International Journal of Systematic and Evolutionary Microbiology (2015), 65, 1360–1368
DOI 10.1099/ijs.0.000065
Methanogenic archaea database containing
physiological and biochemical characteristics
Sławomir Jabłoński,1 Paweł Rodowicz1,2 and Marcin Łukaszewicz1
Correspondence
1
Marcin Łukaszewicz
2
[email protected]
Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
Department of Information, Wrocław University of Technology, Wrocław, Poland
The methanogenic archaea are a group of micro-organisms that have developed a unique
metabolic pathway for obtaining energy. There are 150 characterized species in this group;
however, novel species continue to be discovered. Since methanogens are considered a crucial
part of the carbon cycle in the anaerobic ecosystem, characterization of these micro-organisms is
important for understanding anaerobic ecology. A methanogens database (MDB; http://
metanogen.biotech.uni.wroc.pl/), including physiological and biochemical characteristics of
methanogens, was constructed based on the descriptions of isolated type strains. Analysis of the
data revealed that methanogens are able to grow from 0 to 122 6C. Methanogens growing at the
same temperature may have very different growth rates. There is no clear correlation between the
optimal growth temperature and the DNA G+C content. The following substrate preferences are
observed in the database: 74.5 % of archaea species utilize H2+CO2, 33 % utilize methyl
compounds and 8.5 % utilize acetate. Utilization of methyl compounds (mainly micro-organisms
belonging to the genera Methanosarcina and Methanolobus) is seldom accompanied by an ability
to utilize H2+CO2. Very often, data for described species are incomplete, especially substrate
preferences. Additional research leading to completion of missing information and development of
standards, especially for substrate utilization, would be very helpful.
Methanogenic archaea are a very important part of anaerobic ecosystems. They can be found in many anaerobic
environments, such as aquatic sediments (Romesser et al.,
1979; Worakit et al., 1986), soil (Joulian et al., 2000; Sakai
et al., 2010), anaerobic digesters (Patel & Sprott, 1990), the
gastrointestinal tract (Leadbetter & Breznak, 1996; Smith &
Hungate, 1958), volcanic environments (Burggraf et al.,
1990; Jones et al., 1983) and even coal and oil deposits
(Meslé et al., 2013; Ni & Boone, 1991). After 1936, when
the first methane-producing micro-organism was isolated
(Methanosarcina mazei), the number of isolated methanogenic archaea increased slowly to 13 identified species in
1979; the isolation of methanogenic archaea then accelerated rapidly (68 species were isolated in the years 1980–
2000, and 69 species from 2000 to the present). This
acceleration was enabled by the development of new
cultivation techniques (Carbonero et al., 2010; Janssen,
2003; Miller & Wolin, 1974; Sakai et al., 2009) and the
exploration of novel environments inhabited by methanogenic archaea, such as hydrothermal vents (Jones et al.,
1983).
The ability to form methane as a major product of metabolism plays a significant role in the carbon cycle. It is
estimated that 58 % of the methane released into the
atmosphere as a result of human activity is produced by
methanogenic archaea (Houweling et al., 2008). For instance,
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enteric fermentation in ruminants is responsible for 37 % of
anthropogenic atmospheric methane emission (Patra, 2013).
Since methane is a greenhouse gas (24 times more effective
than carbon dioxide; Forster et al., 2007), its emission may
have a significant impact on the global ecosystem. The substrates used for methane formation include carbon dioxide
and hydrogen, acetic acid (utilized by members of the genera
Methanosaeta and Methanosarcina) and methyl-group-containing molecules. All these substrates are products of the
decay of organic matter; thus, methanogenesis is usually the
final step in the mineralization of organic matter under
anaerobic conditions (if other hydrogen acceptors such as
nitrate or sulfate are absent). Since the formation of methane
is one of the lowest energy-yielding processes performed by
living organisms (Deppenmeier, 2002), methane contains a
large part of the energy contained in the substrates. This fact
makes anaerobic digestion technology successful for transformation of organic matter into fuel. Biogas may be obtained
from various biomass or from H2+CO2. Anaerobic digesters
on an industrial scale are usually operated under mesophilic
conditions (temperature range 30–40 uC). These conditions
require a heat supply in temperate climates. Future research
efforts are focusing on improving net energy and nutrient
recovery (Batstone & Virdis, 2014). There have been various
attempts to design technologies that are more efficient, such
as two-stage systems, lower operating temperatures (Alvarez
et al., 2008), membrane bioreactors (Smith et al., 2012) and
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The methanogenic archaea properties database
Table 1. Examples of species descriptions in the MDB
Description of codes used in the substrate section: 1, substrate used; 21, substrate not used.
Feature
Taxonomy
Class
Order
Family
Genus
Temperature
Tmin
Tmax
Topt. min
Topt. max
Alkalinity
pHmin
pHmax
pHopt. min
pHopt. max
Salinity
[NaCl]min (mol l21)
[NaCl]max (mol l21)
[NaCl]opt. min (mol l21)
[NaCl]opt. max (mol l21)
Growth
Rate (h21)
Doubling time (h)
Growth on:
H2+CO2
Formate
Acetate
Methanol
Methylamine
Dimethylamine
Trimethylamine
Dimethylsulfide
CO
Ethanol
1-Propanol
1-Butanol
2-Propanol
2-Butanol
Cyclopentanol
Isobutanol
H2+methanol
Environment
Reactors
Intestinal tracts
Soil
Water/sediments
Geothermal
Description
DNA G+C content (mol%)
Morphology
Shape
Gram reaction
Motility
http://ijs.sgmjournals.org
ND,
Usage was not determined or no data available.
Methanomethylovorans
thermophila
Methanosarcina
horonobensis
Methanobacterium subterraneum
Methanomicrobia
Methanosarcinales
Methanosarcinaceae
Methanomethylovorans
Methanomicrobia
Methanosarcinales
Methanosarcinaceae
Methanosarcina
Methanobacteria
Methanobacteriales
Methanobacteriaceae
Methanobacterium
42
58
50
50
20
42
37
37
3.5
40
20
40
5
7.5
6.6
6.6
6
7.75
7
7.25
6.75
9.2
7.8
8.8
0
0.3
0.1
0.1
0
0.35
0.1
0.1
0
1.4
0.2
1.25
0.050
13.86
0.14
4.90
0.178
3.89
21
21
21
1
1
1
1
21
21
21
21
21
21
21
21
21
ND
21
21
1
1
21
1
1
1
1
1
21
21
ND
ND
21
21
ND
ND
ND
21
21
21
21
21
21
ND
ND
ND
21
ND
ND
ND
21
21
1
1
1
Bioreactor
37.6
Groundwater
41.4
Underground water
54.4
Irregular cocci
Negative
No
Irregular cocci
Negative
No
Rod
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No
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S. Jabłoński, P. Rodowicz and M. Łukaszewicz
Table 1. cont.
Feature
Cell surface structures
Width (min.) (mm)
Width (max.) (mm)
Length (min.) (mm)
Length (max.) (mm)
Culture collection accession
numbers
DSMZ
ATCC
Literature
Authors
URL
Methanomethylovorans
thermophila
Methanosarcina
horonobensis
Methanobacterium subterraneum
ND
0.7
1.5
0.7
1.5
Absent
1.4
2.9
1.4
2.9
0.1
0.15
0.6
1.2
DSM 17232
ATCC BAA-1173
DSM 21571
–
DSM 11074
ATCC 700657
Jiang et al. (2005)
http://ijs.sgmjournals.org/content/55/
6/2465.long
Shimizu et al. (2011)
http://ijs.sgmjournals.org/
content/61/10/2503.long
Kotelnikova et al. (1998)
http://ijs.sgmjournals.org/
content/48/2/357.long
electrochemical bioreactors (Xafenias & Mapelli, 2014) or
operating at increased pressure (Lindeboom et al., 2012). In
all cases, the methanogen population will be different; thus,
knowledge of their physiological and biochemical characteristics will be useful.
The isolation and description of novel species of methanogenic archaea is an important process for the understanding of the ecology of anaerobic environments. A uniform
database containing data describing methanogenic microorganisms would be very helpful in the description and
assignment of novel methanogenic archaeal species. There
are already databases containing taxonomic and molecular
data (e.g. http://www.ncbi.nlm.nih.gov/, http://www.bacterio.
net), but none of them includes the physiological characteristics of methanogenic archaea. Uniform standards for the
description of physiological features for methanogenic archaea
were proposed by Boone & Whitman (1988). These standards
include the description of growth conditions, substrate requirements, general morphology, determination of DNA
G+C content, etc. Thus, in this work, we have created and
analysed a database of 150 described and named methanogens.
The database structure is based on the minimal standards
proposed by Boone & Whitman (1988). This database
represents a complete set of the available data describing the
physiological traits of methanogenic archaea. It may be used
during the classification and assignment of novel species,
analysis of the ecology of anaerobic environments and the
development of technologies related to anaerobic digestion.
Database preparation, content and methods
The University of Wrocław methanogens database (MDB;
http://metanogen.biotech.uni.wroc.pl/) contains information on 150 methanogenic micro-organisms, each characterized by 42 features organized into nine groups. Table 1
is an example of the description of three species included in
the MDB. For each micro-organism, there are features
taken from the original publication and a link to the electronic version of the source article.
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Database format
The main part of the MDB is a relational database built
with MySQL software. The web page of MDB is based on
the open-source standard Wordpress. For the generation of
graphs, the API Google software was used. Microbiological
Common Language (MCL), aimed at standardizing the
electronic exchange of meta-information about microorganisms, was used (Verslyppe et al., 2010).
The MDB is updated by scientific staff of the Faculty of
Biotechnology, University of Wrocław, based on the scientific literature. Contributions from users will be welcome
through the MDB webpage (http://metanogen.biotech.uni.
wroc.pl/about/) and will be reviewed for scientific accuracy
before inclusion.
The home page contains a scrollable list of methanogenic
archaea. This list may be filtered in accordance with selected
restrictions listed on the left of the page. Elements of the
MDB may be also selected according to their taxonomic
assignment. The user may obtain graphs representing relationships between selected parameters. These graphs may be
downloaded in .csv or .pdf format.
Examples of data analysis applications
The MDB can be used for the taxonomic placement of
novel species, understanding of the basic biochemistry of
methanogenesis and data searches leading to biotechnological applications such as the design of operating conditions in bioreactors. An example of a specific MDB analysis
is presented in Fig. 1.
DNA G+C content
The G+C content of DNA in prokaryotes was found
nearly 60 years ago to cover a broad range, between
approximately 25 and 75 mol% (Barbu et al., 1956). With
the discovery and description of novel species, this range is
now slightly larger (the lowest being for ‘Carsonella ruddii’,
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The methanogenic archaea properties database
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DNA G+C content (mol%)
65
60
55
50
45
40
35
30
25
20
0
40
20
60
80
100
120
Optimal growth temperature (°C)
Fig. 1. Relation between DNA G+C content and optimal
temperature of growth.
16.5 mol%; Nakabachi et al., 2006). Within most classes of
bacteria, the variation tends to be smaller, but the range in
some groups remains extremely large, e.g. in the class
Alphaproteobacteria, values range from 30 to 60 mol%
(Bentley & Parkhill, 2004). In this respect, methanogens are
extremely variable (Fig. 1). The DNA G+C content ranged
from 23 mol% for Methanosphaera cuniculi (Biavati et al.,
1988) to 62 mol% for Methanoculleus horonobensis (Shimizu
et al., 2013), Methanothermobacter defluvii (Kotelnikova
et al., 1993) and Methanoculleus chikugoensis (Dianou et al.,
2001). It has been suggested that the DNA G+C content is
correlated with factors such as genome size, whether or not
the bacterium is free-living, aerobiosis, nitrogen utilization
or temperature (Hildebrand et al., 2010). For the methanogens as a whole, as well as in more phylogenetically homogeneous groups such as orders or families, there is no clear
correlation between the optimal growth temperature and
DNA G+C content. Analysis of the MDB partially supports
the observations made by Hurst & Merchant (2001) that,
among prokaryotic organisms, the G+C content in the
whole genome does not correlate with the optimal growth
temperature (Fig. 1). Our observation confirms the intriguing finding that correlations valid for aerobic, facultative and
microaerophilic species are not valid for anaerobic prokaryotes (Musto et al., 2006).
Growth temperature
According to growth temperature preferences, microorganisms are generally divided into three or four groups,
namely psychrophilic, mesophilic, thermophilic and, eventually, hyperthermophilic. As seen from Fig. 2, there are
no clear-cut borders that enable these four groups to be
distinguished. Methanogens are able to grow from 0 uC
(Methanogenium frigidum; Franzmann et al., 1997) to 122 uC
(Methanopyrus kandleri; Kurr et al., 1991). Considering
optimal growth temperatures, the border line between
http://ijs.sgmjournals.org
psychrophiles and mesophiles would be around 27 uC.
Within the range 25–40 uC, there is a similar number
(around 80, which is around three-quarters of all those in the
database) of species able to grow. Above 40 uC, the number
of species decreases dramatically. For the optimal growth
temperature, there is a clear minimal number of species at
47 uC, which could be the upper limit for mesophiles. The
number of species able to grow above 47 uC drops slowly up
to 70 uC. Above 70 uC, only a few described species are able
to grow. It is worth pointing out that eight species have
growth rate optima around 65 uC, while this temperature is
within the growth range of 25 species. This temperature may
be used in fermentation of substrates that require sanitation.
An increased fermentation temperature should also result in
higher substrate turnover rates.
Equally promising seems to be the possibility of performing methanogenesis at lower temperatures. For example,
while only a few species grow optimally in the range 20–
27 uC, roughly half of all the micro-organisms are able to
grow within this range. Although anaerobic digestion at
temperatures below 20 uC requires much lower energy
input through heating, it is slower. However, the rate of
some reactions involved in anaerobic digestion may be
increased by increasing the pressure (Miller et al., 1988;
Picard et al., 2007). This phenomenon may be particularly
useful in the case of generation of methane by power-togas technologies (production of methane with the use of
hydrogen obtained from water electrolysis).
Growth rate
Growth rate or doubling time is correlated with growth
temperature. Fig. 3 plots doubling time against optimal
growth temperature. The trend line shows that the relationship is very close to the general rule from the Arrhenius
equation (growth rates almost double with every 10 uC
increase; Connors, 1990). Slowly growing micro-organisms
tend to be psychrophiles, such as ‘Methanosaeta pelagica’
(doubling time 298 h; Mori et al., 2012) or Methanogenium
frigidum (doubling time 70 h; Franzmann et al., 1997).
However, the slowly growing micro-organism Methanolinea
tarda is not a psychrophilic methanogen, since it grows
optimally at 50 uC but has doubling time of around 98 h
(Imachi et al., 2008). The fastest growing methanogens are
hyperthermophilic: Methanopyrus kandleri (Kurr et al.,
1991), with an optimal growth temperature of 98 uC and
a doubling time of 0.33 h, Methanocaldococcus fervens
(Jeanthon et al., 1999), with an optimal growth temperature
of 85 uC and a doubling time of 0.33 h, and Methanotorris
igneus (Burggraf et al., 1990), with an optimal growth
temperature of 88 uC and a doubling time of 0.42 h. Thus,
independently of the general rule that the higher the growth
temperature, the shorter the doubling time, methanogenic
archaea growing at the same temperature may have very
different growth rates or the same growth rates at very different optimal growth temperatures. Moreover, the growth
rate of micro-organisms depends on the substrate used. This
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S. Jabłoński, P. Rodowicz and M. Łukaszewicz
90
50
45
80
Number of species growing
Number of species within optimum
70
40
35
60
30
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25
40
20
30
15
20
10
5
0
0
1
3
5
7
9
11
13
15
17
19
21
23
25
27
29
31
33
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37
39
41
43
45
47
49
51
53
55
57
59
61
63
65
67
69
71
73
75
77
79
81
83
85
87
89
91
93
95
97
99
10
Temperature of growth (°C)
Fig. 2. Numbers of species growing at a given temperature and species within their optimal growth temperature.
phenomenon is particularly evident in the case of archaea
capable of acetate utilization (Table 2; substrate utilization
capabilities).
structure influences bioreactor performance (Werner et al.,
2011).
Understanding the underlying molecular mechanisms that
lead to differences in growth rates would be interesting and
valuable. Meanwhile, it is encouraging that the selection in
bioreactors of an appropriate set of methanogens could
result in substantial increases in process efficiency. It could
also explain substantial differences in the efficiency of
similar bioreactors operating under the same conditions. It
has been shown recently that micro-organism populations
within bioreactors are relatively stable and that their
Substrate utilization capabilities
Doubing time (h)
1000
100
10
1
0.1
0
20
40
60
80
100
120
Optimal growth temperature (°C)
Fig. 3. Dependence between doubling time and optimal growth
temperature among methanogenic archaea.
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Data concerning the substrate preferences of described
species are incomplete. While there is a standard set of
substrates to be tested (Boone & Whitman, 1988), it is
seldom followed, making reliable comparisons difficult.
Nevertheless, compounds such as H2+CO2, acetate, formate
and methanol are usually tested (in more than 75 % of
classified methanogenic archaea). Substrates such as methylamine, dimethylamine, ethanol and 2-propanol have been
tested for about 50 % of methanogenic species. The remaining
organic compounds were tested in less than 30 % of classified
methanogenic archaea. Although the utilization of methanol
in the presence of hydrogen has been observed among
methanogenic archaea, it is seldom tested during the description of novel species. This lack of information represents a serious hindrance to the analysis of the metabolic
abilities of methanogenic archaea.
Methanogenic substrates may be divided into four categories:
H2+CO2, acetate, methyl-group-containing compounds
and higher organics. Since formate is converted by a similar
metabolic pathway to CO2, it may be included in the same
group of substrates. However, the capacity for formate
utilization requires additional enzymes, and only 57 % of
archaea that feed on H2+CO2 are capable of formate
utilization (Liu & Whitman, 2008).
The substrate utilized by the majority of methanogenic
archaea is a mixture of H2 and CO2. About 74.5 % of microorganisms included in the database utilize these substrates.
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The methanogenic archaea properties database
Table 2. Growth rates of acetoclastic archaea on different substrates
The term ‘very slow’ was used in the reference publications without precise definition. 2, Not applicable (acetate is the only used substrate).
Growth rate (h”1) on:
Species/strain
Methanosarcina soligelidi
Methanosarcina vacuolata
Methanosarcina mazei
Methanosarcina barkeri MST
Methanosarcina barkeri 227
Methanosarcina thermophila
Methanosarcina horonobensis
Methanosarcina acetivorans
‘Methanosaeta pelagica’
Methanosaeta harundinacea
Methanosaeta concilii
Methanosaeta thermophila
Acetate
Preferred substrate
Very slow
0.012
0.010
0.009
0.013
0.058
Very slow
0.029
0.002
0.030
0.011
0.019
0.060 (H2+CO2)
0.140 (H2+methanol)
0.130 (methanol)
0.100 (H2+methanol)
0.090 (H2+methanol)
0.087 (methanol)
0.140 (methanol)
0.133 (methanol)
2
2
2
2
This tendency can be observed among micro-organisms
isolated from all habitats (Fig. 4). This source of energy may
be favoured among methanogenic archaea because the
reduction of CO2 with H2 provides more energy than the
utilization of other substrates. A second explanation for this
phenomenon may be the selection of enrichment methods
used before the isolation of pure strains (Sakai et al., 2009).
Moreover, 27.1 % of archaea cannot use any source of
energy and carbon for growth other than H2+CO2; in
particular, this phenomenon is observed among archaea
isolated from geothermal environments (in this group,
obligate hydrogen consumers represent 64.3 %). This may
be the result of the absence or low levels of other substrates
in volcanic environments. In these environments, water is
enriched in H2, CO2, hydrogen sulfide and ammonium
ions (Tivey, 2007). The concentration of organic compounds, on the other hand, is low. Such conditions should
favour the development of hydrogen-utilizing archaea.
Reference
Wagner et al. (2013)
Maestrojuan & Boone (1991)
Maestrojuan & Boone (1991)
Maestrojuan & Boone (1991)
Maestrojuan & Boone (1991)
Murray & Zinder (1985)
Shimizu et al. (2011)
Sowers et al. (1984)
Mori et al. (2012)
Ma et al. (2006)
Patel & Sprott (1990)
Patel & Sprott (1990)
The ability to utilize higher alcohols as hydrogen donors is
a rare alternative to the utilization of hydrogen. Only 9 %
of archaea in the database use this metabolic pathway (in
the case of 41 % of the species, these substrates were not
tested). Alcohols are oxidized to aldehydes and ketones.
Electrons from the secondary alcohols are transferred to
coenzyme F420, and the oxidation of ethanol is coupled to
the reduction of NADP. All isolated alcohol-utilizing
archaea are also capable of hydrogen utilization, and the
growth rate on alcohols is reduced in comparison with that
on hydrogen (Liu & Whitman, 2008).
A very important group of methanogenic archaea are those
capable of growth on acetate as a sole carbon and energy
source. All acetate-utilizing archaea belong to the order
Methanosarcinales. Despite the fact that about 75 % of the
methane formed during anaerobic digestion is produced
by acetate cleavage (Garcia et al., 2000), acetate-utilizing
archaea make up only 8.5 % of classified methanogenic
H2/CO2
Acetate
Methyl compounds
Higher alcohols
100%
90%
80%
70%
60%
50%
40%
30%
20%
10%
0%
All
Reactors Intestinal
tracts
http://ijs.sgmjournals.org
Soil
Water Geothermal Other
sediments
Fig. 4. Substrate utilization patterns among
archaea isolated from different environments.
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S. Jabłoński, P. Rodowicz and M. Łukaszewicz
archaea. They have usually been isolated from soil, water
sediments and anaerobic reactors. In this group, archaea
from two families are present: Methanosaetaceae and
Methanosarcinaceae (Jetten et al., 1992). Archaea belonging
to the family Methanosaetaceae grow more slowly (doubling time above 24 h), but are capable of utilization of
acetate at concentrations below 1 mmol dm23. Acetateutilizing micro-organisms belonging to the family Methanosarcinaceae grow more quickly (doubling times below
10 h, usually calculated for substrates other than acetate),
but only in acetate concentrations above 1 mmol dm23
(Madigan et al., 2012). It is worth mentioning that growth
rates observed on acetate are in the same range for these
two groups of archaea (Table 2).
Surprisingly, no acetate-utilizing archaea have been isolated
from the intestinal tracts of animals. This phenomenon may
be a result of the low abundance of these archaea in the
intestinal tract. Analysis of 16S rRNA gene clone libraries
obtained from material isolated from the human gut
revealed a lack of representatives of acetoclastic microorganisms (Mihajlovski et al., 2010), and clones related to
the genus Methanosarcina were isolated from the intestinal
tracts of cattle and other animals in only small numbers
(Jeyanathan et al., 2011; Sundset et al., 2009). This may be
the result of washout due to the short retention time of
biomass in the intestinal tract and the relatively long
generation time of archaea capable of degradation of acetate.
The retention time for the cattle intestinal tract is between
40.6 and 51.7 h (Mambrini & Peyraud, 1997). These values
correspond to a dilution rate ranging from 0.59 to 0.47 day21.
The growth rate of methanogenic archaea capable of acetate
utilization obtained on acetate ranges from 0.056 day21 for
‘Methanosaeta pelagica’ (Mori et al., 2012) up to 0.59 day21
for Methanosaeta concilii (Patel & Sprott, 1990) (usually
around 0.3 day21; Maestrojuan & Boone, 1991) for temperature conditions corresponding to the cattle intestinal tract.
Since the dilution rate is at the same level or greater than the
growth rate of acetoclastic archaea, the development of
stable populations is difficult. Nutritional limitations in this
environment should not be a constraint, since the concentration of acetic acid is similar to that observed in anaerobic
reactors, in which these acetoclastic archaea are present in
significant numbers (Imoto & Namioka, 1978; Nielsen et al.,
2007). The lack of acetoclastic archaea isolated from
intestinal tracts may also be a result of the selection of
enrichment techniques used for the isolation of pure
cultures (Sakai et al., 2009).
Methanogenesis from methyl compounds is limited among
methanogenic archaea; only 33 % of micro-organisms in
the database have this ability. Surprisingly, this metabolic
ability is seldom accompanied by the ability for H2+CO2
utilization. Only seven species (six species of the genus
Methanosarcina and Methanobacterium movilense) can utilize
substrates from both groups. Some species of the genus
Methanosphaera and ‘Methanomassilii coccus’ can grow on
methanol in the presence of hydrogen. While this capability
is not often tested during the description of novel species of
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methanogenic archaea, it is possible that other methanogenic
micro-organisms can utilize this substrate. Only 25 % of
archaea that cannot utilize methanol as a sole substrate were
tested with hydrogen.
Future directions
Since the biological generation of methane has a significant
impact on the global ecosystem and many aspects of
human activity, the MDB will be a helpful tool in resolving
problems connected with this phenomenon. The structure
of the database will be modified in future to provide additional information (for example, the description of substrate utilization patterns will be improved to ensure complete
and unambiguous information, and the susceptibility to
chemical agents and chemotaxonomic data will be added).
Based on the information obtained from the MDB, it will
be possible to select micro-organisms most suitable for
conditions under which methanogenesis is beneficial. For
instance, the start-up and recovery of the anaerobic digestion process could be stimulated by the addition of an
appropriate archaeon.
On the other hand, it will also be possible to find novel
conditions for processes in which reduction of biological
methane production is beneficial. For instance, the reduction of archaea activity in the cattle intestinal tract could
result in better fodder utilization efficiency and reduced
greenhouse gas production.
The analysis of data gathered in the MDB also reveals that,
despite the isolation of pure cultures, the data obtained are
often incomplete, and further research is needed. This
statement is particularly true in regard to substrate utilization patterns. Although the database includes 17 substrates,
in the case of only 11 micro-organisms were more than 13
substrates analysed, and usually only eight substrates are
tested. Another problem related to substrate utilization
patterns is the determination of whether the substrate is an
electron donor, an electron acceptor or a carbon source for
the cell. This issue is particularly important in the case of
methyl substrates which, in some cases, can be utilized only
in the presence of hydrogen.
The data concerning the growth rate are also incomplete
and, in the case of 23 % of the included archaea, this
information is not available. An additional useful piece of
information not yet included in the MDB is the substrate
turnover rate; this deficiency clearly indicates that clear
standards for the description of novel species are required.
In summary, the MDB is a platform dedicated to the
analysis of many aspects of the biology of methanogenic
archaea. It may be useful in the context of basic science (for
example, the placement of novel species) as well as for
the development of technologies involving the biological
generation of methane (optimization of anaerobic digestion of waste). It will also be helpful in the selection of new
directions in research involving methanogenic archaea.
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The methanogenic archaea properties database
Acknowledgements
The research was supported financially by the Politechniki
Wrocławskiej through the key project POIG.01.01.02-00-016/08
‘The model agro-energetic complexes as an example of distracted
co-generation based on local and renewable energy sources’ and by
European Union from the project POKL.04.01.01-00-054/10-0.
Houweling, S., van der Werf, G. R., Klein Goldewijk, K., Röckmann,
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