mitosomes: mitochondria of anaerobic eukaryotes. Springer, Cham, pp 159–175. https://doi.
org/10.1007/978-3-030-17941-0_7
Haferkamp I, Hackstein JH, Voncken FG, Schmit G,
Tjaden J (2002) Functional integration of mitochondrial and hydrogenosomal ADP/ATP carriers
in the Escherichia coli membrane reveals different
biochemical characteristics for plants, mammals
and anaerobic chytrids. Eur J Biochem 269
(13):3172–3181
Haitjema CH, Solomon KV, Henske JK, Theodorou
MK, O’Malley MA (2014) Anaerobic gut fungi:
advances in isolation, culture, and cellulolytic
enzyme discovery for biofuel production. Biotechnol Bioeng 111(8):1471–1482. https://doi.org/
10.1002/bit.25264
Haitjema CH, Gilmore SP, Henske JK, Solomon KV, de
Groot R, Kuo A, Mondo SJ, Salamov AA, LaButti
K, Zhao Z, Chiniquy J, Barry K, Brewer HM, Purvine SO, Wright AT, Hainaut M, Boxma B, van
Alen T, Hackstein JHP, Henrissat B, Baker SE,
Grigoriev IV, O’Malley MA (2017) A parts list for
fungal cellulosomes revealed by comparative
genomics. Nat Microbiol 2:17087. https://doi.org/
10.1038/nmicrobiol.2017.87
Hanafy RA, Elshahed MS, Liggenstoffer AS, Griffith
GW, Youssef NH (2017) Pecoramyces ruminantium, gen. nov., sp. nov., an anaerobic gut fungus
from the feces of cattle and sheep. Mycologia
109(2):231–243.
https://doi.org/10.1080/
00275514.2017.1317190
Hanafy RA, Elshahed MS, Youssef NH (2018) Feramyces austinii, gen. nov., sp. nov., an anaerobic
gut fungus from rumen and fecal samples of
wild Barbary sheep and fallow deer. Mycologia
110(3):513–525.
https://doi.org/10.1080/
00275514.2018.1466610
Hanafy RA, Lanjekar VB, Dhakephalkar PK, Callaghan
TM, Dagar SS, Griffith GW, Elshahed MS, Youssef
NH (2020) Seven new Neocallimastigomycota
genera from wild, zoo-housed, and domesticated
herbivores greatly expand the taxonomic diversity
of the phylum. Mycologia. https://doi.org/10.1080/
00275514.2019.1696619
Hara KY, Kobayashi J, Yamada R, Sasaki D, Kuriya Y,
Hirono-Hara Y, Ishii J, Araki M, Kondo A (2017)
Transporter engineering in biomass utilization by
yeast. FEMS Yeast Res 17(7). https://doi.org/
10.1093/femsyr/fox061
Harhangi HR, Steenbakkers PJM, Akhmanova A, Jetten
MSM, van der Drift C, Op den Camp HJM (2002) A
highly expressed family 1 b-glucosidase with
transglycosylation capacity from the anaerobic
fungus Piromyces sp. E2. Biochimica et Biophysica
Acta 1574(3):293–303. https://doi.org/10.1016/
S0167-4781(01)00380-3
Hassan SS, Williams GA, Jaiswal AK (2018) Emerging
technologies for the pretreatment of lignocellulosic biomass. Bioresour Technol 262:310–318.
https://doi.org/10.1016/j.biortech.2018.04.099
Hazlewood GP, Gilbert HJ (1993) Recombinant xylanases. International patent number: WO9325693.
https://patents.google.com/patent/
WO1993025693A1/en
Henske JK, Gilmore SP, Knop D, Cunningham FJ, Sexton JA, Smallwood CR, Shutthanandan V, Evans JE,
Theodorou MK, O’Malley MA (2017) Transcriptomic characterization of Caecomyces churrovis: a
novel, non-rhizoid-forming lignocellulolytic anaerobic fungus. Biotechnol Biofuels 10(1):305. https://
doi.org/10.1186/s13068-017-0997-4
Henske JK, Gilmore SP, Haitjema CH, Solomon KV,
O’Malley MA (2018a) Biomass-degrading enzymes
are catabolite repressed in anaerobic gut fungi.
AIChE J. https://doi.org/10.1002/aic.16395
Henske JK, Wilken SE, Solomon KV, Smallwood CR,
Shutthanandan V, Evans JE, Theodorou MK,
O’Malley MA (2018b) Metabolic characterization
of anaerobic fungi provides a path forward for
bioprocessing of crude lignocellulose. Biotechnol
Bioeng 115(4):874–884. https://doi.org/10.1002/
bit.26515
Hillman ET, Readnour LR, Solomon KV (2017) Exploiting the natural product potential of fungi with
integrated -omics and synthetic biology
approaches. Curr Opin Syst Biol 5:50–56. https://
doi.org/10.1016/j.coisb.2017.07.010
Hooker CA, Hillman ET, Overton JC, Ortiz-Velez A,
Schacht M, Hunnicutt A, Mosier NS, Solomon
KV (2018) Hydrolysis of untreated lignocellulosic
feedstock is independent of S-lignin composition
in newly classified anaerobic fungal isolate, Piromyces sp. UH3-1. Biotechnol Biofuels 11:293.
https://doi.org/10.1186/s13068-018-1292-8
Irvine HL, Stewart CS (1991) Interactions between
anaerobic cellulolytic bacteria and fungi in the
presence of Methanobrevibacter smithii. Lett
Appl Microbiol 12(2):62–64. https://doi.org/
10.1111/j.1472-765X.1991.tb00504.x
James TY, Kauff F, Schoch CL, Matheny PB, Hofstetter
V, Cox CJ, Celio G, Gueidan C, Fraker E, Miadlikowska J, Lumbsch HT, Rauhut A, Reeb V, Arnold
AE, Amtoft A, Stajich JE, Hosaka K, Sung G-H,
Johnson D, O’Rourke B, Crockett M, Binder M,
Curtis JM, Slot JC, Wang Z, Wilson AW, Schu ¨ßler
A, Longcore JE, O’Donnell K, Mozley-Standridge
S, Porter D, Letcher PM, Powell MJ, Taylor JW,
White MM, Griffith GW, Davies DR, Humber RA,
Morton JB, Sugiyama J, Rossman AY, Rogers JD,
Pfister DH, Hewitt D, Hansen K, Hambleton S,
Shoemaker RA, Kohlmeyer J, VolkmannKohlmeyer B, Spotts RA, Serdani M, Crous PW,
Hughes KW, Matsuura K, Langer E, Langer G,
Untereiner WA, Lu ¨cking R, Bu ¨del B, Geiser DM,
Aptroot A, Diederich P, Schmitt I, Schultz M, Yahr
R, Hibbett DS, Lutzoni F, McLaughlin DJ, Spatafora JW, Vilgalys R (2006) Reconstructing the
early evolution of fungi using a six-gene phylogeny. Nature 443(7113):818–822. https://doi.org/
10.1038/nature05110
432
V. Flad et al.
org/10.1007/978-3-030-17941-0_7
Haferkamp I, Hackstein JH, Voncken FG, Schmit G,
Tjaden J (2002) Functional integration of mitochondrial and hydrogenosomal ADP/ATP carriers
in the Escherichia coli membrane reveals different
biochemical characteristics for plants, mammals
and anaerobic chytrids. Eur J Biochem 269
(13):3172–3181
Haitjema CH, Solomon KV, Henske JK, Theodorou
MK, O’Malley MA (2014) Anaerobic gut fungi:
advances in isolation, culture, and cellulolytic
enzyme discovery for biofuel production. Biotechnol Bioeng 111(8):1471–1482. https://doi.org/
10.1002/bit.25264
Haitjema CH, Gilmore SP, Henske JK, Solomon KV, de
Groot R, Kuo A, Mondo SJ, Salamov AA, LaButti
K, Zhao Z, Chiniquy J, Barry K, Brewer HM, Purvine SO, Wright AT, Hainaut M, Boxma B, van
Alen T, Hackstein JHP, Henrissat B, Baker SE,
Grigoriev IV, O’Malley MA (2017) A parts list for
fungal cellulosomes revealed by comparative
genomics. Nat Microbiol 2:17087. https://doi.org/
10.1038/nmicrobiol.2017.87
Hanafy RA, Elshahed MS, Liggenstoffer AS, Griffith
GW, Youssef NH (2017) Pecoramyces ruminantium, gen. nov., sp. nov., an anaerobic gut fungus
from the feces of cattle and sheep. Mycologia
109(2):231–243.
https://doi.org/10.1080/
00275514.2017.1317190
Hanafy RA, Elshahed MS, Youssef NH (2018) Feramyces austinii, gen. nov., sp. nov., an anaerobic
gut fungus from rumen and fecal samples of
wild Barbary sheep and fallow deer. Mycologia
110(3):513–525.
https://doi.org/10.1080/
00275514.2018.1466610
Hanafy RA, Lanjekar VB, Dhakephalkar PK, Callaghan
TM, Dagar SS, Griffith GW, Elshahed MS, Youssef
NH (2020) Seven new Neocallimastigomycota
genera from wild, zoo-housed, and domesticated
herbivores greatly expand the taxonomic diversity
of the phylum. Mycologia. https://doi.org/10.1080/
00275514.2019.1696619
Hara KY, Kobayashi J, Yamada R, Sasaki D, Kuriya Y,
Hirono-Hara Y, Ishii J, Araki M, Kondo A (2017)
Transporter engineering in biomass utilization by
yeast. FEMS Yeast Res 17(7). https://doi.org/
10.1093/femsyr/fox061
Harhangi HR, Steenbakkers PJM, Akhmanova A, Jetten
MSM, van der Drift C, Op den Camp HJM (2002) A
highly expressed family 1 b-glucosidase with
transglycosylation capacity from the anaerobic
fungus Piromyces sp. E2. Biochimica et Biophysica
Acta 1574(3):293–303. https://doi.org/10.1016/
S0167-4781(01)00380-3
Hassan SS, Williams GA, Jaiswal AK (2018) Emerging
technologies for the pretreatment of lignocellulosic biomass. Bioresour Technol 262:310–318.
https://doi.org/10.1016/j.biortech.2018.04.099
Hazlewood GP, Gilbert HJ (1993) Recombinant xylanases. International patent number: WO9325693.
https://patents.google.com/patent/
WO1993025693A1/en
Henske JK, Gilmore SP, Knop D, Cunningham FJ, Sexton JA, Smallwood CR, Shutthanandan V, Evans JE,
Theodorou MK, O’Malley MA (2017) Transcriptomic characterization of Caecomyces churrovis: a
novel, non-rhizoid-forming lignocellulolytic anaerobic fungus. Biotechnol Biofuels 10(1):305. https://
doi.org/10.1186/s13068-017-0997-4
Henske JK, Gilmore SP, Haitjema CH, Solomon KV,
O’Malley MA (2018a) Biomass-degrading enzymes
are catabolite repressed in anaerobic gut fungi.
AIChE J. https://doi.org/10.1002/aic.16395
Henske JK, Wilken SE, Solomon KV, Smallwood CR,
Shutthanandan V, Evans JE, Theodorou MK,
O’Malley MA (2018b) Metabolic characterization
of anaerobic fungi provides a path forward for
bioprocessing of crude lignocellulose. Biotechnol
Bioeng 115(4):874–884. https://doi.org/10.1002/
bit.26515
Hillman ET, Readnour LR, Solomon KV (2017) Exploiting the natural product potential of fungi with
integrated -omics and synthetic biology
approaches. Curr Opin Syst Biol 5:50–56. https://
doi.org/10.1016/j.coisb.2017.07.010
Hooker CA, Hillman ET, Overton JC, Ortiz-Velez A,
Schacht M, Hunnicutt A, Mosier NS, Solomon
KV (2018) Hydrolysis of untreated lignocellulosic
feedstock is independent of S-lignin composition
in newly classified anaerobic fungal isolate, Piromyces sp. UH3-1. Biotechnol Biofuels 11:293.
https://doi.org/10.1186/s13068-018-1292-8
Irvine HL, Stewart CS (1991) Interactions between
anaerobic cellulolytic bacteria and fungi in the
presence of Methanobrevibacter smithii. Lett
Appl Microbiol 12(2):62–64. https://doi.org/
10.1111/j.1472-765X.1991.tb00504.x
James TY, Kauff F, Schoch CL, Matheny PB, Hofstetter
V, Cox CJ, Celio G, Gueidan C, Fraker E, Miadlikowska J, Lumbsch HT, Rauhut A, Reeb V, Arnold
AE, Amtoft A, Stajich JE, Hosaka K, Sung G-H,
Johnson D, O’Rourke B, Crockett M, Binder M,
Curtis JM, Slot JC, Wang Z, Wilson AW, Schu ¨ßler
A, Longcore JE, O’Donnell K, Mozley-Standridge
S, Porter D, Letcher PM, Powell MJ, Taylor JW,
White MM, Griffith GW, Davies DR, Humber RA,
Morton JB, Sugiyama J, Rossman AY, Rogers JD,
Pfister DH, Hewitt D, Hansen K, Hambleton S,
Shoemaker RA, Kohlmeyer J, VolkmannKohlmeyer B, Spotts RA, Serdani M, Crous PW,
Hughes KW, Matsuura K, Langer E, Langer G,
Untereiner WA, Lu ¨cking R, Bu ¨del B, Geiser DM,
Aptroot A, Diederich P, Schmitt I, Schultz M, Yahr
R, Hibbett DS, Lutzoni F, McLaughlin DJ, Spatafora JW, Vilgalys R (2006) Reconstructing the
early evolution of fungi using a six-gene phylogeny. Nature 443(7113):818–822. https://doi.org/
10.1038/nature05110
432
V. Flad et al.