[1] GRUNINGER R J,PUNIYA A K,CALLAGHAN T M,et al.Anaerobic fungi (phylum Neocallimastigomycota):advances in understanding their taxonomy,life cycle,ecology,role and biotechnological potential[J].FEMS Microbiology Ecology,2014,90(1):1-17.
[2] THEODOROU M K,ZHU W Y,RICKERS A,et al.Biochemistry and ecology of anaerobic fungi[M]//HOWARD D H,MILLER J D.Human and animal relationships.Berlin,Heidelberg:Springer,1996:265-295.
[3] SOLOMON K V,HAITJEMA C H,HENSKE J K,et al.Early-branching gut fungi possess a large,comprehensive array of biomass-degrading enzymes[J].Science,2016,351(6278):1192-1195.
[4] SIJTSMA L,TAN B.Degradation of perennial ryegrass leaf and stem cell walls by the anaerobic fungus
Neocallimastix sp. strain CS3b[J].Applied and Environmental Microbiology,1996,62(4):1437-1440.
[5] ORPIN C G.The rumen flagellate
Piromonas communis:its life-history and invasion of plant material in the rumen[J].Journal of General Microbiology,1977,99(1):107-117.
[6] HESS M,PAUL S S,PUNIYA A K,et al.Anaerobic fungi:past,present,and future[J].Frontiers in Microbiology,2020,11:584893.
[7] STABEL M,HANAFY R A,SCHWEITZER T,et al.
Aestipascuomyces dupliciliberans gen. nov,sp. nov.,the first cultured representative of the uncultured SK4 clade from aoudad sheep and alpaca[J].Microorganisms,2020,8(11):1734.
[8] ORPIN C G,GREENWOOD Y.The role of haems and related compounds in the nutrition and zoosporogenesis of the rumen chytridiomycete
Neocallimastx frontalis H8[J].Journal of General Microbiology,1986,132(8):2179-2185.
[9] ORPIN C G,BOUNTIFF L.Zoospore chemotaxis in the rumen phycomycete
Neocallimastix frontalis[J].Journal of General Microbiology,1978,104(1):113-122.
[10] WUBAH D A,KIM D S.Chemoattraction of anaerobic ruminal fungi zoospores to selected phenolic acids[J].Microbiological Research,1996,151(3):257-262.
[11] ORPIN C G.On the induction of zoosporogenesis in the rumen phycomycetes
Neocallimastix frontalis,
Piromonas communis and
Sphaeromonas communis[J].Journal of General Microbiology,1977,101(2):181-189.
[12] LOWE S E,GRIFFITH G G,MILNE A,et al.The life cycle and growth kinetics of an anaerobic rumen fungus[J].Journal of General Microbiology,1987,133(7):1815-1827.
[13] EDWARDS J E,KINGSTON-SMITH A H,JIMENEZ H R,et al.Dynamics of initial colonization of nonconserved perennial ryegrass by anaerobic fungi in the bovine rumen[J].FEMS Microbiology Ecology,2008,66(3):537-545.
[14] ORPIN C G.Studies on the rumen flagellate
Neocallimastix frontalis[J].Journal of General Microbiology,1975,91(2):249-262.
[15] BARR D J S,KUDO H,JAKOBER K D,et al.Morphology and development of rumen fungi:
Neocallimastix sp.,
Piromyces communis,and
Orpinomyces bovis gen. nov.,sp. nov.[J].Canadian Journal of Botany,1989,67(9):2815-2824.
[16] HANAFY R A,ELSHAHED M S,LIGGENSTOFFER A S,et al.
Pecoramyces ruminantium,gen. nov.,sp. nov.,an anaerobic gut fungus from the feces of cattle and sheep[J].Mycologia,2017,109(2):231-243.
[17] JOSHI A,LANJEKAR V B,DHAKEPHALKAR P K,et al.
Liebetanzomycespolymorphus gen. et sp. nov.,a new anaerobic fungus (Neocallimastigomycota) isolated from the rumen of a goat[J].MycoKeys,2018,40:89-110.
[18] HANAFY R A,ELSHAHED M S,YOUSSEF N H.
Feramyces austinii,gen. nov.,sp. nov.,an anaerobic gut fungus from rumen and fecal samples of wild Barbary sheep and fallow deer[J].Mycologia,2018,110(3):513-525.
[19] HANAFY R A,LANJEKAR V B,DHAKEPHALKAR P K,et al.Seven new Neocallimastigomycota genera from wild,zoo-housed,and domesticated herbivores greatly expand the taxonomic diversity of the phylum[J].Mycologia,2020,112(6):1212-1239.
[20] GOLD J J,HEATH I B,BAUCHOP T.Ultrastructural description of a new chytrid genus of caecum anaerobe,
Caecomyces equi gen. nov.,sp. nov.,assigned to the Neocallimasticaceae[J].BioSystems,1988,21(3/4):403-415.
[21] CHEN Y C,TSAI S D,CHENG H L,et al.
Caecomyces sympodialis sp. nov.,a new rumen fungus isolated from
Bos indicus[J].Mycologia,2007,99(1):125-130.
[22] OZKOSE E,THOMAS B J,DAVIES D R,et al.
Cyllamyces aberensis gen. nov. sp. nov.,a new anaerobic gut fungus with branched sporangiophores isolated from cattle[J].Canadian Journal of Botany,2001,79(6):666-673.
[23] ORPIN C G.Isolation of cellulolytic phycomycete fungi from the caecum of the horse[J].Journal of General Microbiology,1981,123(2):287-296.
[24] WUBAH D A,FULLER M S,AKIN D E.Resistant body formation in
Neocallimastix sp.,an anaerobic fungus from the rumen of a cow[J].Mycologia,1991,83(1):40-47.
[25] BROOKMAN J L,MENNIM G,TRINCI A P J,et al.Identification and characterization of anaerobic gut fungi using molecular methodologies based on ribosomal ITS1 and 18S rRNA[J].Microbiology,2000,146(2):393-403.
[26] GRIFFITH G W,OZKOSE E,THEODOROU M K,et al.Diversity of anaerobic fungal populations in cattle revealed by selective enrichment culture using different carbon sources[J].Fungal Ecology,2009,2(2):87-97.
[27] HAITJEMA C H,SOLOMON K V,HENSKE J K,et al.Anaerobic gut fungi:advances in isolation,culture,and cellulolytic enzyme discovery for biofuel production[J].Biotechnology and Bioengineering,2014,111(8):1471-1482.
[28] DAGAR S S,KUMAR S,GRIFFITH G W,et al.A new anaerobic fungus (
Oontomyces anksri gen. nov.,sp. nov.) from the digestive tract of the Indian camel (
Camelus dromedarius)[J].Fungal Biology,2015,119(8):731-737.
[29] GRUNINGER R J,NGUYEN T T M,REID I D,et al.Application of transcriptomics to compare the carbohydrate active enzymes that are expressed by diverse genera of anaerobic fungi to degrade plant cell wall carbohydrates[J].Frontiers in Microbiology,2018,9:1581.
[30] HENSKE J K,GILMORE S P,KNOP D,et al.Transcriptomic characterization of
Caecomyces churrovis:a novel,non-rhizoid-forming lignocellulolytic anaerobic fungus[J].Biotechnology for Biofuels,2017,10:305.
[31] COUGER M B,YOUSSEF N H,STRUCHTEMEYER C G,et al.Transcriptomic analysis of lignocellulosic biomass degradation by the anaerobic fungal isolate
Orpinomyces sp. strain C1A[J].Biotechnology for Biofuels,2015,8:208.
[32] LOMBARD V,GOLACONDA RAMULU H,DRULA E,et al.The carbohydrate-active enzymes database (CAZy) in 2013[J].Nucleic Acids Research,2013,42(D1):D490-D495.
[33] FONTES C M G A,GILBERT H J.Cellulosomes:highly efficient nanomachines designed to deconstruct plant cell wall complex carbohydrates[J].Annual Review of Biochemistry,2010,79:655-681.
[34] LAMED R,SETTER E,BAYER E A.Characterization of a cellulose-binding,cellulase-containing complex in
Clostridium thermocellum[J].Journal of Bacteriology,1983,156(2):828-836.
[35] HAITJEMA C H,GILMORE S P,HENSKE J K,et al.A parts list for fungal cellulosomes revealed by comparative genomics[J].Nature Microbiology,2017,2:17087.
[36] KRAUSS J,ZVERLOV V V,SCHWARZ W H.
In vitro reconstitution of the complete
Clostridium thermocellum cellulosome and synergistic activity on crystalline cellulose[J].Applied and Environmental Microbiology,2012,78(12):4301-4307.
[37] MURPHY C L,YOUSSEF N H,HANAFY R A,et al.Horizontal gene transfer as an indispensable driver for evolution of Neocallimastigomycota into a distinct gut-dwelling fungal lineage[J].Applied and Environmental Microbiology,2019,85(15):e00988-19.
[38] GARCIA-VALLVÉ S,ROMEU A,PALAU J.Horizontal gene transfer of glycosyl hydrolases of the rumen fungi[J].Molecular Biology and Evolution,2000,17(3):352-361.
[39] WANG Y,YOUSSEF N H,COUGER M B,et al.Molecular dating of the emergence of anaerobic rumen fungi and the impact of laterally acquired genes[J].mSystems,2019,4(4):e00247-19.
[40] FANUTTI C,PONYI T,BLACK G W,et al.The conserved noncatalytic 40-residue sequence in cellulases and hemicellulases from anaerobic fungi functions as a protein docking domain[J].Journal of Biological Chemistry,1995,270(49):29314-29322.
[41] NAGY T,TUNNICLIFFE R B,HIGGINS L D,et al.Characterization of a double dockerin from the cellulosome of the anaerobic fungus
Piromyces equi[J].Journal of Molecular Biology,2007,373(3):612-622.
[42] BAYER E A,BELAICH J P,SHOHAM Y,et al.The cellulosomes:multienzyme machines for degradation of plant cell wall polysaccharides[J].Annual Review of Microbiology,2004,58:521-554.
[43] HAGEN L H,BROOKE C G,SHAW C A,et al.Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber[J].The ISME Journal,2021,15(2):421-434.
[44] EDWARDS J E,FORSTER R J,CALLAGHAN T M,et al.PCR and omics based techniques to study the diversity,ecology and biology of anaerobic fungi:insights,challenges and opportunities[J].Frontiers in Microbiology,2017,8:1657.
[45] GILMORE S P,LILLINGTON S P,HAITJEMA C H,et al.Designing chimeric enzymes inspired by fungal cellulosomes[J].Synthetic and Systems Biotechnology,2020,5(1):23-32.
[46] YOUSSEF N H,COUGER M B,STRUCHTEMEYER C G,et al.The genome of the anaerobic fungus
Orpinomyces sp. strain C1A reveals the unique evolutionary history of a remarkable plant biomass degrader[J].Applied and Environmental Microbiology,2013,79(15):4620-4634.
[47] LI Y F,LI Y Q,JIN W,et al.Combined genomic,transcriptomic,proteomic,and physiological characterization of the growth of
Pecoramyces sp. F1 in monoculture and co-culture with a syntrophic methanogen[J].Frontiers in Microbiology,2019,10:435.
[48] WILKEN S E,MONK J M,LEGGIERI P A,et al.Experimentally validated reconstruction and analysis of a genome-scale metabolic model of an anaerobic Neocallimastigomycota fungus[J].mSystems,2021,6(1):e00002-21.
[49] CHENG Y F,JIN W,MAO S Y,et al.Production of citrate by anaerobic fungi in the presence of co-culture methanogens as revealed by 1H NMR spectrometry[J].Asian-Australasian Journal of Animal Sciences,2013,26(10):1416-1423.
[50] BOXMA B,VONCKEN F,JANNINK S,et al.The anaerobic chytridiomycete fungus
Piromyces sp. E2 produces ethanol via pyruvate:formate lyase and an alcohol dehydrogenase E[J].Molecular Microbiology,2004,51(5):1389-1399.
[51] HACKSTEIN J H P,BAKER S E,VAN HELLEMOND J J,et al.Hydrogenosomes of anaerobic chytrids:an alternative way to adapt to anaerobic environments[M]//TACHEZY J.Hydrogenosomes and mitosomes:mitochondria of anaerobic eukaryotes.Berlin,Heidelberg:Springer,2008:147-162.
[52] HACKSTEIN J H P,TJADEN J,KOOPMAN W,et al.Hydrogenosomes (and related organelles,either) are not the same[M]//MARTIN W F,MVLLER M.Origin of Mitochondria and Hydrogenosomes.Berlin,Heidelberg:Springer,2007:135-159.
[53] KELLER N P,TURNER G,BENNETT J W.Fungal secondary metabolism-from biochemistry to genomics[J].Nature Reviews Microbiology,2005,3(12):937-947.
[54] PODOLSKY I A,SEPPÄLÄ S,LANKIEWICZ T S,et al.Harnessing nature's anaerobes for biotechnology and bioprocessing[J].Annual Review of Chemical and Biomolecular Engineering,2019,10:105-128.
