Environmental Microbiology (2011) 13(8), 1903–1907 doi:10.1111/j.1462-2920.2011.02512.

Editorial

Life and applications of extremophiles emi_2512 1903..1907

Ricardo Cavicchioli,1 Ricardo Amils,2 Dirk Wagner3 considering what constitutes an extreme environment and
and Terry McGenity4 what defines an extremophile – in particular, the match
1
School of Biotechnology and Biomolecular Sciences, between the organism and the specific environmental
The University of NSW, Sidney, NSW 2052, Australia. extreme, and the mechanisms that lead to survival and in
2
Centro de Biología Molecular, CSIC- Universidad some cases ecological dominance. Consider for example,
Autónoma de Madrid, 28049 Cantoblanco, Madrid, that many microorganisms found in hot acidic environ-
Spain. ments require low pH and high temperature for growth –
3
Alfred Wegener Institute for Polar and Marine at low temperature or alkaline pH the same organisms
Research, Research Unit Postdam, D-14473 Postdam, cease growth and/or lyse and die. In this regard it is
Germany. straightforward to consider the microorganisms as ther-
4
Department of Biological Sciences, Univeristy of Essex, moacidophiles, where ‘phile’ denotes ‘love’ or in essence,
Colchester, CO43SQ Essex, UK. a ‘requirement’ for those conditions. Consistent with this
line of reasoning, in the case of halophiles, there is an
The Earth contains a plethora of environments that, from obligate requirement for high levels of salt in the growth
an anthropocentric perspective, might be classified as medium. However, radically different mechanisms have
extreme. Relative to the typical standard conditions of evolved to achieve ‘halo’ extremophily, with obligate
temperature, pressure, humidity, air quality, light, nutrient extreme halophiles from the domains Archaea and
supply, shelter, lack of predation, etc. that many humans Bacteria accumulating very high concentrations of salt in
encounter in everyday life, almost all other forms of life the cell, whereas moderate halophiles or halotolerant
live under more constrained conditions. From this per- microbes adopt a more flexible strategy, largely excluding
spective, the world is clearly full of extremes – tempera- salt and synthesizing instead compatible organic solutes
ture, salinity and pH being the abiotic factors that first to to maintain osmotic balance.
spring to mind. Even environments that represent large It is interesting to consider other types of extremophiles,
portions of the biosphere, such as cold environments (e.g. such as radiation resistant Deinococcus radiodurans
> 80% of the Earth’s biosphere is permanently below (bacteria), Methanosarcina species (archaea) from per-
5°C), are considered extreme – clearly not because they mafrost and Pyrococcus furiosus (archaea) from hydro-
are extreme to the large number of organisms that can thermal vents – all are highly resistant to g-radiation, yet
survive there, but because the extreme cold greatly none have evolved to ‘love’ or even tolerate extremely
restricts human colonization (e.g. the cold deep ocean). high levels of radiation. Instead, extreme radiation resis-
Still, even with this concept of extreme not aptly reflect- tance is a result of cross protection having arisen from
ing the ‘viewpoint’ of many life-forms on the planet, by selection pressure to repair damaged DNA caused by
recognizing what are anthropocentric extremes and pon- dehydration or thermal injury. In one further example,
dering how life prevails in such environments, strong lines many microorganisms from naturally cold environments
of scientific research have been generated that have display a relatively slow rate of growth when cultivated at
resulted in important discoveries being made about the in situ temperatures compared with higher temperatures.
resident ‘extremophiles’ and life on Earth as a whole. While at first glance this may appear to indicate that
Breakthroughs have provided completely new levels of these psychrophiles are poorly adapted to the cold,
understanding about biological mechanisms of adapta- temperature-dependent growth rate is in fact a very poor
tion, informed us about the evolution of life on Earth, indicator of fitness for psychrophiles. Studies of psychro-
expanded the repertoire of locations suitable for search- philic bacteria and archaea have demonstrated both
ing for extra-terrestrial life, and provided a boon for bio- physiological adaptation and ecological competitiveness
technology and related commercial industries. at in situ temperatures – responses that do not occur at
With regard to the concept of extremophiles and what relatively high temperatures such as Topt (the temperature
has been learned about them, there is value in further at which microorganisms grow the fastest).
© 2011 Society for Applied Microbiology and Blackwell Publishing Ltd
1904 Editorial

As a result of the awareness about the diversity of and desiccation, as well as protection against toxic metals
extreme environments (often involving multiple types of in the environment.
extremes), the range of evolutionary paths that have led A number of reports and reviews highlight the develop-
to individual microorganisms becoming extremophiles, ment of methodology for advancing studies of extremo-
and the overall lack of understanding about the adaptive philes: the use of proteomics for studying extremophiles
mechanisms of individual extremophiles and whole micro- (Burg et al., 2011), RNA stable isotope probing for study-
bial communities, knowledge in the field has been most ing methanotrophic communities (Graef et al., 2011),
effectively gained through studies that have incorporated quantitative PCR to measure the abundance of syntrophic
a thorough evaluation of the particular environmental acetate-oxidizing microorganisms in ammonia-stressed
extreme. This combined with letting empirical determina- biogas reactors (Westerholm et al., 2011) and high tem-
tion (and not preconception) guide the work, and keeping perature petroleum reservoirs (Mayumi et al., 2011),
a wise eye open to the capacity of discovery to surprise metagenomics for studying viruses from hypersaline
has allowed the successful augmentation of this important lakes (Sime-Ngando et al., 2011), a multiplex approach
knowledge base. for quantification of fine-scale temperature-induced
‘Life and Applications of Extremophiles’ is the focus of changes in the proteome (Williams et al., 2011) and a
special issues in Environmental Microbiology and Envi- microarray for gene regulation studies (Campanaro et al.,
ronmental Microbiology Reports and a thematic issue in 2011) of a psychrophilic archaeon, and development of
Microbial Biotechnology. Reflecting the broad coverage of gene transfer systems for manipulating halophiles (Calo
the journals, the thirty-plus papers cover diverse topics et al., 2011 and Köcher et al., 2011a,b), psychrophiles
about a wide range of extremophiles. Several papers (Cavicchioli et al., 2011) and thermophiles (Taylor et al.,
arose out of the MicroPerm Workshop held 8–10 Novem- 2011).
ber 2010 in Potsdam, Germany – the first workshop The development of tractable genetic systems
aimed at bringing together microbiologists working on has paved the way for breakthroughs in both discovery
Arctic and Antarctic permafrost environments. science and commercially orientated research of many
All life requires water for growth. Lithotrophs living on biological systems. For extremophiles, developing a suit-
or just below rock surfaces, survive for long periods with able system can be complicated by the challenges
low water activity. Bjelland and colleagues (2011) used imposed by the extreme cultivation and plating conditions.
molecular phylogenetic analyses to characterize lichen– Taylor and colleagues (2011) review gene transfer
rock-associated microbial metacommunities from areas of systems developed for (hyper) thermophilic archaea and
Norway. Their work revealed that lichens are much more bacteria, focusing on the value of genetic systems for
than a symbiosis between algae and fungi but additionally learning about cellular physiology, and particularly for
house a diverse mix of bacteria and archaea, with an whole cell conversion of lignocellulose to alcohols. Koba-
apparent association between community composition yashi and colleagues (2011) demonstrated a role for the
and species of lichen that may account for the specific s32-mediated heat-shock response in organic-solvent tol-
rock weathering characteristics observed with different erance in Pseudomonas putida. Calo and colleagues
species of lichen. Perfumo and colleagues (2011) used (2011) developed a system for enabling glycoproteins to
both molecular phylogenetic and cultivation-dependent be synthesized in haloarchaea. The study flows from pre-
techniques to study the microbial communities associated vious studies that defined the pathway for synthesis of
with ferromagnetic sand from an arid coastal mine area in novel N-linked glycans in Haloferax volcanii. In their article
Italy. Similar to the lithotrophs studied by Bjelland and in Environ. Microbiol., Köcher et al. (2011a) describe the
colleagues (2011), microbial communities are exposed to development of a markerless mutagenesis gene deletion
dehydration and UV, but in this case the ferromagnetic system for the moderately halophilic bacterium, Haloba-
sand communities are also exposed to high temperature cillus halophilus, and demonstrate its use for deleting the
and very high iron content. Reflecting some of the proHJA operon. In their accompanying study in EMI
common selection pressures, some microbial groups (e.g. Reports, Köcher et al. (2011b) examine the regulation of
Deinococcus) were detected in both studies. A related proline synthesis in response to physiological perturba-
story that speaks to survival by avoiding extremes, is the tion, rationalizing the role of proline as a carbon and
report by Reeb and colleagues (2011) on the microbial energy source, and as a compatible solute.
communities present within buffalo bones found in a high The role of compatible solutes in archaea and bacteria
altitude region of Yellowstone National Park. Members of is discussed in several reports (Schwibbert et al., 2011;
the Stichococcus clade of green algae were found to be Empadinhas and Costa, 2011; Oren, 2011). Empadinhas
abundant, and the authors speculated that similar to and Costa describe the role of sugar glycerates, in par-
endolithic communities in Antarctic soil, they might prolif- ticular mannosylglycerate and glucosylglycerate in stress
erate in the bone due to protection from high UV radiation adaptation by functioning as osmolytes, as protectors

© 2011 Society for Applied Microbiology and Blackwell Publishing Ltd, Environmental Microbiology, 13, 1903–1907
 Editorial 1905

against thermal stress or as precursors to larger macro- taining a functional cellular environment, therefore the
molecules in bacteria and archaea, including (hyper) ther- study by Hamilton and colleagues (2011) was interesting
mophiles and halophiles. The extensive review covers in providing the first evidence of thermoacidophilic nitro-
physiological responses, biosynthetic pathways and gen fixation in hot and acid geothermal springs in Yellow-
biotechnological/medical applications. Schwibbert and stone National Park. The freshwater of Yellowstone Lake
colleagues (2011) describe the complete genome supports fish that are pivotal to the ecology of the park’s
sequence of Halomonas elongata DSM 2581T, and larger and enigmatic fauna; however, Clingenpeel and
genomic and experimental analyses leading to a compre- colleagues (2011) show that, while dominated by typical
hensive view of the entire ectoine metabolism pathways, freshwater-lake bacteria, chemolithotrophs, fuelled by
including the development of a metabolic flux model for underwater hydrothermal vents, are also likely to
ectoine metabolism. The model was used for not only contribute to the lake’s ecology, together with the cyano-
learning about the ways in which H. elongata survives salt bacterium, Prochlorococcus, more typical of marine envi-
stress, but also for improving industrial production of ronments. Le Fourn and colleagues (2011) report on
ectoine. Oren (2011) provides an analysis of the bioener- the role of horizontal gene transfer in providing the ability
getics surrounding growth and survival in hypersaline of diverse clades of anaerobic (hyper)thermophiles to
environments. By reflecting on principles of thermody- withstand exposure to oxygen. By defining pathways of
namics he explains that the limits to various biogeochemi- oxygen consumption in the bacterium Thermotoga mar-
cal processes in hypersaline environments can be itima, and performing phylogenetic analyses of the genes
explained by whether the relevant halophilic microbes involved, the authors inferred that gene exchange
have evolved the energy-demanding compatible-solute between (hyper)thermophilic members of the Bacteria
strategy or the less energy expensive salt-in-cell strategy (Thermotogales) occurred with members of the Archaea
to cope with high salt concentrations. In so doing he (Thermococcales) – selection pressure for the gene
highlights areas where knowledge is lacking, providing exchange events arising from the need to cope with fluc-
important foci for future studies. Indeed, the study by tuating environmental oxidative conditions.
Lazar and colleagues (2011) extends the known salinity Two studies serve to further blur the distinction between
limit of one such process, acetoclastic methanogenesis. geosphere and biosphere, including discussions of the
The types of minerals in hypersaline environments can role of terrestrial subsurface communities in seeding geo-
vary a great deal depending on the origin of the water thermal spring environments (Tin et al., 2011), and the
basins. Soda lakes are rich in carbonate and sodium and long-term survival of haloarchaea in subterranean halite
as a result have a high pH. Lefèvre and colleagues (2011) from the Salar Grande in Chile (Gramain et al., 2011). By
studied a number of alkaline sites in California and iso- comparing the microbial community composition of a cold,
lated microorganisms that were not only alkaliphiles, but acidic, metal-rich pyrite mine in Wales with previous
were anaerobic, sulfate reducing, magnetotactic bacteria studies of acid-mine drainage in warmer environments,
that produced bullet-shaped, magnetite-containing mag- Kimura and colleagues (2011) were able to infer the
netosomes. In contrast to soda lakes, deep-sea anoxic importance of iron-oxidizing acidithiobacilli in generating
brines arise in areas characterized by diverse tectonic acid in the colder mines.
activity where evaporitic deposits are dissolved or The pelagic and subsurface reaches of the deep sea
expelled as interstitial brine producing a range of hyper- are cold, high pressure, oligotrophic environments that
saline environments that differ in temperature, pH and are technically challenging to study. Three reports cover
chemical composition. Antunes and colleagues (2011) different aspects of the deep sea and its sediments:
review these systems describing, for example, the micro- Kawamoto and Kurihara (2011) elucidate a role for the
biology of Atlantis II Deep in the Red Sea which is cytoplasmic membrane polyunsaturated fatty acid,
~ 2200 m deep basin that contains a 200 m thick brine eicosapentaenoic acid, in facilitating cell division under
with a pH 5.3 and a temperature up to 68°C. While the high pressure in Shewanella violacea; Eloe and col-
logistics of studying these environments is challenging, leagues (2011) describe the microbial composition of
Antunes and colleagues (2011) describe the advances particle-associated and free-living Archaea, Bacteria and
being made in understanding the ecology of the diverse Eucarya from the 6000 m deep Puerto Rico Trench in the
archaea and bacteria that have been identified, as well as Atlantic Ocean; and Engelhardt and colleagues (2011)
some interesting findings about eucaryotes and viruses. report on the role of phage in structuring microbial com-
Although the ability to fix atmospheric nitrogen offers munity composition within sediment (up to 420 m deep) at
a selective advantage to microbes living in nitrogen- depths of up to 5000 m below the surface of the Pacific
depleted environments it requires significant input of Ocean. These reports offer base-line information about
energy. In many extreme environments a higher propor- abyssal microorganisms, highlighting the lack of data for
tion of the microbes’ resources are directed towards main- comparison. Interestingly, a different level of incomplete

© 2011 Society for Applied Microbiology and Blackwell Publishing Ltd, Environmental Microbiology, 13, 1903–1907
1906 Editorial

understanding was described by Bouman and colleagues metacommunities in the lichen-rock habitat. Envrion
(2011) for subtropical upper ocean communities. Focus- Microbiol Rep 3: 434–442. doi: 10.1111/j.1758-2229.2010.
ing on phytoplankton, they described the stratification of 00206.x.
Bouman, H.A., Ulloa, O., Barlow, R., Li, W.K.W., Platt, T.,
cyanobacterial versus eucaryotic microbial communities,
Zwirglmaier, K., et al. (2011) Water-column stratification
noting the effect of genomic streamlining on Prochloro- governs the community structure of subtropical marine
coccus species to facilitate growth in highly stable, olig- picophytoplankton. Environ Microbiol Rep 3: 473–482. doi:
otrophic systems, but only within zones that were subject 10.1111/j.1758-2229.2011.00241.x.
to dynamic mixing. Burg, D., Ng, C., Ting, L., and Cavicchioli, R. (2011) Pro-
Two reports focus on the cycling of C1 compounds teomics of extremophiles. Environ Microbiol 13: 1934–
through methanogenic and methanotrophic pathways in 1955. doi:10.1111/j.1462-2920.2011.02484.x.
Calo, D., Guan, Z., and Eichler, J. (2011) Glyco-engineering
distinct cold environments. Lazar and colleagues (2011)
in Archaea differential N-glycosylation of the S-layer glyco-
describe the methanogenic diversity and activity in hyper- protein in a transformed Haloferax volcanii strain. Microb
saline sediments collected from the centre of the Napoli Biotech 4: 461–470. doi:10.1111/j.1751-7915.2011.
mud volcano at 1940 m of water depth in the Eastern 00250.x.
Mediterranean Sea, and Graef and colleagues (2011) Campanaro, S., Williams, T.J., Burg, D.W., De Francisi, D.,
describe communities from the upper soil layers in the Treu, L., Lauro, F.M., and Cavicchioli, R. (2011)
high Arctic Svalbard wetlands. Graef and colleagues Temperature-dependent global gene expression in the Ant-
arctic archaeon Methanococcoides burtonii. Environ Micro-
(2011) determined that the diversity of methanotrophs
biol 13: 2018–2038. doi:10.1111/j.1462-2920.02367.
was relatively low, inferring that Arctic communities may Cavicchioli, R., Charlton, T., Ertan, H., Mohd, O.S., Siddiqui,
therefore be vulnerable to ecosystem change, and so K.S., and Williams, T.J. (2011) Biotechnological uses of
compromise the effectiveness of microbial capture of the enzymes from psychrophiles. Microbiol Biotech 4: 449–
greenhouse gas, methane. 460. doi.10.1111/j.1751-7915.2011.00258.x.
A number of studies revolve around the use of model Clingenpeel, S., Macur, R.E., Kan, J., Inskeep, W.P., Lovalvo,
extremophiles. These include, the psychrophilic archaeon D., Varley, J., et al. (2011) Yellowstone Lake: high-energy
geochemistry and reich bacterial diversity. Environ
Methanococcoides burtonii (Campanaro et al., 2011; De
Microbiol 13: 2172–2185. doi:10.1111/j.1462-2920.2011.
Francisci et al., 2011; Pilak et al., 2011; Williams et al., 02466.x.
2011), the ectoine-producing halophile H. elongata De Francisci, D., Campanaro, S., Kornfeld, G., Siddiqui, K.S.,
(Schwibbert et al., 2011; Köcher et al., 2011a,b), and Williams, T.J., Ertan, H., et al. (2011) The RNA polymerase
N-glycosylation in the haloarchaeon H. volcanii (Calo subunits E/F from the Antarctic archaeon Methnococcoides
et al., 2011). While the studies on M. burtonii focused on burtonii bind to specific species of mRNA. Environ
the roles of RNA polymerase subunits E and F, chaper- Microbiol 13: 2039–2055. doi:10.1111/j.1462-2920.2010.
02385.x.
onins, and global gene regulation and expression on
Eloe, E.A., Shulse, C.N., Fadrosh, D.W., Williamson, S.J.,
thermal adaptation, they also shed light on fundamental Allen, E.E., and Bartlett, D.H. (2011) Compositional differ-
aspects of transcription (both the transcription machinery ences in particle-associated and free-living microbial
and operon structure) and protein folding (including the assemblages from a extreme deep-ocean environment.
first crystal structure of a protein from a psychrophilic Environ Microbiol Rep 3: 449–458. doi:10.1111/j.1758-
archaeon). The review by Piette and colleagues (2011) 2229-2010.00223.x.
describe the present state of knowledge about protein Empadinhas, N., and Costa, M.S. (2011) Diversity, biological
roles and biosynthetic pathways for sugar-glicerate con-
folding in the cold. An important aspect of the review was
taining compatible solutes in bacteria and archaea. Environ
highlighting the value of having studies available for Microbiol 13: 2056–2077. doi:10.1111/j.1462-2920.2010.
numerous model psychrophilic systems so that principles 02390.x.
versus specific features of adaptation could be inferred. Engelhardt, T., Sahlberg, M., Cypionka, H., and Engelen, B.
For the same reasons, this rationale can be applied to (2011) Induction of prophages from deep-subseafloor bac-
studies of all types of extremophiles. The thirty-plus teria. Environ Microbiol Rep 3: 459–465. doi:10.1111/
papers presented in this series make an important contri- j.1758-2229.2010.00232.x.
Graef, C., Hestnes, A.G., Svenning, M.M., and Frenzel, P.
bution to the vibrant field of extremophile research.
(2011) The active methanotrophic community in a wetland
from the High Arctic. Environ Microbiol Rep 3: 466–472.
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© 2011 Society for Applied Microbiology and Blackwell Publishing Ltd, Environmental Microbiology, 13, 1903–1907