Bauchop T, Mountfort DO (1981) Cellulose fermentation by a rumen anaerobic fungus in both the
absence and the presence of rumen methanogens.
Appl Environ Microbiol 42(6):1103–1110. https://
www.ncbi.nlm.nih.gov/pubmed/16345902
Bayer EA, Belaich JP, Shoham Y, Lamed R (2004) The
cellulosomes: multienzyme machines for degradation of plant cell wall polysaccharides. Annu Rev
Microbiol 58:521–554. https://doi.org/10.1146/
annurev.micro.57.030502.091022
Blum DL, Li X-L, Chen H, Ljungdahl LG (1999) Characterization of an acetyl xylan esterase from the
anaerobic fungus Orpinomyces sp. strain PC-2.
Appl Environ Microbiol 65(9):3990–3995. https://
aem.asm.org/content/aem/65/9/3990.full.pdf
Boxma B, Voncken F, Jannink S, Van Alen T, Akhmanova A, Van Weelden SWH, Van Hellemond JJ,
Ricard G, Huynen M, Tielens AGM, Hackstein JHP
(2004) The anaerobic chytridiomycete fungus Piromyces sp. E2 produces ethanol via pyruvate:formate lyase and an alcohol dehydrogenase E. Mol
Microbiol
51(5):1389–1399.
https://doi.org/
10.1046/j.1365-2958.2003.03912.x
Caldwell DR, Bryant MP (1966) Medium without rumen
fluid for nonselective enumeration and isolation of
rumen bacteria. Appl Microbiol 14(5):794–801.
https://www.ncbi.nlm.nih.gov/pubmed/5970467
Calkins S, Elledge NC, Hanafy RA, Elshahed MS, Youssef N (2016) A fast and reliable procedure for spore
collection from anaerobic fungi: application for
RNA uptake and long-term storage of isolates. J
Microbiol Methods 127:206–213. https://doi.org/
10.1016/j.mimet.2016.05.019
Calkins SS, Elledge NC, Mueller KE, Marek SM, Couger
MB, Elshahed MS, Youssef NH (2018) Development of an RNA interference (RNAi) gene knockdown protocol in the anaerobic gut fungus
Pecoramyces ruminantium strain C1A. PeerJ 6:
e4276. https://doi.org/10.7717/peerj.4276
Callaghan TM, Podmirseg SM, Hohlweck D, Edwards
JE, Puniya AK, Dagar SS, Griffith GW (2015)
Buwchfawromyces eastonii gen. nov., sp. nov.: a
new anaerobic fungus (Neocallimastigomycota)
isolated from buffalo faeces. MycoKeys 9:11–28.
https://doi.org/10.3897/mycokeys.9.9032
Catalano V, Vergara M, Hauzenberger JR, Seiboth B,
Sarrocco S, Vannacci G, Kubicek CP, Seidl-Seiboth
V (2011) Use of a non-homologous end-joiningdeficient strain (delta-ku70) of the biocontrol fungus Trichoderma virens to investigate the function
of the laccase gene lcc1 in sclerotia degradation.
Curr Genet 57(1):13–23. https://doi.org/10.1007/
s00294-010-0322-2
Chen H, Li XL, Ljungdahl LG (1995) A cyclophilin from
the polycentric anaerobic rumen fungus Orpinomyces sp. strain PC-2 is highly homologous to
vertebrate cyclophilin B. Proc Natl Acad Sci USA
92(7):2587–2591.
https://doi.org/10.1073/
pnas.92.7.2587
Chen H, Li XL, Ljungdahl LG (1997) Sequencing of a
1,3-1,4-beta-D-glucanase (lichenase) from the
anaerobic fungus Orpinomyces strain PC-2: properties of the enzyme expressed in Escherichia coli
and evidence that the gene has a bacterial origin. J
Bacteriol 179(19):6028–6034. https://doi.org/
10.1128/jb.179.19.6028-6034.1997
Chen H, Li X-L, Blum DL, Ljungdahl LG (1998) Two
genes of the anaerobic fungus Orpinomyces sp.
strain PC-2 encoding cellulases with endoglucanase activities may have arisen by gene duplication. FEMS Microbiol Lett 159(1):63–68. https://
doi.org/10.1111/j.1574-6968.1998.tb12842.x
Chen H, Li XL, Xu H, Ljungdahl LG, Cerniglia CE
(2006) High level expression and characterization
of the cyclophilin B gene from the anaerobic fungus Orpinomyces sp. strain PC-2. Protein Pept Lett
13(7):727–732.
https://doi.org/10.2174/
092986606777790511
Chen YC, Chen WT, Liu JC, Tsai LC, Cheng HL (2014) A
highly active beta-glucanase from a new strain of
rumen fungus Orpinomyces sp.Y102 exhibits cellobiohydrolase and cellotriohydrolase activities.
Bioresour Technol 170:513–521. https://doi.org/
10.1016/j.biortech.2014.08.016
Cheng YF, Edwards JE, Allison GG, Zhu WY, Theodorou MK (2009) Diversity and activity of
enriched ruminal cultures of anaerobic fungi and
methanogens grown together on lignocellulose in
consecutive batch culture. Bioresour Technol 100
(20):4821–4828.
https://doi.org/10.1016/j.biortech.2009.04.031
Conrad R (1999) Contribution of hydrogen to methane
production and control of hydrogen concentrations in methanogenic soils and sediments. FEMS
Microbiol Ecol 28(3):193–202. https://doi.org/
10.1111/j.1574-6941.1999.tb00575.x
Couger MB, Youssef NH, Struchtemeyer CG, Liggenstoffer AS, Elshahed MS (2015) Transcriptomic
analysis of lignocellulosic biomass degradation
by the anaerobic fungal isolate Orpinomyces sp.
strain C1A. Biotechnol Biofuels 8(1):208. https://
doi.org/10.1186/s13068-015-0390-0
Dagar SS, Kumar S, Mudgil P, Singh R, Puniya AK
(2011) D1/D2 domain of large-subunit ribosomal
DNA for differentiation of Orpinomyces spp. Appl
Environ Microbiol 77(18):6722–6725. https://doi.
org/10.1128/AEM.05441-11
Dagar SS, Kumar S, Griffith GW, Edwards JE, Callaghan
TM, Singh R, Nagpal AK, Puniya AK (2015) A new
anaerobic fungus (Oontomyces anksri gen. nov.,
sp. nov.) from the digestive tract of the Indian
camel (Camelus dromedarius). Fungal Biol 119
(8):731–737.
https://doi.org/10.1016/j.funbio.2015.04.005
Dalrymple BP, Cybinski DH, Layton I, McSweeney CS,
Xue G-P, Swadling YJ, Lowry JB (1997) Three
Neocallimastix patriciarum esterases associated
with the degradation of complex polysaccharides
430
V. Flad et al.
absence and the presence of rumen methanogens.
Appl Environ Microbiol 42(6):1103–1110. https://
www.ncbi.nlm.nih.gov/pubmed/16345902
Bayer EA, Belaich JP, Shoham Y, Lamed R (2004) The
cellulosomes: multienzyme machines for degradation of plant cell wall polysaccharides. Annu Rev
Microbiol 58:521–554. https://doi.org/10.1146/
annurev.micro.57.030502.091022
Blum DL, Li X-L, Chen H, Ljungdahl LG (1999) Characterization of an acetyl xylan esterase from the
anaerobic fungus Orpinomyces sp. strain PC-2.
Appl Environ Microbiol 65(9):3990–3995. https://
aem.asm.org/content/aem/65/9/3990.full.pdf
Boxma B, Voncken F, Jannink S, Van Alen T, Akhmanova A, Van Weelden SWH, Van Hellemond JJ,
Ricard G, Huynen M, Tielens AGM, Hackstein JHP
(2004) The anaerobic chytridiomycete fungus Piromyces sp. E2 produces ethanol via pyruvate:formate lyase and an alcohol dehydrogenase E. Mol
Microbiol
51(5):1389–1399.
https://doi.org/
10.1046/j.1365-2958.2003.03912.x
Caldwell DR, Bryant MP (1966) Medium without rumen
fluid for nonselective enumeration and isolation of
rumen bacteria. Appl Microbiol 14(5):794–801.
https://www.ncbi.nlm.nih.gov/pubmed/5970467
Calkins S, Elledge NC, Hanafy RA, Elshahed MS, Youssef N (2016) A fast and reliable procedure for spore
collection from anaerobic fungi: application for
RNA uptake and long-term storage of isolates. J
Microbiol Methods 127:206–213. https://doi.org/
10.1016/j.mimet.2016.05.019
Calkins SS, Elledge NC, Mueller KE, Marek SM, Couger
MB, Elshahed MS, Youssef NH (2018) Development of an RNA interference (RNAi) gene knockdown protocol in the anaerobic gut fungus
Pecoramyces ruminantium strain C1A. PeerJ 6:
e4276. https://doi.org/10.7717/peerj.4276
Callaghan TM, Podmirseg SM, Hohlweck D, Edwards
JE, Puniya AK, Dagar SS, Griffith GW (2015)
Buwchfawromyces eastonii gen. nov., sp. nov.: a
new anaerobic fungus (Neocallimastigomycota)
isolated from buffalo faeces. MycoKeys 9:11–28.
https://doi.org/10.3897/mycokeys.9.9032
Catalano V, Vergara M, Hauzenberger JR, Seiboth B,
Sarrocco S, Vannacci G, Kubicek CP, Seidl-Seiboth
V (2011) Use of a non-homologous end-joiningdeficient strain (delta-ku70) of the biocontrol fungus Trichoderma virens to investigate the function
of the laccase gene lcc1 in sclerotia degradation.
Curr Genet 57(1):13–23. https://doi.org/10.1007/
s00294-010-0322-2
Chen H, Li XL, Ljungdahl LG (1995) A cyclophilin from
the polycentric anaerobic rumen fungus Orpinomyces sp. strain PC-2 is highly homologous to
vertebrate cyclophilin B. Proc Natl Acad Sci USA
92(7):2587–2591.
https://doi.org/10.1073/
pnas.92.7.2587
Chen H, Li XL, Ljungdahl LG (1997) Sequencing of a
1,3-1,4-beta-D-glucanase (lichenase) from the
anaerobic fungus Orpinomyces strain PC-2: properties of the enzyme expressed in Escherichia coli
and evidence that the gene has a bacterial origin. J
Bacteriol 179(19):6028–6034. https://doi.org/
10.1128/jb.179.19.6028-6034.1997
Chen H, Li X-L, Blum DL, Ljungdahl LG (1998) Two
genes of the anaerobic fungus Orpinomyces sp.
strain PC-2 encoding cellulases with endoglucanase activities may have arisen by gene duplication. FEMS Microbiol Lett 159(1):63–68. https://
doi.org/10.1111/j.1574-6968.1998.tb12842.x
Chen H, Li XL, Xu H, Ljungdahl LG, Cerniglia CE
(2006) High level expression and characterization
of the cyclophilin B gene from the anaerobic fungus Orpinomyces sp. strain PC-2. Protein Pept Lett
13(7):727–732.
https://doi.org/10.2174/
092986606777790511
Chen YC, Chen WT, Liu JC, Tsai LC, Cheng HL (2014) A
highly active beta-glucanase from a new strain of
rumen fungus Orpinomyces sp.Y102 exhibits cellobiohydrolase and cellotriohydrolase activities.
Bioresour Technol 170:513–521. https://doi.org/
10.1016/j.biortech.2014.08.016
Cheng YF, Edwards JE, Allison GG, Zhu WY, Theodorou MK (2009) Diversity and activity of
enriched ruminal cultures of anaerobic fungi and
methanogens grown together on lignocellulose in
consecutive batch culture. Bioresour Technol 100
(20):4821–4828.
https://doi.org/10.1016/j.biortech.2009.04.031
Conrad R (1999) Contribution of hydrogen to methane
production and control of hydrogen concentrations in methanogenic soils and sediments. FEMS
Microbiol Ecol 28(3):193–202. https://doi.org/
10.1111/j.1574-6941.1999.tb00575.x
Couger MB, Youssef NH, Struchtemeyer CG, Liggenstoffer AS, Elshahed MS (2015) Transcriptomic
analysis of lignocellulosic biomass degradation
by the anaerobic fungal isolate Orpinomyces sp.
strain C1A. Biotechnol Biofuels 8(1):208. https://
doi.org/10.1186/s13068-015-0390-0
Dagar SS, Kumar S, Mudgil P, Singh R, Puniya AK
(2011) D1/D2 domain of large-subunit ribosomal
DNA for differentiation of Orpinomyces spp. Appl
Environ Microbiol 77(18):6722–6725. https://doi.
org/10.1128/AEM.05441-11
Dagar SS, Kumar S, Griffith GW, Edwards JE, Callaghan
TM, Singh R, Nagpal AK, Puniya AK (2015) A new
anaerobic fungus (Oontomyces anksri gen. nov.,
sp. nov.) from the digestive tract of the Indian
camel (Camelus dromedarius). Fungal Biol 119
(8):731–737.
https://doi.org/10.1016/j.funbio.2015.04.005
Dalrymple BP, Cybinski DH, Layton I, McSweeney CS,
Xue G-P, Swadling YJ, Lowry JB (1997) Three
Neocallimastix patriciarum esterases associated
with the degradation of complex polysaccharides
430
V. Flad et al.