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Anaerobic Fungi and Their Potential for Biogas Production

Article  in  Advances in Biochemical Engineering/Biotechnology · September 2015

DOI: 10.1007/978-3-319-21993-6_2

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Anaerobic Fungi and Their Potential
for Biogas Production

Veronika Dollhofer, Sabine Marie Podmirseg,

Tony Martin Callaghan, Gareth Wyn Griffith
and Kateřina Fliegerová

Abstract Plant biomass is the largest reservoir of environmentally friendly

renewable energy on earth. However, the complex and recalcitrant structure of these
lignocellulose-rich substrates is a severe limitation for biogas production. Microbial
pro-ventricular anaerobic digestion of ruminants can serve as a model for
improvement of converting lignocellulosic biomass into energy. Anaerobic fungi
are key players in the digestive system of various animals, they produce a plethora
of plant carbohydrate hydrolysing enzymes. Combined with the invasive growth of
their rhizoid system their contribution to cell wall polysaccharide decomposition
may greatly exceed that of bacteria. The cellulolytic arsenal of anaerobic fungi
consists of both secreted enzymes, as well as extracellular multi-enzyme complexes
called cellulosomes. These complexes are extremely active, can degrade both
amorphous and crystalline cellulose and are probably the main reason of cellulo-
lytic efficiency of anaerobic fungi. The synergistic use of mechanical and enzymatic
degradation makes anaerobic fungi promising candidates to improve biogas

V. Dollhofer (&)
Bavarian State Research Center for Agriculture, Central Department for Quality Assurance
and Analytics, Micro- and Molecular Biology, Lange Point 6, 85354 Freising, Germany
e-mail: [email protected]
S.M. Podmirseg
Institut für Mikrobiologie, Universität Innsbruck, Technikerstraße 25d,
6020 Innsbruck, Austria
e-mail: [email protected]
T.M. Callaghan
G.W. Griffith
Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Adeilad
Cledwyn Penglais, Aberystwyth, Ceredigion SY23 3DD, Wales, UK
e-mail: [email protected]
G.W. Griffith
e-mail: [email protected]
K. Fliegerová
Institute of Animal Physiology and Genetics, v.v.i, Academy of Sciences of the Czech
Republic, 142 20, Prague 4, Czech Republic
e-mail: [email protected]

© Springer International Publishing Switzerland 2015 41

G.M. Guebitz et al. (eds.), Biogas Science and Technology,
Advances in Biochemical Engineering/Biotechnology 151,
DOI 10.1007/978-3-319-21993-6_2
42 V. Dollhofer et al.

production from recalcitrant biomass. This chapter presents an overview about their
biology and their potential for implementation in the biogas process.

Keywords Anaerobic fungi Neocallimastigomycota
Phylogeny

Cellulosomes Biogas process improvement Recalcitrant cellulosic substrates

Contents

1 Anaerobic Fungi: An Overview .......................................................................................... 42

1.1 Classical and Pragmatic Taxonomy of Anaerobic Fungi .......................................... 43
1.2 Life Cycle.................................................................................................................... 43
1.3 Anaerobic Fungi and Their Interactions with Methanogens and Bacteria ................ 45
2 Anaerobic Fungi and Their Potential for Biogas Production ............................................. 46
2.1 Lignocelluloytic Enzymes of Anaerobic Fungi and Their Potential Use.................. 46
2.2 Anaerobic Fungi in the Biogas Production Process................................................... 50
3 Anaerobic Fungi: Methodological State of the Art ............................................................ 51
3.1 Detection Techniques for Anaerobic Fungi ............................................................... 51
3.2 Cultivation Techniques and Cryopreservation ........................................................... 53
4 Conclusions.......................................................................................................................... 54
References .................................................................................................................................. 54

1 Anaerobic Fungi: An Overview

Anaerobic fungi belonging to the phylum Neocallimastigomycota, are the most

basal lineage of the kingdom Fungi. These fungi are principally known from the
digestive tracts of larger mammalian herbivores, where they play an important role
as primary colonisers of ingested forage [1, 2]. Recent studies indicate their
appearance in herbivorous reptiles like the green iguana [2] and termites [3] also.
Anaerobic fungi are characterised by several distinctive traits which stem from their
obligately anaerobic physiology; mitochondria, cytochromes and other biochemical
features of the oxidative phosphorylation pathway are absent. Energy generation
occurs in hydrogenosomes where ATP is formed by malate decarboxylation to form
acetate, CO2, and H2 [4]. The Neocallimastigales are fungi that do not require
molecular oxygen for any of their physiological processes, and for which the
presence of oxygen is toxic. This trait raises the question how anaerobic fungi
defend themselves against the toxic effects of oxygen, for instance when colonizing
freshly ingested forage or during dispersal between host animals. Respective
insights are presented in the following section “life cycle”. Additionally, their
genomes are peculiar having the highest AT-content hitherto found (often
exceeding 90 % in non-coding regions) and with a substantial expansion of
important hydrolytic and cellulolytic gene families [5].
Anaerobic fungi are the only fungi which possess cellulosomes. These
extraordinary features are presented in more detail in Sect. 2.1. The position of
Anaerobic Fungi and Their Potential for Biogas Production 43

anaerobic fungi as a basal fungal lineage is reflected in the genome characteristics,

which are also present in other early-branching fungal lineages and/or non-fungal
Opisthokonts, but are absent in the later diverging Dikarya (Ascomycetes and
Basidiomycetes) genomes [6]. Such phylogenetic determinants and unique taxon-
omy of anaerobic fungi are discussed in the following Sect. 1.1.

1.1 Classical and Pragmatic Taxonomy of Anaerobic Fungi

The atypical morphology and physiology of anaerobic fungi has caused some
taxonomic uncertainty. After misleading classification as Protozoa [7],
Phycomycetes [8] and Chytridiomycetes [9, 10] the anaerobic fungi were finally
placed into the distinct phylum Neocallimastigomycota [11]. The phylum contains
only one order (Neocallimastigales) and one family (Neocallimastigaceae) within
which eight genera are currently described: The monocentric rhizoidal genera
Neocallimastix, Piromyces, Ontomyces and Buwchfawromyces, the polycentric
rhizoidal genera Anaeromyces and Orpinomyces, and the two bulbous genera,
monocentric Caecomyces and polycentric Cyllamyces, respectively [12–14].
The genera are defined on the basis of thallus morphology, the formation of
rhizoidal filaments or bulbous holdfasts within the substrate and their zoospore
morphology. A distinction is made between monoflagellate and polyflagellate
zoospores. The latter possessing 7–20 posterior flagella inserted in two rows.
Formation of polyflagellate zoospores is a trait unique to Orpinomyces and
Neocallimastix spp., not known from any other Opisthokonta, and these two genera
form a distinct clade within the Neocallimastigomycota [15].
Differentiation by the shape of sporangia may additionally be possible, but can
be misleading as it is varying depending on culture conditions. Currently about 20
species have been described [16]. Uncertainties created by difficulties in inter-lab
comparisons and the loss of many viable type cultures, can only now be resolved by
the use of DNA barcoding and the concerted effort to exchange cultures [17].
Culture-independent analysis of environmental nucleic acid sequences, provided
evidence for much greater fungal diversity than previously suspected in the
digestive tract of wild and domestic herbivores. Based on data from these more
recent studies, it appears that twelve or more hitherto un-named genera may exist
[2, 15, 18]. Several of these novel clades are now recognized from sequences of
cultured fungi [15], while other clades still consist of environmental nucleic
sequences (ENAS) only.

1.2 Life Cycle

The life cycle of anaerobic fungi alternates between a motile zoospore stage and a
non-motile vegetative stage. The latter consists of a thallus associated to plant
44 V. Dollhofer et al.

Fig. 1 Different culture morphologies of anaerobic fungi: a Neocallimastix sp. sporangia and
rhizomycelium (CLSM: superimposed z-stacks (26.7 µm total depth) showing culture auto
fluorescence (excitation at 561 nm and emission from 570 to 620 nm); b Piromyces sp. light
microscopy of native preparation; c Rhizoid of Anaeromyces mucronatus with apical sporangia.
Light microscopy of lugol-stained preparation (×200); d Bulbous species Caecomyces communis.
Light microscopy of native preparation (×400); e Neocallimastix frontalis sporangium and rhizoid.
Light microscopy (×400); f Orpinomyces sp. with sporangia and rhizoid. Light microscopy of
native preparation; g Light microscopy of a biflagellated zoospore of Piromyces sp. (×1000)

material and fruiting bodies known as sporangia (Fig. 1) [13]. Flagellate zoospores
(see Fig. 1g) released from mature sporangia actively swim towards freshly
ingested plant tissues using chemotactic response to soluble sugars and/or phenolic
acids [19]. After attachment to the feed particles, flagella are shed and a cyst is
formed. The cyst then germinates to form the thallus. In all monocentric species
(Piromyces, Neocallimastix and Buwchfawromyces), the nucleus remains in the
enlarging cyst which forms the sporangium. In the polycentric species Anaeromyces
Anaerobic Fungi and Their Potential for Biogas Production 45

and Orpinomyces, the nuclei migrate through the rhizoidal system to form multiple
sporangia on a single thallus. The terms exogenous and endogenous germination
(nuclei migrate into the thallus or not), that are widely used in describing chytrid
development, are less clearly applicable to the bulbous anaerobic fungi which do
not form rhizoids but do form multiple sporangia (i.e. Cyllamyces) [20].
The rhizoidal system penetrates the plant tissue by a combination of enzymatic
activity and hydrostatic pressure using appressorium-like penetration structures [21,
22]. In the non-rhizoidal bulbous species (Caecomyces, Cyllamyces), the expanding
holdfast formed within the substrate causes a splitting of the plant fibers [23–25].
Sporangium maturation and release of asexual zoospores can occur as quickly as
eight hours after encystment [26, 27].The complete life cycle, is conducted within
24–32 h [25]. Propagules of the anaerobic fungi are known to survive up to and
probably over a year in feces [28] and have also been found to be transferred to
neonatal hosts through saliva [29]. Putative aero-tolerant survival structures have
been observed only rarely [14, 30, 31] and many questions as to the formation of
these structures and their occurrence in the various genera of anaerobic fungi
remain to be answered.

1.3 Anaerobic Fungi and Their Interactions

with Methanogens and Bacteria

Close association of anaerobic fungi with methanogens is well known [23, 32], with
inter-species hydrogen transfer leading to both methane production and also more
efficient re-generation of oxidized nucleotides (NAD+, NADP+). Syntrophic
co-cultivation markedly increases fungal growth rate, with increased rates of cel-
lulolysis and xylanolysis, consequently enhancing dry matter reduction [33].
However the anaerobic fungus—methanogen interaction is more complex than
simple cross-feeding. Hydrogen transfer also influences fungal catabolic pathways
and specific enzyme profiles, shifting fungal product formation away from more
oxidized end products (lactate, ethanol) towards production of more reduced
products (acetate, formate). Acetate, and in the rumen especially formate, are the
preferred growth substrates for methanogens [32, 33]. This interaction is so pivotal,
that some species of anaerobic fungi cannot be isolated as axenic cultures, but only
in combination with the permanent archaeal symbiont [34].
Syntrophic interactions between acetogenic bacteria and methanogens are well
known to occur in the biogas biocoenosis [35]. Since anaerobic fungi show
improved growth in the presence of methanogens, the idea of augmenting biogas
reactors with this microbial group seems a logical step.
Interactions of anaerobic fungi with bacteria can be of antagonistic and sym-
biotic nature as shown by Bernalier and coworkers [36], who tested the degradation
efficiency in different culture combinations of three anaerobic fungi and two cel-
lulolytic bacterial strains. In general both groups are competing for the same
46 V. Dollhofer et al.

ecological niche, but the breaking up of plant tissue through fungal rhizoids may
also enhance the overall efficiency of cellulolytic bacteria [36]. This improved
degradation was also confirmed when testing the contribution of different microbial
groups (fungi, bacteria, protozoa) on orchard grass decomposition [37]. Presence of
protozoa was, however attributed with lower degradation efficiency and inhibition
of both, bacteria and fungi.
Most of these studies are based on in vitro co-cultures, that may not completely
reflect conditions of whole rumen or biogas reactor consortia and still more research
is needed in this field.

2 Anaerobic Fungi and Their Potential for Biogas

Production

Under oxygen-free conditions organic matter is decomposed by a complex of

microorganisms which are so far divided into three functional groups: hydrolysing
and fermenting bacteria, obligate hydrogen-producing acetogenic bacteria, and
methanogenic archaea. Only little is known on the role and the potential of
anaerobic fungi for biogas production. Great potential lies in biogas production
from lignocellulosic wastes but, slow and inefficient degradation processes, the
formation of toxic intermediates and the necessity for long incubation times are
only a few examples of the problems encountered [38, 39]. A promising strategy is
the use of microorganisms, which are able to successfully perform such compli-
cated degradation processes in their natural environment [40, 41]. Herbivores as
biogas reactors evolved the need for fungal symbionts for this purpose and over
millions of years natural selection has created a highly specialised and niche spe-
cific community of anaerobic fungi.
The following paragraphs will give an overview about useful features of
anaerobic fungi and will present the actual knowledge about anaerobic fungi and
biogas production.

2.1 Lignocelluloytic Enzymes of Anaerobic Fungi and Their

Potential Use

Lignin-embedded cellulose and hemicellulose [42] represent a physical barrier

against microbial and enzymatic attack. Known as the primary digesters of plant
biomass in the rumen anaerobic fungi [37] have the ability to open up the plant
tissue through rhizoidal growth and produce a cocktail of enzymes to degrade and
separate the different compounds of lignocellulosic biomass, while lignin itself
remains anaerobically indigestible. Some of these enzymes are secreted freely but
most of them are bound to a multi-enzyme complex the so called cellulosome.
Anaerobic Fungi and Their Potential for Biogas Production 47

Genome sequencing of Orpinomyces strain C1A revealed a broader enzyme range

compared to aerobic fungi with a repertoire of 357 glycosyl hydrolases, 92 car-
bohydrate esterases and 24 pectate lyases [5]. Horizontal gene transfer from bacteria
is suggested as one of the main reasons why anaerobic fungi have evolved such
robust and impressive cellulolytic and hemicellulolytic capability.
A group of enzymes often termed cellulases synergistically hydrolyze β-1, 4
glucosidic bonds in cellulose through three discrete enzymatic activities involving
three different types of enzymes. Endoglucanases (EC 3.2.1.4) cut within amorphous
regions of cellulose strands, releasing oligosaccharides and creating new free chain
ends for the enzymatic attack by exoglucanases (EC 3.2.1.176; EC 3.2.1.91). Since
the latter liberate cellobiose disaccharides from either reducing (EC 3.2.1.176) or
non-reducing (EC 3.2.1.91) ends, they are also termed cellobiohydrolases. In a
cellulosomal complex extracted from a Neocallimastix frontalis culture, enzymes
from glycosyl hydrolase family 5 (GH5) operated by the endo- and enzymes from
GH6 and GH48 by the exo-mechanism [43]. The residual cellobiose is then
hydrolyzed to glucose by β-glucosidases (EC 3.2.1.21) [40, 44]. Auxiliary enzymes
like the recently discovered lytic polysaccharide mono-oxygenases (LPMO) (family
AA9) have been reported to enhance or complete the utilization of cellulose in many
fungal species [45]. In contrast to the hydrolyzing enzymes they cleave glucosidic
bonds with a copper dependent oxidation mechanism and are able to attack crys-
talline regions of cellulose [46]. But it seems that basal fungal groups including the
anaerobic fungi lack those enzymes [45].
All three major cellulase types have been reported for the Neocallimastigomycota
([5, 47, 48, 49, 50] and many more) confirming the potential of anaerobic fungi as a
reservoir for highly efficient cellulases. The fact that glucose is the main product of
anaerobic fungal cellulose degradation is an advantage for biotechnological appli-
cations. Cellobiose is not accumulated and therefore cannot act as end-product
inhibitor for cellulose hydrolysis, as known for Trichoderma reesei or many bac-
terial species. Thus costly addition of β-glucosidase becomes unnecessary [51].
Due to the heterogeneous structure of hemicelluloses, several enzymes are
needed for their catabolism. Until now anaerobic fungi have been reported to
provide all enzymes needed to degrade the major hemicelluloses constituents of the
plant cell wall, namely β-glucans, mannans and xylans. And in some cases xylanase
activity was even higher than cellulase activity [52]. In contrast to aerobic higher
fungi (Dikarya), anaerobic fungi lack the enzymatic machinery to catabolise lignin.
The enzymatic reaction to cleave the aromatic ring requires oxygen and can
therefore not take place in an anaerobic environment [53]. But it was shown that a
Neocallimastix sp. could mediate the loss of up to 34 % of plant biomass associated
lignin, however this loss probably due to physical alteration or chemical modifi-
cation of the lignin rather than enzymatic catabolism [54]. Additional feruloyl (EC
3.1.1.73) esterases are produced which cleave the bond between hemicelluloses and
lignin and by separating these two compounds, making cellulose and hemicellulose
more easily accessible for further degradation [55].
48 V. Dollhofer et al.

2.1.1 Anaerobic Fungal Cellulosomes

As mentioned above, most of the cellulolytic and hemicellulolytic enzymes are part
of a multi-enzyme complex known as the cellulosome. Cellulosomes were first
identified in the bacterial family Clostridiaceae [56] and the anaerobic fungi are the
only eukaryotic representatives showing this feature. The fungal cellulosome is
structurally and phylogenetically similar to that found in bacteria and is thought to
have arisen through a horizontal gene transfer event [57]. Up to now cellulosomes
have been described for species of Piromyces [58, 59], Orpinomyces [48], and
Neocallimastix [52, 60]. Anaerobic fungi invade plant tissues with their rhizoid and
it is assumed that in addition to the secretion of soluble enzymes, they form cell-
ulosomes anchored to the cell walls of rhizoid tips [55]. Unfortunately the
molecular structure of the anaerobic fungal cellulosome is still unclear and mis-
cellaneous theories exist (see [61] for a schematic overview). In anaerobic bacteria a
non-catalytic protein, the ‘scaffolding protein’, is anchored to the cell wall and
contains several repeating domains, the cohesins. This structure forms the backbone
to which the enzymatic subunits assemble by non-catalytic domains, the dockerins.
Additionally the scaffolding connects to the substrate, in this case the (hemi) cel-
lulose molecules, via a cellulose-binding domain [62].
Compared to the enzymes of anaerobic bacteria, which contain only one
species-specific dockerin domain, the fungal enzymes contain one to three copies of
dockerin domains which show an interspecies specificity. It is believed that the
amount of dockerin regulates the affinity of the enzymes towards the scaffolding
molecule [63]. Recently it was reported that the anaerobic fungal cellulosome
contains a scaffolding backbone as well, raising the suggestion that the catalytic
components also interact with it via dockerin domains [43]. Other studies have
shown that some types of docking domains attach to several individual proteins,
concluding that there might be various different scaffolding proteins in anaerobic
fungal cellulosomes [64]. Additionally it could be shown that a double-dockerin
domain and a β-glucosidase enzymatic subunit from glycosyl hydrolase family 3
(GH 3), both belonging to one fungal species, could bind to each other [58, 61].
This leads to the third theory that dockerins mediate the binding of different
secreted enzymes to each other, forming the cellulosome without scaffolding as
structural molecule. Despite the detailed structure remaining unsolved, cellulo-
somes permit the anaerobic fungi to use their cellulolytic enzymes in a synergistic
and more efficient way, unequalled by individually secreted enzymes [61]. It also
provides protection against proteases from the surrounding environment in the form
of a serine protease inhibitor named celpin [65].

2.1.2 Substrates Utilized by Anaerobic Fungi

In addition to municipal solid waste (MSW) and animal wastes, lignocellulose-rich

materials potentially useful for biogas production are by-products of various
industrial processes, including agriculture, forestry, pulp-, paper- and food
Anaerobic Fungi and Their Potential for Biogas Production 49

Table 1 Examples for lignocellulosic residues degraded by anaerobic fungi

Lignocellulosic Lignin Organism Reference
residue content %
[66]
Wheat straw 16-21 Neocallimastix frontalis [67]
Coastal 6.4 Piromyces MC-1, Orpinomyces PC-1-3, [49]
Bermuda grass Neocallimastix MC-2
Sugar cane 19-24 Piromyces strain E2 [68]
bagasse
Hard wood 18-25 Neocallimastix sp. [69]
Rice straw 18 Piromyces M014, Orpinomyces [3]
GSRI-001, Neocallimastix T010

production [51, 66]. However, the recalcitrance and variability of these materials
leads to low gas yields in biogas fermentations, thus making their exploitation
uneconomical. Since anaerobic fungi are efficient physical and enzymatic degraders
of lignocellulose-rich substrates (see Table 1), they have the potential to make the
biogas production from these lignocellulose-rich materials more efficient and
profitable.

2.1.3 Production of Recombinant Enzymes

One strategy to overcome the bottleneck of enzymatic hydrolysis of lignocellulose

in the biogas production process is the development and use of recombinant potent
polysaccharide-degrading enzymes. Such a strategy could involve the transfer of
the cellulolytic genes of efficient degraders (e.g. anaerobic fungi) into other
well-established enzyme production hosts or biofuel producers (e.g. yeast) or
alternatively the modification of the genetic capability of the anaerobic fungi
themselves. Improving the efficiency of known enzymes and the creation of opti-
mized enzyme mixtures, along with the identification of new and more active
enzymes has been the focus of some studies [70]. Efforts to produce recombinant
fibrolytic enzymes from anaerobic fungi have focused on expressing a range of
carbohydrate-active enzymes into a number of aerobic fungal expression hosts. But
catalytic activity of anaerobic fungal xylanases, cellulases, β-glucosidases, or cel-
lobiohydrolases in the tested aerobic strains (Saccharomyces cerevisiae, Hypocrea
jecorina, Pichia pastoris and P. methanolica) was low or else the recombinant
proteins were not catalytically active [71–74]. Genetic modification of S. cerevisiae
integrating a xylose isomerase from anaerobic fungi allowing the yeast to metab-
olize monosaccharide xylose was more successful. Conversion of xylose into
xylulose using the isomerases of Piromyces and/or Orpinomyces species [75–77]
represents at this time the most promising technique for improving the industrial
production of ethanol [78] and several patents have been filed so far [79]. In
addition to the incorporation of single enzymes, the creation of artificial cellulo-
somes and xylanosomes, to profit from the synergy between certain enzymes is on
50 V. Dollhofer et al.

the rise. For example Doi and colleagues built a cellulosome from Clostridium
thermocellum enzymes which show synergistic activity against cellulose [66].
Mingardon et al. designed mini-cellulosomes combining free fungal endoglucanase
of glycosyl hydrolase family 6 from Neocallimastix patriciarum with bacterial
cellulosomal endoglucanase of glycosyl hydrolase family 9 from Clostridium cel-
lulolyticum, achieving superior cellulose activity, compared to complexes assem-
bled only with bacterial enzymes [80]. But even if recombinant anaerobic fungal
enzymes could be produced and implemented in biotechnological processes, the
physical degradation abilities of anaerobic fungi would still remain unused.

2.2 Anaerobic Fungi in the Biogas Production Process

A commonly encountered issue during anaerobic digestion is limited degradability

of plant biomass, 40–60 % of organic carbon remains unused [81]. This problem is
due to the physical structure and the recalcitrant chemical nature of these polymers.
In detail, lignin remains indigestive under anaerobic conditions and shields cellu-
lose and hemicellulose from enzymatic degradation. Thus, technologies that can
improve anaerobic degradation of lignocellulosic biomass are needed. Partial dis-
ruption of plant tissues, can be achieved by mechanical [82], thermal [83, 84],
chemical [85], oxidative [86] or ultrasonic [87, 88] pre-treatment.
However, in the rumen the natural biogas system these techniques are not
available. There bacteria, archaea, protozoa and anaerobic fungi account for the key
players in plant tissue degradation. Some important parameters of anaerobic
digestion in biogas fermenters resemble conditions of the fermentation processes
found in the rumen, namely a strong negative redox potential, a nearly neutral pH
and a temperature between 37 ± 2 °C. Microbial pre-treatment or the implemen-
tations of rumen microorganisms into the biogas process seem to be possible
strategies to deal with recalcitrant substrates.
Improvement of anaerobic biomass hydrolysis through the addition of specific
microorganisms has been experimentally tested in several studies for bacteria. Miah
and co-workers [89] described a 210 % increase in biogas production during
thermophilic digestion (65 °C) of sewage sludge caused by the protease activity of a
Geobacillus sp. strain. Similarly, Bagi and colleagues [90] applied mesophilic
Enterobacter cloacae and thermophilic Caldicellulosyruptor saccharolyticus
strains during anaerobic digestion of waste water sludge, pig manure and dried
plant biomass of artichoke, and achieved a remarkable increase of biogas produc-
tion (160 %). This increase was explained by the enhanced H2 level as both tested
strains are excellent hydrogen-producing bacteria, and C. saccharolyticus has
moreover cellulolytic activity. Also introduction of an aerobic pre-treatment step for
plant residues through e.g. white and brown rot fungi or the potent cellulose
degrading Trichoderma viride has shown promising results on improving the
subsequent anaerobic digestibility in biogas reactors [91, 92].
Anaerobic Fungi and Their Potential for Biogas Production 51

In contrast, the direct introduction of anaerobic fungi into these bioreactors

would eliminate the requirement of an aerobic pre-digestion. With respect to the
presented intention, of course only mesophilic conditions are eligible. In recent
years, several studies have dealt with the application of anaerobic fungi to improve
anaerobic digestion of cellulosic material [3]. In more detail, the digestive tract of
animals fed with very specific, fibre-rich diets have been chosen for the isolation of
potent anaerobic fungal strains, that could be best suited for a technical imple-
mentation [34]. The possibility of Anaeromyces and Piromyces strains to integrate
into biogas-producing anaerobic sludge bacterial communities, to improve degra-
dation of substrate polysaccharides and consequently to influence methane pro-
duction has already been tested in laboratory conditions. Promising results were
obtained during the bioaugmentation of swine manure fed biogas reactors with
different strains of anaerobic fungi. Amendment with fungal biomass led to 4–22 %
higher gas yields and up to 2.5 % higher methane concentration [81, 93]. A recent
study showed that bioaugmentation with anaerobic fungi did not increase the
overall methane yield, but that it speeds up initial gas production and thus may help
to reduce retention time [94]. In most cases, however, it was not possible to pre-
serve fungal activity and the fungal beneficial effect on hydrolysis seems to decline
after about ten days of incubation. The factors permitting fungal growth in habitats
other than the digestive tract of their hosts still require thorough research and it is
unclear if full-scale application of these microorganisms will become feasible.

3 Anaerobic Fungi: Methodological State of the Art

3.1 Detection Techniques for Anaerobic Fungi

The monitoring of anaerobic fungi sampled from the digestive tract or feces of
herbivores requires accurate and reliable detection techniques, and the same
methods are also applicable to axenic cultures and industrial fermentations [95].
Here we summarize the range of approaches that have been used so far, or which
may be of relevance to detect and quantify the activity of anaerobic fungi.
Microscopy is still the most straightforward method for a general determination
of growth status and initial phylogenetic classification of fungal biomass. However
it requires a certain level of skill and experience to assign identity and mistakes can
be made even with the help of identification keys as found in e.g. Ho and Barr [96]
and Orpin [97]. Classification into rhizoidal or bulbous genera is relatively easy, for
a more exact attribution of anaerobic fungi to the monocentric or polycentric group,
the DNA binding fluorescent dyes DAPI (4’,6-diamidino-2-phenylindole) or stains
of the Hoechst-group (bisbenzimides) must be employed. A microscopic approach
reaches its limit when differentiation between e.g. Piromyces and Neocallimastix, or
Orpinomyces and Anaeromyces is needed and often no zoospore release can be
witnessed to check for monoflagellate or polyflagellate zoospores. Another
52 V. Dollhofer et al.

drawback, especially in microscopy of environmental samples that contain plant

debris, is the clear differentiation of fungal- and plant biomass. During fluorescence
microscopy, autofluorescence of plant material over a wide wavelength range
clearly impedes distinct identification of fungal structures. Staining with Calcofluor
white [98] or the more recently proposed stains Solophenyl Flavine 7GFE 500 and
Pontamine Fast Scarlet 4B [99] will help to highlight chitinous structures of the
fungal biomass, such as cell walls, septa and bud scars, but the affinity of these dyes
for cellulose and other sugar polymers can be problematic. Specific staining pro-
tocols can be performed to circumvent this issue. One possibility is the staining
with lactofuchsin as described in Leis et al. [34], an approach originally used to
bring out plant root fungi, e.g. arbuscular myccorhizas.
Measurement of fungal abundance with culture-dependent techniques i.e. thallus
forming units (TFU) is generally performed through the most probable number
(MPN) method [29, 100] and by using the roll-tube method as described by Joblin
[101]. A work that can be tedious and also requires certain expertise. The roll-tube
approach is further well suited to obtain pure fungal cultures during the isolation
procedure.
An indirect way to determine fungal biomass/growth is through their gas pro-
duction that can be monitored by the use of a pressure transducer and then corre-
lated to the amount of biomass [102].
Anaerobic fungi produce a wide range of potent enzymes, e.g. cellulase, en-
doglucanase, xylanase or amylase amongst others, that help to degrade plant
material [93, 103, 104]. Thus enzyme activity can be used as indirect parameter for
fungal activity. For instance Fliegerová and co-workers could, based on these
parameters, demonstrate the improved hydrolytic activity of biogas reactors after
fungal amendment, but also detected the relatively fast decrease of this enzyme
activity over time [93].
Another very promising approach that has yet to be tested for anaerobic fungi is
the raising of enzyme-specific antibodies. Li and coworkers [103] were able to
produce specific antibodies for the catalytic domain of xylanases found in
Orpinomyces and Neocallimastix. By fluorescence-labelling of these antibodies that
could maybe also be raised for other fungi specific structures, an elegant detection
technique could be established.
Culture independent, molecular techniques and DNA-based approaches have
revolutionized microbial ecology over the last two decades and helped to confirm
the monophyly of the Neocallimastigomycota. The most commonly used target
genes, that allow not only for anaerobic fungi detection and community analysis but
also quantification through qPCR are the small ribosomal subunit (18S rRNA gene)
and the internal spacer (ITS) region [15, 32, 95, 105–109]. However, both gene
regions also bear certain drawbacks that should be considered and are discussed in
[13]. To summarize these drawbacks, the sequence of the 18S rRNA gene is too
conserved within the Neocallimastigomycota phylum to allow for a clear differ-
entiation of closely related taxa [110], and the ITS region, despite its prevalent
utilization in fungal phylogeny [111], does not allow for direct sequencing of PCR
products and exhibits high variability for this microbial group that might impair
Anaerobic Fungi and Their Potential for Biogas Production 53

sequence alignments. The 28S rRNA gene however seems to be best suited for
detection and phylogenetic assignment of anaerobic fungi and should be considered
as the best target gene thus far utilized. A recent study even suggests to combine all
three DNA regions (18S, 28S and ITS) for a more accurate representation of fungal
diversity in environmental samples [112], indicating that each chosen DNA region
leads to a different result. Quantification of anaerobic fungi through qPCR gives a
good insight into fungal abundance but is difficult to correlate with culture
dependent enumeration results (TFU) or the actual biomass due to varying ratios of
the DNA/biomass content within the Neocallimastigomycota members and
depending on specific growth phase of each culture.

3.2 Cultivation Techniques and Cryopreservation

This chapter has highlighted the potential of this unusual group of fungi to address a
range of problems associated with the degradation of lignocellulose-rich waste
materials. The fact that these fungi are obligate anaerobes is an important com-
ponent of their biotechnological potential, since scale-up issues are less problematic
with anaerobic fermentation. However, the associated difficulty in the culturing and
maintenance of obligate anaerobic fungi does impede the exchange of materials
between scientists, and could cause problems in future biotechnological deployment
of these fungi. First there is a need for an international culture collection, with
moves underway to exchange cryogenically stored cultures between interested
parties. This will avoid the loss of cultures that has beset past research—we note
with sadness that most of the type cultures that define the ca. 20 species are no
longer extant. However, the growth in the routine use of DNA barcoding will
facilitate the process of reliable identification of these fungi both in pure culture and
from environmental samples.
Storage in liquid nitrogen appears to provide the only means for long term
storage of anaerobic fungi cultures and it is strongly advised to store such cryovials
in several locations. Storage at −80 °C is possible but there is progressive loss of
viability of cultures over periods of more than a few months. Given the fragility of
pure cultures, there is a need to elucidate the mechanism whereby these fungi form
aerotolerant structures. It is clear that all the anaerobic fungi must be able to do this
in order to disperse between hosts and furthermore it is clear that they are very
efficient in dispersal. The ability to generate such aerotolerant structures from
axenic cultures would be extremely useful for long-term preservation of cultures
and important in the context of this chapter for the inoculation of industrial fer-
mentations with desired cultures or culture mixtures. Fliegerová et al. [93] has
already demonstrated that biogas fermentation can be enhanced by addition of
anaerobic fungi, as have Puniya et al. in their use of ‘direct fed’ microbials for the
enhancement of the rumen fermentation [113]. However, they used actively
growing cultures, a process difficult to scale up. The ability to add aerotolerant
structures to such fermentations would be most advantageous.
54 V. Dollhofer et al.

4 Conclusions

One of the major research goals in biogas science is to find an efficient tool to
circumnavigate the bottleneck possessed by hydrolysis of lignocellulose-rich resi-
dues. Besides several physical, mechanical chemical or microbial pretreatment
techniques, the use of anaerobic lignocellulolytic fungi should be beneficial and
even more cost-efficient. The rumen of herbivores can be seen as a natural resource
for potent biomass degraders. Especially anaerobic fungi, known to act as primary
digesters, could be good candidates.
They produce a superior set of hemi/cellulolytic enzymes which they excrete
separately or combined in cellulosomes. Additionally they are able to attack the
plant material mechanically by their rhizoidal growth and open up the tissue for
further digestion by bacteria. These two features are of capital interest to the biogas
industry.
Until now several attempts have been made to produce recombinant anaerobic
fungal enzymes for biotechnological application and even artificial cellulosomes
have been built. Production in yeast has been the most profitable way, but still more
research has to be done to provide recombinant enzymes in an industrial scale.
Experiments to use anaerobic fungi directly in the biogas production process
showed positive effects on gas production, but enzymatic activity and fungal
growth decreased quickly under these conditions. Maybe anaerobic fungi cannot be
implemented into conventional biogas reactors, but an individual anaerobic fungal
pre-hydrolysis stage might be a possible solution facing this problem.
To summarize, anaerobic fungi have the potential to make biogas production
much more efficient and the utilization of lignocellulose-rich substrates more viable.
But for use in the industrial scale a greater understanding of the underlying ecology
of these fungi and there cohorts is needed.

Acknowledgments TMC is grateful for funding from the Aberystwyth Postgraduate Research
Studentship. VD is grateful for funding of the project BE/14/22 from the Bavarian State Ministry
of Food, Agriculture and Forestry and the Bavarian State Ministry of Economics.

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