17 The Biotechnological Potential of Anaerobic Gut Fungi
VERONIKA FLAD
1
, DIANA YOUNG
1 , SUSANNA SEPPA ¨ LA ¨ 2 , CASEY HOOKER
3 , NOHA YOUSSEF
4
,
SABINE M. PODMIRSEG
5
, MAGDALENA NAGLER
5
, MATTHEW REILLY
6,7 , YUANFEI LI
8 , KATER ˇ INA
FLIEGEROVA ´ 9 , YANFEN CHENG
8
, GARETH W. GRIFFITH
10
, MOSTAFA ELSHAHED
4
, KEVIN V. SOLOMON
3
,
MICHELLE A. O’MALLEY
2
, MICHAEL K. THEODOROU
7
CONTENTS
I. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 413
A. Background and Taxonomy . . . . . . . . . . . . . . . . 414
B. Culture Methodology . . . . . . . . . . . . . . . . . . . . . . . 416
C. Physiology and Metabolism . . . . . . . . . . . . . . . . 418
II. Identification of Useful Enzymes . . . . . . . . . . . . . 420
A. “Omics” Analyses Identify Enzymes and
Their Regulation Patterns . . . . . . . . . . . . . . . . . . 421
B. Systems for Heterologous Enzyme
Expression . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 421
C. Progress Toward Direct Genetic
Manipulation of Anaerobic Fungi . . . . . . . . . . 423
III. Anaerobic Fungi and Their Applications in
Agriculture and Biotechnology . . . . . . . . . . . . . . . 423
A. Anaerobic Fungi for Animal Nutrition . . . . . 423
B. Bioethanol Production with Anaerobic
Fungi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 424
C. Biogas Production with Anaerobic Fungi . . 425
IV. Current and Future Opportunities for
Exploitation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 427
A. Potential Source of Commodity via
Secondary Metabolites . . . . . . . . . . . . . . . . . . . . . 427
B. Characterization and Metabolic Engineering
with Membrane Proteins . . . . . . . . . . . . . . . . . . . 427
C. Opportunities Identified from Published
Patents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 428
V. Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 429
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 429
I. Introduction
Anaerobic gut fungi belong to the early diverging phylum Neocallimastigomycota and are
commonly found in the digestive tract of ruminants and hindgut fermenters. Animal hosts
include a wide range of important livestock
and wild animals such as cattle, sheep, horses,
and elephants (Liggenstoffer et al. 2010).
Instead of producing biomass-degrading
enzymes of their own, these large herbivores
rely on the synergistic action of an intestinal
microbial community, composed of fungi, cellulolytic bacteria, protozoa, and archaea (Peng
et al. 2016). The Neocallimastigomycota fungi
are key members of these microbial communities, as they function as initial colonizers of
the ingested plant fibers (lignocellulose) and
contribute to the biomass breakdown process
both physically and enzymatically (Podolsky
et al. 2019). Digestion of such recalcitrant mixtures requires the synergistic action of a large
1 Bavarian State Research Center for Agriculture (LfL), Central
Department for Quality Assurance and Analytics, Freising,
Germany;
e-mail:
veronika.flad@lfl.bayern.de;
diana.
young@lfl.bayern.de
2 Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, USA; e-mail: sseppala@ucsb.edu; momalley@ucsb.edu
3 Agriculture and Biological Engineering, Purdue University,
West Lafayette, IN, USA; e-mail: hookerc@purdue.edu;
kvs@purdue.edu
4 Department
of
Microbiology
and
Molecular
Genetics, Oklahoma State University, Stillwater, OK, USA;
e-mail: noha@okstate.edu; mostafa@okstate.edu
5 Institute of Microbiology, Universita ¨t Innsbruck, Innsbruck,
Austria; e-mail: Sabine.Podmirseg@uibk.ac.at; Magdalena.
Nagler@uibk.ac.at
6 Department of Biology, University of York, York, UK; e-mail:
matthew.reilly@york.ac.uk
7 Agriculture Centre for Sustainable Energy Systems, Harper
Adams University, Newport, Shropshire, UK; e-mail: mtheodorou@harper-adams.ac.uk
8 Laboratory of Gastrointestinal Microbiology, Nanjing Agricultural University, Nanjing, China; e-mail: yanfencheng@njau.edu.cn
9 Institute of Animal Physiology and Genetics, v.v.i, Academy
of Sciences of the Czech Republic, Prague 4, Czech Republic;
e-mail: fliegerova@iapg.cas.cz
10 Institute of Biological, Environmental and Rural
Sciences, Aberystwyth University, Penglais, Aberystwyth, Ceredigion, Wales, UK; e-mail: gwg@aber.ac.uk
Genetics and Biotechnology, 3 rd Edition
The Mycota II
J.P. Benz, K. Schipper (Eds.)
© Springer Nature Switzerland AG 2020
VERONIKA FLAD
1
, DIANA YOUNG
1 , SUSANNA SEPPA ¨ LA ¨ 2 , CASEY HOOKER
3 , NOHA YOUSSEF
4
,
SABINE M. PODMIRSEG
5
, MAGDALENA NAGLER
5
, MATTHEW REILLY
6,7 , YUANFEI LI
8 , KATER ˇ INA
FLIEGEROVA ´ 9 , YANFEN CHENG
8
, GARETH W. GRIFFITH
10
, MOSTAFA ELSHAHED
4
, KEVIN V. SOLOMON
3
,
MICHELLE A. O’MALLEY
2
, MICHAEL K. THEODOROU
7
CONTENTS
I. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 413
A. Background and Taxonomy . . . . . . . . . . . . . . . . 414
B. Culture Methodology . . . . . . . . . . . . . . . . . . . . . . . 416
C. Physiology and Metabolism . . . . . . . . . . . . . . . . 418
II. Identification of Useful Enzymes . . . . . . . . . . . . . 420
A. “Omics” Analyses Identify Enzymes and
Their Regulation Patterns . . . . . . . . . . . . . . . . . . 421
B. Systems for Heterologous Enzyme
Expression . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 421
C. Progress Toward Direct Genetic
Manipulation of Anaerobic Fungi . . . . . . . . . . 423
III. Anaerobic Fungi and Their Applications in
Agriculture and Biotechnology . . . . . . . . . . . . . . . 423
A. Anaerobic Fungi for Animal Nutrition . . . . . 423
B. Bioethanol Production with Anaerobic
Fungi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 424
C. Biogas Production with Anaerobic Fungi . . 425
IV. Current and Future Opportunities for
Exploitation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 427
A. Potential Source of Commodity via
Secondary Metabolites . . . . . . . . . . . . . . . . . . . . . 427
B. Characterization and Metabolic Engineering
with Membrane Proteins . . . . . . . . . . . . . . . . . . . 427
C. Opportunities Identified from Published
Patents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 428
V. Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 429
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 429
I. Introduction
Anaerobic gut fungi belong to the early diverging phylum Neocallimastigomycota and are
commonly found in the digestive tract of ruminants and hindgut fermenters. Animal hosts
include a wide range of important livestock
and wild animals such as cattle, sheep, horses,
and elephants (Liggenstoffer et al. 2010).
Instead of producing biomass-degrading
enzymes of their own, these large herbivores
rely on the synergistic action of an intestinal
microbial community, composed of fungi, cellulolytic bacteria, protozoa, and archaea (Peng
et al. 2016). The Neocallimastigomycota fungi
are key members of these microbial communities, as they function as initial colonizers of
the ingested plant fibers (lignocellulose) and
contribute to the biomass breakdown process
both physically and enzymatically (Podolsky
et al. 2019). Digestion of such recalcitrant mixtures requires the synergistic action of a large
1 Bavarian State Research Center for Agriculture (LfL), Central
Department for Quality Assurance and Analytics, Freising,
Germany;
e-mail:
veronika.flad@lfl.bayern.de;
diana.
young@lfl.bayern.de
2 Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, USA; e-mail: sseppala@ucsb.edu; momalley@ucsb.edu
3 Agriculture and Biological Engineering, Purdue University,
West Lafayette, IN, USA; e-mail: hookerc@purdue.edu;
kvs@purdue.edu
4 Department
of
Microbiology
and
Molecular
Genetics, Oklahoma State University, Stillwater, OK, USA;
e-mail: noha@okstate.edu; mostafa@okstate.edu
5 Institute of Microbiology, Universita ¨t Innsbruck, Innsbruck,
Austria; e-mail: Sabine.Podmirseg@uibk.ac.at; Magdalena.
Nagler@uibk.ac.at
6 Department of Biology, University of York, York, UK; e-mail:
matthew.reilly@york.ac.uk
7 Agriculture Centre for Sustainable Energy Systems, Harper
Adams University, Newport, Shropshire, UK; e-mail: mtheodorou@harper-adams.ac.uk
8 Laboratory of Gastrointestinal Microbiology, Nanjing Agricultural University, Nanjing, China; e-mail: yanfencheng@njau.edu.cn
9 Institute of Animal Physiology and Genetics, v.v.i, Academy
of Sciences of the Czech Republic, Prague 4, Czech Republic;
e-mail: fliegerova@iapg.cas.cz
10 Institute of Biological, Environmental and Rural
Sciences, Aberystwyth University, Penglais, Aberystwyth, Ceredigion, Wales, UK; e-mail: gwg@aber.ac.uk
Genetics and Biotechnology, 3 rd Edition
The Mycota II
J.P. Benz, K. Schipper (Eds.)
© Springer Nature Switzerland AG 2020