenstoffer AS, Griffith GW, Youssef NH. Pecoramyces ruminantium, gen. nov., sp. nov., an anaerobic gut fungus from the feces of cattle and sheep. Mycologia 2017; 109:231–243 [View Article]
    [Google Scholar]
  7. Hanafy RA, Elshahed MS, Youssef NH. Feramyces austinii, gen. nov, sp. nov., an anaerobic gut fungus from rumen and fecal samples of wild barbary sheep and fallow deer. Mycologia 2018; 110:513–525
    [Google Scholar]
  8. Hanafy RA, Lanjekar VB, Dhakephalkar PK, Callaghan TM, Dagar SS et al. Seven new Neocallimastigomycota genera from wild, zoo-housed, and domesticated herbivores greatly expand the taxonomic diversity of the phylum. Mycologia 2020; 112:1212–1239 [View Article] [PubMed]
    [Google Scholar]
  9. Hanafy RA, Youssef NH, Elshahed MS. Paucimyces polynucleatus gen. nov, sp. nov., a novel polycentric genus of anaerobic gut fungi from the faeces of a wild blackbuck antelope. Int J Syst Evol Microbiol 2021; 71:1466–5034 [View Article] [PubMed]
    [Google Scholar]
  10. Stabel M, Hanafy RA, Schweitzer T, Greif M, Aliyu H et al. Aestipascuomyces dupliciliberans gen. nov, sp. nov., the first cultured representative of the uncultured SK4 clade from aoudad sheep and alpaca. Microorganisms 2020; 8:1734 [View Article]
    [Google Scholar]
  11. Ariyawansa HA, Hyde KD, Jayasiri SC et al. Fungal diversity notes 111–252—taxonomic and phylogenetic contributions to fungal taxa. Fungal Divers 2015; 75:27–274 [View Article]
    [Google Scholar]
  12. Hanafy RA, Johnson B, Elshahed MS, Youssef NH. Anaeromyces contortus, sp. nov., a new anaerobic gut fungal species (Neocallimastigomycota) isolated from the feces of cow and goat. Mycologia 2018; 110:502–512 [View Article] [PubMed]
    [Google Scholar]
  13. Li GJ, Hyde KD, Zhao RL et al. Fungal diversity notes 253–366: taxonomic and phylogenetic contributions to fungal taxa. Fungal Divers 2016; 78:1–237 [View Article]
    [Google Scholar]
  14. Ozkose E, Thomas BJ, Davies DR, Griffith GW, Theodorou MK. Cyllamyces aberensis gen.nov. sp.nov., a new anaerobic gut fungus with branched sporangiophores isolated from cattle. Can J Bot 2001; 79:666–673 [View Article]
    [Google Scholar]
  15. Ho YW, Barr DJS. Classification of anaerobic gut fungi from herbivores with emphasis on rumen fungi from Malaysia. Mycologia 2018; 87:655–677 [View Article]
    [Google Scholar]
  16. James TY, Kauff F, Schoch CL, Matheny PB, Hofstetter V et al. Reconstructing the early evolution of fungi using a six-gene phylogeny. Nature 2006; 443:818–822 [View Article] [PubMed]
    [Google Scholar]
  17. Wang Y, Youssef N, Couger M, Hanafy R, Elshahed M et al. Comparative genomics and divergence time estimation of the anaerobic fungi in herbivorous mammals. mSystems 2019; 4:e00247-19 [View Article]
    [Google Scholar]
  18. Ke H-M, Lee H-H, Lin C-Y, Liu Y-C, Lu MR et al. Mycena genomes resolve the evolution of fungal bioluminescence. Proc Natl Acad Sci USA 2020; 117:31267–31277 [View Article] [PubMed]
    [Google Scholar]
  19. Wibberg D, Stadler M, Lambert C, Bunk B, Spröer C et al. High quality genome sequences of thirteen Hypoxylaceae (Ascomycota) strengthen the phylogenetic family backbone and enable the discovery of new taxa. Fungal Divers 2020; 106:7–28 [View Article]
    [Google Scholar]
  20. Hanafy RA, Dagar SS, Griffith GW, Pratt CJ, Youssef NH et al. Taxonomy of the anaerobic gut fungi (Neocallimastigomycota): a review of classification criteria and description of current taxa. Int J Syst Evol Microbiol 2022
    [Google Scholar]
  21. Gold JJ, Heath IB, Bauchop T. Ultrastructural description of a new chytrid genus of caecum anaerobe, Caecomyces equi gen. nov., sp. nov., assigned to the Neocallimasticaceae. Biosystems 1988; 21:403–415 [View Article]
    [Google Scholar]
  22. Li J, Heath IB, Bauchop T. Piromyces mae and Piromyces dumbonica, two new species of uniflagellate anaerobic chytridiomycete fungi from the hindgut of the horse and elephant. Can J Bot 1990; 68:1021–1033 [View Article]
    [Google Scholar]
  23. Webb J, Theodorou MK. Neocallimastix hurleyensis sp.nov., an anaerobic fungus from the ovine rumen. Can J Bot 1991; 69:1220–1224 [View Article]
    [Google Scholar]
  24. Hanafy RA, Johnson B, Youssef NH, Elshahed MS. Assessing anaerobic gut fungal diversity in herbivores using D1/D2 large ribosomal subunit sequencing and multi-year isolation. Environ Microbiol 2020; 22:3883–3908 [View Article] [PubMed]
    [Google Scholar]
  25. Breton A, Bernalier A, Bonnemoy F, Fonty G, Gaillard B et al. Morphological and metabolic characterization of a new species of strictly anaerobic rumen fungus: Neocallimastix joyonii. FEMS Microbiol Lett 1989; 58:309–314 [View Article]
    [Google Scholar]
  26. Edwards JE, Hermes GDA, Kittelmann S, Nijsse B, Smidt H. Assessment of the accuracy of high-throughput sequencing of the ITS1 region of Neocallimastigomycota for community composition analysis. Front Microbiol 2019; 10:2370 [View Article] [PubMed]
    [Google Scholar]
  27. Koetschan C, Kittelmann S, Lu J, Al-Halbouni D, Jarvis GN et al. Internal transcribed spacer 1 secondary structure analysis reveals a common core throughout the anaerobic fungi (Neocallimastigomycota). PLoS One 2014; 9:e91928 [View Article] [PubMed]
    [Google Scholar]
  28. Edwards JE, Shetty SA, van den Berg P, Burden F, van Doorn DA et al. Multi-kingdom characterization of the core equine fecal microbiota based on multiple equine (sub)species. Anim Microbiome 2020; 2:6 [View Article] [PubMed]
    [Google Scholar]
  29. Edwards JE, Schennink A, Burden F, Long S, van Doorn DA et al. Domesticated equine species and their derived hybrids differ in their fecal microbiota. Anim Microbiome 2020; 2:8 [View Article] [PubMed]
    [Google Scholar]
  30. Liu J, Ma J, Liu Y, Yang Y, Yue D et al. Optimized production of a novel bioflocculant M-C11 by Klebsiella sp. and its application in sludge dewatering. J Environ Sci 2014; 26:2076–2083 [View Article] [PubMed]
    [Google Scholar]
  31. Ljungdahl LG. The cellulase/hemicellulase system of the anaerobic fungus Orpinomyces PC-2 and aspects of its applied use. Ann NY Acad Sci 2008; 1125:308–321 [View Article] [PubMed]
    [Google Scholar]
  32. Mustefa Beyan S, Venkatesa Prabhu S, Mumecha TK, Gemeda MT. Production of alkaline proteases using Aspergillus sp. isolated from injera: RSM-GA based process optimization and enzyme kinetics aspect. Curr Microbiol 2021; 78:1823–1834 [View Article] [PubMed]
    [Google Scholar]
  33. Preczeski KP, Dalastra C, Czapela FF, Kubeneck S, Scapini T et al. Fusarium oxysporum and Aspergillus sp. as keratinase producers using swine hair from agroindustrial residues. Front Bioeng Biotechnol 2020; 8:71 [View Article] [PubMed]
    [Google Scholar]
  34. Ali BR, Zhou L, Graves FM, Freedman RB, Black GW et al. Cellulases and hemicellulases of the anaerobic fungus Piromyces constitute a multiprotein cellulose-binding complex and are encoded by multigene families. FEMS Microbiol Lett 1995; 125:15–21 [View Article] [PubMed]
    [Google Scholar]
  35. Steenbakkers PJM, Freelove A, Van Cranenbroek B, Sweegers BMC, Harhangi HR et al. The major component of the cellulosomes of anaerobic fungi from the genus Piromyces is a family 48 glycoside hydrolase. DNA Seq 2002; 13:313–320 [View Article] [PubMed]
    [Google Scholar]
  36. Wang X, Kan G, Shi C, Xie Q, Ju Y et al. Purification and characterization of a novel wild-type α-amylase from Antarctic sea ice bacterium Pseudoalteromonas sp. M175. Protein Expr Purif 2019; 164:105444 [View Article] [PubMed]
    [Google Scholar]
  37. Knig E, Schlesner H, Hirsch P. Cell wall studies on budding bacteria of the Planctomyces/Pasteuria group and on a Prosthecomicrobium sp. Arch Microbiol 1984; 138:200–205 [View Article]
    [Google Scholar]
  38. Calkins S, Youssef NH. Insights into the utility of the focal adhesion scaffolding proteins in the anaerobic fungus Orpinomyces sp. C1A. PLoS One 2016; 11:e0163553 [View Article] [PubMed]
    [Google Scholar]
  39. Joshi A, Lanjekar VB, Dhakephalkar PK, Callaghan TM, Griffith GW et al. Liebetanzomyces polymorphus gen. et sp. nov., a new anaerobic fungus (neocallimastigomycota). MycoKeys 2018; 40:89–110
    [Google Scholar]
  40. Calkins S, Elledge NC, Hanafy RA, Elshahed MS, Youssef N. A fast and reliable procedure for spore collection from anaerobic fungi: application for RNA uptake and long-term storage of isolates. J Microbiol Methods 2016; 127:206–213 [View Article] [PubMed]
    [Google Scholar]
  41. Nicholson MJ, McSweeney CS, Mackie RI, Brookman JL, Theodorou MK. Diversity of anaerobic gut fungal populations analysed using ribosomal ITS1 sequences in faeces of wild and domesticated herbivores. Anaerobe 2010; 16:66–73 [View Article] [PubMed]
    [Google Scholar]
  42. Edwards JE, Kingston-Smith AH, Jimenez HR, Huws SA, Skøt KP et al. Dynamics of initial colonization of nonconserved perennial ryegrass by anaerobic fungi in the bovine rumen. FEMS Microbiol Ecol 2008; 66:537–545 [View Article] [PubMed]
    [Google Scholar]
  43. Fliegerová K, Mrázek J, Voigt K. Differentiation of anaerobic polycentric fungi by rDNA PCR-RFLP. Folia Microbiol 2006; 51:273–277 [View Article]
    [Google Scholar]
  44. Dagar SS, Kumar S, Mudgil P, Singh R, Puniya AK. D1/D2 domain of large-subunit ribosomal DNA for differentiation of Orpinomyces spp. Appl Environ Microbiol 2011; 77:6722–6725 [View Article] [PubMed]
    [Google Scholar]
  45. Nagler M, Podmirseg SM, Griffith GW, Insam H, Ascher-Jenull J. The use of extracellular DNA as a proxy for specific microbial activity. Appl Microbiol Biotechnol 2018; 102:2885–2898 [View Article] [PubMed]
    [Google Scholar]
  46. Sridhar M, Kumar D, Anandan S, Prasad CS, Sampath KT. Morphological and molecular characterization of polycentric rumen fungi belonging to the genus Orpinomyces isolated from Indian cattle and buffaloes. Res J Microbiol 2010; 5:581–594 [View Article]
    [Google Scholar]
  47. Wang X, Liu X, Groenewald JZ. Phylogeny of anaerobic fungi (phylum Neocallimastigomycota), with contributions from yak in China. Antonie van Leeuwenhoek 2017; 110:87–103 [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005449
Loading
/content/journal/ijsem/10.1099/ijsem.0.005449
Loading

Data & Media loading...

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error