Extremophilic Bacteria and Microbial Diversity

10 Pages·2000·8.4 MB·

by  Michael T Madigan

EXTREMOPHILIC BACTERIA
Madigan
Michael
T.
AND
MICROBIAL DIVERSITY
1
Abstract
—
Many prokaryolic microorganisms inhabit "extreme environments" habitats in which some chemical or physical
variable(s) differs significantly from that found in habitats that support plant and animal life. Great strides have been
made in recent years in the isolation and characterization of extremophilic prokaryoles, and many of them turn out to
have fascinating metabolic properties and interesting evolutionary histories. Prokaryotes that grow at very high tem-
peratures are perhaps the most dramatic in these regards, as all cellular components need to be made heat stable and
their evolutionary position is that of the least evolved of all known life forms. As our knowledge of bacterial diversity
phylogeny and and from
improves, primarily from the introduction of molecular tools for assessing bacterial diversity
new advances in isolation and laboratory culture, is becoming clear that the bulk of evolutionary diversity on Earth
it
There now
does not reside in plants and animals, but instead in the invisible prokaryotic world. is great interest in
mining the diverse genetic resources of Earth's smallest cells for use in biotechnology and related areas.
Key words: extremophilic bacteria, evolutionary history, microbial diversity, prokaryotes.
when orw
Since the days almost 100 years ago Robert bacteria. This giant 1
Koch and his associates isolated the pure cul- tools of molecular bic ogy.
first
worldwide have development of rapid gene sequencing methods and
microbiologists
tures of bacteria,
been isolating laboratory cultures of literally thou- powerful algorithms for the comparative analysis of
sands of different bacteria. These include, of course, nucleic acid sequences. But for these advances to
gene genes
most of the causative agents of infectious diseases, impact microbial evolution, a or that
web an organism
but more important from the standpoint of the reflected the evolutionary history of
many had be Such an evolutionary "Rosetta
of on Earth, of the bacteria that carry out to identified.
life
critical chemical reactions that form the "life sup- Stone" had long been sought, but not until the ad-
RNA
sequencing
port" system for plants and animals (Madigan et al., vent of comparative ribosomal as
2000). Despite the diversity of organisms that are a rapid and specific means for deducing bacterial
already known, now clear that microbiologists phylogenies (Woese, 1987) did microbiologists have
is
it
have only seen the of iceberg; most microorgan- nat
tip tl
—
way and had
isms that exist in nature, in particular the bacteria, ural fashion the botanists zoologists
have not yet been obtained in laboratory culture! classified their subjects for over a century using
Indeed, with the help of new molecular tools micro- primarily phenotypic characteristics such as bones
biologists have explored a variety of microbial hab- or leaf arrangements as evolutionary guideposts.
and have detected not only new species of bac- Two key concepts have emerged from compara-
itats
RNAs:
new and even molecular sequencing of ribosomal
teria, but genera, families, orders, tive (1)
phyla (Bams 1994; Hugenholtz, 1998). that cells evolved along three major lineages, the
et al., el al.,
Imagine finding a new phylum of plants or animals Bacteria, the Archaea, and the Eukarya, instead of
now and
The prokaryotes
today! challenge for microbiologists is to
between
isolate these organisms, learn alx)ut their basic bi- 1); and (2) that the evolutionary difference
ology, and harness their vast genetic resources for a mouse and an elephant (or between Chlorella and
the benefit of mankind. Trillium, for the more botanically oriented) pales by
between
comparison the evolutionary distance
to
common
any two bacteria you might
A World virtually soil
Natural Picture of the Bacterial
want mention, Pseudomx>nas and Bacillus.
like
to
Great excitement has pervaded the field of mi- The first of these conclusions, that prokaryotic
crobial diversity in recent years because of the life contains two major evolutionary lineages, is
new-found ability of microbiologists to experimen- slowly but surely becoming mainstream thinking
among and even gaining support
:rmme microbiologists,
is
OPP
980919S.
The research of M. Madigan supported by National Science Foundation grant
T. is
'
Department of Microbiology and Center for Systematic Biology, Mailcode 6508, Southern Illinois University, Car-
^
bondale, 62901-6508, U.S.A. [email protected]
Illinois
Ann. Missouri Bot. Card. 87: 3-12. 2000
4 Annals the
of
Garden
Missouri Botanical
(0
0)
o
03
O
o.
^
O
a?
c/)
c5
^
D
i;
o
a;
4;
u>
o
E
o
LL c
3
3
S
(0
>
O
CO
O o
o
c
o
a;
a;
o
e
a
<
^
a
tZ
Volume Number
Madigan
5
87,
1
2000
Extremophilic Bacteria
from macrobiologists as evidenced by the inclusion relationships of prokaryotes (Fig. but can also
1),
of this concept in recent biology textbooks (Raven use phylogenetic information to construct highly
&
Johnson, 1999; Raven 1999). However, specific nucleic acid probes as a means of identi-
et
al.,
the second conclusion, that morphologically quite fying and tracking specific microorganisms in the
A
different plants or animals can be extremely closely environment. natural application of this technol-
related in a molecular evolutionary sense, has been ogy has been to take these tools into various ex-
for many a harder pill to swallow. If one steps back treme environments and probe for the diversity of
The
for a moment and considers that is not the evo- microbial life therein. fallout from these stud-
it
many
lution of the mouse and the elephant, or the alga ies, which historically followed by years more
enrichment and approaches, has
and mo- classical isolation
the flowering plant, as intact entities, that
been an awareness that extreme environments are
lecular sequencing speaks but instead, the evo-
to,
make them "ot a place for "hangers on," but instead are hab-
lutionary history of the cells that up,
it
that flourish with microbial especially pro-
why itats life,
understand bulk
easier the of evolutionar>'
is to
&
(Bams
karyotes 1994; Horikoshi Grant,
et al.,
hange has occurred in the prokaryotic worid; pro-
The
1998; Hugenholtz et al., 1998). rest of this
have some
kar}otes existed for 3.8 billion years,
some
introduce the reader of
^^1^ try to to
P^P^^
while the mouse and the elephant have only very
these organisms and their homes, and discuss what
recently evolved and diverged.
laboratoiy studies of these remarkable prokaryotes
Prokaryotes ruled the Earth for at least 2 billion
^ave revealed our understandmg of the physi-
for
modem
years before the (organelle-containing) eu-
ochemical
limits to Hfe.
And
karyotic cell appears in the fossil record.
metazoans (multi-celled plants and animals) have
ENVIRONMENTS AND EXTREMOPHFLKS
EXTF^EMK
only existed for some half billion years or so. So by
was what and
the time the stage set for botanists
Microbiological examination of extreme environ-
zoologists consider the "evolutionary diversification
many new By
ments has revealed prokaryotes. "ex-
of plants and animals," most of cellular evolution
meant an
treme environment" here, environ-
is
it
mouse
had already occurred. Diversification of the
ment humans would consider extreme or
that
and the elephant, for example, was simply a matter
pH,
uninhabitable: extremes of heat or cold, salin-
ways what
of arranging cells in different to yield
As
and even previously
pressure, radiation.
ity,
appears to the eye to be highly divergent organisms.
mentioned, extreme environments are inhabited by
mouse
But in terms of their evolutionary' history, the
diverse populations of microior*ganuisms, most of
ii*t
iii
and the elephant are virtually identical organisms.
D f
^ y which have evolved to live only in the presence oi
In contrast higher organisms, prokaryotes have
to
^j^^ ^^^reme. These organisms are the extremo-
had more evolutionary time to show great genetic & &
Madigan
(Horikoshi Grant, 1998;
^j^j^^^,,
divergence. However, unlike metazoans, evolution-
&
^997. Madigan 2000; Madigan
j^^^^^ al,
et
ary change prokaryotes not manifest in mor-
in is ^g^y
q^.^^^ Several classes of extremophiles are
For whatever bac-
phological variation. reason(s),
and
recognized microbiology, laboratory cultures
in
teria maintained a ver)^ small size and changed
known
^f representatives of each class are (Table
(compared with metazoans) mor-
relatively in
little
Organisms in each class are denoted by a de-
1).
phology through billions of years of evolutionary
scriptive term, usually a word with Greek or Latin
history. But that is not to say they did not evolve. followed by the combining orm "phile,"
^^^^s f
Molecular sequencing us they have
tells that in- Greek for "loving." Thus there are thermophiles and
deed evolved but that the product of this evolution-
hyperthermophiles (organisms growing at high or
ary change invisible— instead of big changes in
is y^^y high temperatures, respectively),
/;.sjc/iro/>/zi7e.s
size or shape, evolutionary change in the prokary- (organisms that grow best at low temperatures),
otes focused on metabolic diversity and the genetic acidophiles and alkaliphiles (organisms optimally
pH
capacities to explore and eventually colonize every adapted acidic or basic values, respectively),
to
conceivable environment on Earth, including ex- grow under
barophiles (organisms that best pres-
treme environments. Thus we must go to the genes sure), and halophiles (organisms that require NaCl
of the prokaryotes to see their true phylogenetic for growth) (Table Instead of trying to be inclu-
1).
diversification, and with advances in nucleic acid sive here, as literally hundreds of different species
sequencing, this world is now beginning to open up could be included, the organisms listed in Table 1
(Madigan 2000). are the current "record holders" in each of the
et al.,
RNA
The column most
Using comparative ribosomal sequencing tremophile categories. of interest
microbiologists can now not only construct natural in Table 1 is the one labeled "optimum," for here
6 Annals the
of
Garden
Missouri Botanical
Table Classes and examples of extremophiles\
1.
Descriptive
Minimum Optimum Maximum
Extreme term Genus/species
Temperature
113X
High Hyperthemiophile Pyrulobus fumarii 90°C 106°C
OX
w
Lo Psychrophile Pularumonas vacuolata 4°C 12°C
PH
x>w Acidophile Picrophilas oshimae 0.06 0.7 (60T)* 4
I
High Alkaliphile Natronobacterium grego- 8.5 10 (20% NaCl>' 12
ryi
MT41
Pressure Barophile (Mariana 500 atm 700 atm (4X) 1000 atm
Trench)''
saUnarum 15% 25% 32%
(NaCl) Halophile Halobacterium
Salt (saturation)
^ In each category the organism listed is the current "record holder" for requiring a particular exl condition for
growth.
MT41 name
Strain does not yet have a formal genus and species and also a psychrophile.
'• is
oshimae also a thermophile, growing optimally 60X.
P. is at
*
20%
N. gregoryi also an extreme halophile, growing optimally NaCI.
*' is at
modem
becomes
cleeir that these organisms are not mere- isms set the stage for the evolution of
it life
do
ly tolerating their but that they actually best forms,
lot,
punishing indeed most
in their habitats; actually
require their extreme condition(s) in order to repro- at High Temperature
\jyy.
duce
at all.
Extremophiles are of interest to both basic and Although thermophilic bacteria (organisms with
applied biology. In a basic sense, these organisms growth temperature optima between 45^C and 80°C)
hold many interesting biological secrets, such as have been known for over 80 years, hyperthermo-
—
the biochemical limits to macromolecular stability philic bacteria organisms with optima above
—
and the genetic instructions for constructing mac- 80°C have only been recognized more recently
romolecules stable to one or another extreme (Ma- (Stetter, 1996). Following the pioneering work of
&
Thomas
digan Oren, 1999). But in an applied sense, Broc;k in the 1960s and 1970s (reviewed
these organisms have yielded an amazing array of in Brock, 1978), Karl Stetter and co-workers at Re-
enzymes capable of catalyzing specific biochemical gensburg (Germany) have proceeded to isolate over
&
reactions under extreme conditions (Adams Kel- 30 genera (> 70 species) of hyperthermophiles.
ly, 1995). Such enzymes have served as grist for Brock was the first to demonstrate, often using sim-
industry in applications as diverse as laundry de- pie but ingenious field experiments, that bacteria
and were
tergent additives (proteases, lipases) the ge- present in boiling hot springs in Yellowstone
DNA
netic identification of criminals {Taq poly- National Park (Brock, 1978). By contrast, Stetters
merase and use in the polymerase chain group, whose focus has been on isolation and cul-
its
reaction, PCR). ture, has isolated many of the hyperthermophiles
Another important realization that has emerged known today, including Pyrolohus fumarii^ a re-
113X
from the study of extremophiles is that some of markable prokaryote that can grow up to (Ta-
Many
these organisms form the cradle of life itself. ble 1, Fig. 2) (Blochl et al., 1997).
extremophiles, in particular the hyperthermophiles. Thermophilic microorganisms can be isolated
lie close to the "universal ancestor" of all extant from virtually any environment that receives inter-
life on Earth (Fig. Thus, an understanding of mittent heat, such as soil, compost, and the like.
1).
the basic biology of these organisms an oppor- But hyperthermophiles thrive only in very hot and
is
backward
tunity for biologists to "look in time" so constantly hot environments, including hot springs,
to speak, to a period of early life on Earth. This both terrestrial and undersea (hydrothermal vents),
much
exciting realization has fueled research on and active sea mounts, where volcanic lava emit-
is
these organisms in order to understand the nature ted directly onto the sea floor (Stetter, 1999). It is
of primitive life forms, how the first cells "made a also strongly suspected, and some supportive evi-
living" in Earth's early days, and how early organ- dence exists, that hyperthermophiles reside deep
Volume Number
Madigan
7
87,
1
2000
Extremophilic Bacteria
the chimneys, which are often only about 0.5
^
T * f
show
thick, a temperature gradient from about
2°C Because
300*^C inside outside. prokaryotes
to
are so small, microenvironments differing in tem-
chimney
perature exist across the wall leading to
ideal habitats for various species of heat-loving
bacteria.
Using nucleic acid probe technology several
morphological types of bacteria have been detected
chimney (Harmsen
in hydrothermal vent walls et
1997), suggesting that these compact thermal
al.,
may many
gradients contain different microbial
populations in addition to those already isolated.
And my
for botanical friends reading this paper,
I
would be remiss did not point out that P.famarii
if I
and M, kandleri are good examples of primary pro-
Figure 2. Transmission (^Icclron mirrogra[)h of a cell
Pyrolohus fHiruird, llic riiosi tlieniio[)liili(; of all known ducers totally divorced from sunlight, a capacity
i}{
fnmani grows
living organisms. PyrolobiLs opiirtially at widespread in the microbial world. Besides growing
\{Y}\] and an grow up to Kv<^n higher leniper- R
at 1.5'^C.
< I almost unbelievably high temperatures, fu-
at
alures are lolcratetl hut <lo not support growth. Mi<Tograph
and M. capable
marii kandleri are also autotrophs,
courtesy of HeinhanI Karhf^I, liniversilat R(*genshurg.
me-
of growing in a simple anaerobic mineral salts
(Hum CO2 and
supplied with H^; neither sunlight
nor a key product of photosynthesis, O2, required
is
within the earth, Hving a buried existence and re- for either organism. Indeed, has been hypothe-
it
lying on geoihermal heat for their metabolic activ- sized that long before the process of photosynthesis
was
and reproduction 1999). evolved, anaerobic H^-based chemolithotrophy
ities (Stetter,
The most extreme of known hyperthermophiles, the major means by which new organic material
those with temperature optima above lOO^C, have was synthesized on Earth (Madigan et al., 2000).
conu! from submarine hydrothermal vents (Stetter, For an organism to grow at high temperatures.
1996, 1999), and examples include fumarii especially as high as those of the hyperthermo-
P.
(Bl(k:hl et al., 1997, and Fig. 2) and the methano- philes discussed here, all cellular components, in-
gen Methanopyrus kandleri (Kurr el al., 1991). Both eluding proteins, nucleic acids, and lipids, must be
& &
of these amazing prf)karyotes are members of the heat stable (Adams Kelly, 1995; Ladenstein
&
Archaea and are chcmolilhotrophs (organ- Antranikian, 1998; Wiegel Adams, 1998; van de
(Fig.
1)
The
isms that use inorganic com[)ounds as energy Vossenberg et al., 1998a). thermostability of
sources), using molecular hydrogen, H^, as their enzymes from various hyperthermophiles, referred
electron donor (energy source), reducing either to as extremozynieSj has been documented, and
NOi fumarii) or CO^ {M. kandleri) as electron some have been found to remain active up to 140°C
(P.
&
(Adams The
acceptors grow by anat^robic respiration (Madi- Kelly, 1995). structural features that
to
gan 2000; 1999). Besides requiring dictate thermal stability in proteins are not well
et al., Sti^ttcr,
number
substantial heat for growth, these bacteria can sur- understood, but a small of noncovalent fea-
vive temperatures substantially above their upper tures seem characteristic of thermostable proteins.
growth temp<'ratun» limits, making a conventional These include a highly apolar core, which appar-
121^) makes and
autoclave regimen (15 min. at insufficient ently the inside of the protein "sticky"
for sterilizing cultures of either species! thus more resistant to unfolding, a small surface-
Both fumarii and M. kandleri originated from to-volume which confers a compact form on
ratio,
P,
hydrothermal vent chimneys (Blochl 1997; the protein, a reduction in glycine content that
et al.,
StettiT, 1999). These cire precipitated iron mineral tends to remove options for flexibility and thus in-
and
deposits that form as extremely hot water (up to troduce rigidity to the molecule, extensive ionic
400°C) containing various minerals emerges from bonding across the protein's surface that helps the
deep-sea h)(lroth(*rmal vents (note that although compacted protein resist unfolding at high temper-
&
water superheated, does not boil because ature (Ladenstein Anthranikian, 1998). In ad-
this
is
il
of the hydrostatic pressure of the water column, dition to these intrinsic stability factors, special
usually 2000-3000 m, that overlies these vents). proteins called chaperonins are synthesized by hy-
Althoiigh the water that rges too hot for perthermophiles. Chaperonins function to bind heat
is life,
—
Annals
8 of the
Garden
Missouri Botanical
denatured proteins and refold them into their active the opposing hydrophobic residues from each layer
The
form. thermosome a type of chaperonin that of the brane together (van de Vossenberg et
is al.,
among
widespread hyperthermophiles capable of 1998a). This forms a lipid monolayer instead of a
is
R
growth above 100°C, like fumarii and M. han- bilayer, and prevents the membrane from melting
died (Stetter, 1999). at high temperature. Although the precise chemis-
DNA
Several factors may combine to prevent try of lipid monolayer membranes can vary some-
common
from melting in hyperthermophiles. However, the what from species to species, they are
among
two most important features appear to be the en- hyperthermophiles and are likely an impor-
DNA
zyme reverse gyrase, which catalyzes the pas- tant evolutionary response to life at high tempera-
DNA
itive supercoiling of closed circular (by con- ture.
DNA
nonhypcrthermophiles
contain gyrase,
trast,
DNA
an enzyme
that supercoils in a negative twist- l^^ Temperatures
Lij,^ ^^y
DNA
ed fashion), and various types of binding pro-
&
How
teins, Including histone-like proteins (Madigan about life at the other end of the thermom-
&
Oren, 1999; Pereira Reeve, 1998). For various eter? Cold environments on Earth are actually
much common
physicochemical reasons, positively supercoiled more than hot ones. For e*xample,
DNA
is more resistant to thermal denaturation than the oceans, which make up over one half the
DNA. And
is negatively supercoiled the fact that Earth s surface, maintain an average temperature of
And
reverse gyrase seems to be the only protein thus far about 2'^C. vast land masses are intermittently
found universally among hyperthermophiles (re- cold and in some cases permanently cold, or even
&
gardless of their metabolic pattern) (Madigan frozen. However, cold temperatures are no barrier
Oren, 1999) points to an important role for in the to microbial as various microorganisms flourish
life,
it
&
DNA.
heat stability of in cold environments, even in ice (Horikoshi
DNA &
Several hyperthermophiles contain binding Grant, 1998; Madigan Marrs, 1997). Many mi-
proteins that appear to play a role in maintaining croorganisms have been isolated capable of growth
DNA
in a double-stranded form at high tempera- at refrigerator temperatures (4—8X). These are usu-
Some
meaning
ture. of these proteins are stnacturally related ally psychrotolerant, that although they
to the core histones of eukaryotic cells and function capable of growth in the cold, they grow better at
DNA
wind and compact warmer 25—
to the into rmcleosome-like temperatures, usually 35°C. True psy-
&
structures (Pereira Reeve, 1998). Others have no chrophiles, defined as microorganisms that grow best
structural relationship to histones but when bound at 15°C or lower, are usually only present in per-
DNA
to alter its structure in such a way as to sig- manently cold environments like the Arctic, or in
& &
nificantly raise its melting temperature (Madigan particular, the Antarctic (Horikoshi Grant, 1998).
A
Oren, 1999). likely that the combination of variety of microorganisms including algae and
It is
DNA
positive supercoiling of along with proteins diatoms have been found in Antarctic sea ice
DNA
much
that prevent melting is a major solution to the ocean water that remains frozen for of the
DNA
maintenance and integrity of in hyperther- year. Sea ice the habitat for one well-character-
is
mophiles. ized bacterium, Polaromonas vacuolata^ the genus
Heat can membrane As name
also affect stability. all indicating its affinity for cold temperatures
biologists know, in organisms living at moderate (Irgens et al., 1996). Polaromonas vacuolata grows
membranes
temperatures cell are constructed along optimally at 4°C and finds temperatures above 12°C
warm
the typical "lipid bilayer" model: hydrophobic res- too for growth (Table Other psychrophiles
1).
idues (fatty acids) inside oppose each other and are known, but because some of them appear to be
retain an affinity for one another while hydrophilic very sensitive to warming, great care must be taken
residues (such as glycerol phosphate) lie at the sur- in their isolation and culture to prevent killing them
face of the environment and the cytoplasm, respec- off at temperatures as low as room temperature,
An
tively, maintaining contact with the aqueous phase. understanding of the biochemistry and mo-
If one applies sufficient heat to such a membrane lecular biology of psychrophilic bacteria in a
is
membrane much
hitecture the two leaflets of the will earlier stage than that of the hyperthermo-
pull apart, leading to membrane damage and cy- philes. From what known about the biochemistry
is
toplasmic leakage. To prevent this from occurring of psychrophiles, appears that their proteins func-
it
at very high temperatures, hyperthennophiles have tion optimally at low temperatures because they are
membrane
evolved a novel structure. Instead of constructed in such a way so as maximize
to flex-
rmmg
brane
fo a as a lipid bilayer, as just dis- ibility; this is essentially the opposite strategy- from
some
cussed, hyperthennophiles chemically bond that of hyperthermophiles (see Moreover,
earlier).
Volume Number
Madigan
9
87,
1
2000
Extremophilic Bacteria
pH
proteins frf)m psychrophiles are typically more po- (< 1) solfatara in Italy, and the organism has
lar and less hydrophobic than proteins from hy- clearly evolved to require these highly acidic con-
perthermophiles, a fact that undoubtedly also as- ditions for very existence.
its
sists in their relative flexibility. Interestingly, however, acid-loving extremo-
Besides keeping their enzymes functional, psy- philes, even those as extreme as oshimae, cannot
P.
chrophiles have other biological problems to con- tolerate great acidity inside their cells, where
it
mem- DNA.
tend with, transport of nutrients across the would destroy such important molecules as
brane being chief among them. However, just as They thus survive by keeping the acid out. The
pH pH
margarine, with higher content of unsaturated internal of oshimae about and
its P, is 5, is
it
membrane
fats, can stay softer than butter at cold tempera- the cytoplasmic of this organism that
tures, psychrophiles regulate the chemical compo- keeps protons from passively entering the cell.
R
membrane
sition of their membranes, including in particular However, studies of the oshimae have
the length and degree of unsaturation of fatty acids, shown that can only retain its integrity in acidic
it
pH R
to keep them sufficiently fluid to allow for transport solutions; above an external of about 4 the
membrane
processes, even temperatures below freezing oshimae spontaneously disintegrates.
at
&
(Horikoshi Grant, 1998). Applications of en- Major unanswered questions concerning the metab-
R
zymes from psychrophiles include the cold food in- olism of oshimae and other extreme acidophiles
how
dustry, where enzymes that work at refrigerator tem- concern they generate a proton motive force
peratures are sometimes desirable, as well as during respiration and related issues of bioenerget-
membrane-mediated
producers of cold-water laundry detergents (see ics involving proton translo-
more on this below). cation (van de Vossenberg et 1998b).
al.,
Various acid-tolerant enzymes from acidophiles,
Bath primarily ones located on the cell surface or ones
hy Acid or
Life S()D\
in
have
excreted from the cell into the acidic milieu,
Many
extremophiles have evolved to grow best been studied and potential industrial applications
extremes of pH: these are the acidophiles and These are primarily as animal-feed sup-
at identifie<l.
&
the alkaliphiles (Horikoshi Grant, 1998). Al- plements where the enzymes function to break
pH
down more
though extremely acidic or alkaline (below 3 or inexpensive grains nutritionally ben-
to
pH
above 10) habitats are rare on earth, in such eficial forms directly in the animal's stomach. Such
environments one can find a variety of microorgan- enzymes have been widely used in the poultry in-
isms thriving in chemistry the equivalent of battery dustry and have been shown to reduce feed costs
acid or soda-lime. Highly acidic environments can and the time necessary to get birds to market.
result naturally from geochemical activities, such Extreme alkaliphiles live in soils laden with soda
pH
as from the oxidation of SO2 and H^S produced in (natron) or in soda lakes where the can rise to
N
hydrothermal vents and hot springs, and from the as high as 12. atronobacterium gregoryi (Table
1),
metabolic activities of certain acidophiles them- for example, was isolated from Lake Magadi, a soda
selves. For example, the iron sulfide-oxidizing bac- lake located in the Rift Valley of Africa; gregoryi
A^.
pH
terium Thiohacillns ferrooxidans can generate acid grows optimally at a of about 10 (Table (Hor-
1)
&
by oxidizing Fe-^ to Fe^^, the latter of which pre- ikoshi Grant, 1998). In the opposite scenario
—
+
cipitates out as Fe(OH)j (Fe^"^ 3H;^0 Fe(OH)^ from the acidophiles, alkaliphiles have to contend
>
+ HS +
3H'), or by oxidizing to SO^'^ (HS" 2O2 with the problems associated with high pH. Above
—
SO/" + H). pH 8 RNA,
Thiohacillns ferrooxidans is par- a of or so, certain biomolecules, notably
>
ticularly active in surface coal mining operations break down. Consequently, like acidophiles, alka-
where exposure to oxygen of pyrite (FeS2) in the liphiles must maintain their cytopl nearer to
coal seam triggers acid production from the meta- neutrality than their environment. Nevertheless,
mem-
bolic activities of this and related bacteria. Runoff any proteins found in the cell wall or in the
pH
make
from these habitats can often have a of less than brane that contact with the environment must
many
2, fueling conditions for further acidophile activity. be stable to high pH. Indeed, such enzymes
The most acidophilic of bacteria known thus have been studied and a number have found in-
all
pH
whose optimum
far Picrophiliis oshimae^ for dustrial applications, especially in the laundry de-
is
"enzyme
growth is just 0.7 (Schleper et al., 1995) (Table 1). tergent industry. Detergents that are en-
Picrophilus oshimae also a thermophile (temper- riched" contain proteases and lipases (enzymes that
is
ature optimum, 60°C) so this organism must be sta- degrade proteins or fats, respectively, in clothing
pH
and
ble to both hot acidic conditions. Cultures of stains) that function at the high of soapy solu-
&
oshimae were isolated from an extremely acidic tions (Horikoshi Grant, 1998). In addition, alkali-
R.
10 Annals the
of
Garden
Missouri Botanical
active enzymes from thermophiles and psychro- molyte, the archaeon Haloharterium (Tahle ron-
1)
philes have been discovered and commercialized to centrates large amounts of potassium (K^, as KCl)
KCl
better target detergent additives to hot water or cold from its environment. Dissolv(Hl in the cyto-
water applications, respectively. plasm of Halobacterium cells is present at a con-
Besides keeping their cytoplasm near neutrality, centralion etjual to or slightly above that of the dis-
alkaliphiles have other biological problems to con- solved NaCl outside, and in this way c(41s maintain
tend with. For example, consider the problem of the tendency for water to enter and then^by prevent
—
membrane-mediated bioenergetics protons ex- dehydration. As would be expected from such a
traded to the external surface of the membrane en- salty cytoplasm, enzymes that function inside of
ter a sea of hydroxyl ions. Nevertheless, bio(;hem- cells of Ilalohacterium have evolved to require this
problem have shown dose K^
ical studies of this that a large of for catalytic activity, fiy contrast,
membrane
proton motive force is indeed formed by extreme or cell wall-positioned prot<nns in Hal-
alkaliphiles and drives some of the energy-requir- obarterium require Na^ and are typically stable
&
ing reactions in the cell, such as motility and trans- only in the presence of high Na^ (Madigan Orcn,
ATP
Sometimes an
port. in synthesis, ion gradient 1999).
of Na^, rather than H^, drives this key bioenergetic F]xtreme halophiles are sourc(*s of a vari(»ty of
&
process in extreme alkaliphiles (Horikoshi Grant, biomolecules that can function under salty condi-
when
1998). This is probably not surprising one tions. Applications of salt-active enzymes include
many down
considers that (but not extreme alkali- those that can break viscous materials pres-
all)
phlles are also extreme halophiles (see below), re- ent in oil wells (oil is often found in geographic
pH
quiring high salt as well as high for metabolism strata that contain salt) as well as enzymes tliat can
and cany
reproduction. out desirable transformations in highly salted
some produce
foods. In addition, halophiles that
organic compatible solutes have been commercial-
BkINE
LiFF A
IN
ized for the production of these solutes as skin rare
&
Another remarkable group of extremophiles are supplements (Madigan Orcn, 1999).
—
the halophiles organisms adapted to grow best in
salty solutions (Oren, 1999; Ventosa et 1998).
al., ExTUKMOIMULls
OlllFR
And
for extreme halophiles like Halobacterium, a
25%
"salty solution" means anywhere from NaCl Extrt^mophilic microorganisms adapti^d high
to
up to saturation (32% NaCl) (Table Halophilic pressure or which show no deleterious t^huts from
1).
microorganisms abound in hypersaline lakes such exposure to high levels of radiation are also known,
Dead
as the Sea, the Great Salt Lake, and solar salt Barophiles are microorganisms thai grow best under
evaporation ponds. Such lakes are often colored red pressure greater than atmosphere. Extreme bar-
1
by the dense microbial communities of pigmented ophiles are the most interesting in this regard as
halophiles such as Halobacterium (Javor, 1989). they actually require pressure, and in some cases.
Other habitats for halophilic microorganisms in- extreme pressure, for growth (Table Strain
1).
elude highly salted foods, saline soils, and under- MT41, for example, a bacterium isolated from ma-
ground salt deposits. To date, a very large number rine sediments in the Mariana Trench near the Phil-
of halophilic bacteria have been grown in culture ippines (a depth of greater than 10,000 m), rccjuires
including members of all domains of life, including at letLst 500 atmospheres of pressun* in order to
the Eukarya (Kamekura, 1998). However, the ar- grow and grows optimally al 700 atmospheres (and
MT41
chaeal halophiles as exemplified by Halobacterium. at a temperature of 4°C because strain also
is
species remain the most halophilic organisms a psychrophile). Because laboratory culture of ex-
k nown. treme barophiles rather comparatively
is difficult,
known
Halophiles are able to live in salty conditions by about thtur important biomolecules.
little is
preventing dehydration of their cytoplasm. They do However, although probably all macromolecules in
this by either producing large amounts of an inter- extreme barophiles need to be biochemically tai-
nal organic solute or by concentrating an organic lored to high pressure to some extent, experiments
or inorganic solute from their environment (Hori- with moderately barophilic bacteria, some of which
&
koshi Grant, 1998; Oren, 1999). The term "com- be grown without pressure, have pointed nu-
to
mcm-
patible solutes" is often used to describe organic trient transport proteins in the cytoplasmic
osmolytes, of which there are several types, but not brane as key cell components requiring structural
&
all halophiles employ such solutes (Madigan modifications in order to function high pressure
at
&
Oren, 1999; Oren, 1999). For example, as os- (Horikoshi Grant, 1998).
its
Volume Number Madigan
87, 11
1
2000
Extremophilic Bacteria
The bacterium Deinococcus radiodurans is an otherwise, will yield the data needed to confirm
microorganism (Mur-
ingly radiation-resistant this,
ray, 1992). This remarkable organism can survive It may indeed be humbling to many biologists to
30,000 Grays of ionizing radiation, sufficient to think that prokaryotes dominate living diversity,
lit-
erally shatter chromosome into hundreds of But within the rich genetic resources of the pro-
its
pieces (by contrast, a human can be killed by ex- kaiyotes undoubtedly lies more benefit for human-
A DNA we
posure as as 5 Grays). powerful kind than will extract from any other group of
to little
and
organisms. Antibiotics, fermentation, biotech-
repair machinery exists in cells of D. radiodurans
The
chromosome back nology are only the beginning. best is yet to
that able to piece the shattered
is
come.
and Because
together yield viable cells. of re-
its
markable Deinococcus has
radiation resistance,
Literature Cited
been proposed as a cleanup agent for the biore-
&
mediation of toxic materials in contaminated soils Adams, M. W. W. R. M. Kelly 1995. Enzymes from
microorganisms extreme environments. Chemieal and
that are also radioactive from the leakage of radio- in
News 32^2.
Engineering
73:
active materials; these conditions exist primarily at
&
Bams, S. M., R. E. Fundyga, M. W. Jeffries N. K. Pace.
nuclear weapons production
sites.
1994. Remarkable archaeal diversity detected in a Yel-
lowstone National Park hot spring environment. Proc.
1609-1613.
Acad. U.S.A. 91:
Natl. Sci.
the Evolution of
Extfu:mophi[.es Life
in
Blochl, E., R. Rachel, S. Bnrggraf, D. Hafenbradl, H. W.
&
Jannasch K. 0. 1997. Pyrolobus fumarii^ gen.
Stetler.
A
focus of research on extremophiles has cen-
and sp. nov. represents a novel group of archaea, ex-
As
tered on the hyperthermophiles. discussed ear- tending the upper temperature for life to 113°C. Extre-
mophiles 14^21.
there good reason to believe that at least 1:
lier, is
u ^u u J 1* Brock, D. 1978. Thermophilic Microorganisms and Life
u-i »• T.
some hyperthermophiles have evol1 ved rel1 ativel1 y ^ J^ m C
lit-
,'
, . New
nigh temperatures. J^pnnger, i
^^ Yorlc.
r
.
from their ancestors present on eart1h over 3.5 &
tie
Harmsen, H. M., D. Prieur C. Jeanthon. 1997. Dis-
J.
billion years ago (Figs. 1, 2). If true, an understand- tribution of mit^roorganisms in deep-sea hydrothermal
ing of the biology of hyperthermophiles may yield vent chimneys investigated by whole-cell hybridization
and enrichment culture of thermophilic subpopulations.
a glimpse of what was like eons ago. In this
life
Appl. Environm. Microbiol. 63: 2876-2883.
connection the genomes of several hyperthermo-
&
Horikoshi, K. W. D. Grant. 1998. Extremophiles—Mi-
&
have been sequenced (Madigan Oren, New
philes crohial Life Extreme Environments. Wiley, York.
in
&
1999), and the large number of genes they contain Hugenholtz, P., C. Pitulle, K. L. Hershberger N. R.
Pace. 1998. Novel division level bacterial diversity in
that lack counterparts in other organisms suggests
366-373.
a Yellowstone hot spring. Bacteriol. 180:
J.
that their biological secrets have at this point only &
j^^^^^^ j^ l., Gosink' T. Staley. 1996. Polaro-
J. J. J.
As
been partially revealed. living in boiling water ma-
if mofuus vacaolaia gen. nov. sp. nov., a psychrophilic,
enough, just imagine what other tricks hy- rine, gas vacuolate bacterium from Antarctica. Int.
isn't J.
822-826.
Syst. Bacteriol. 46:
—
perthermophiles might be able perform!
to
1989. Hypersaline Environments Microbi-
Javor, B.
J.
As
previously mentioned, the excitement in mi-
ology and Biogeochemistry. Springer- Verlag, Berlin,
crobial diversity these days comes from the fact that Kamekura, M. 1998. Diversity of extremely halophilic
the evolutionary history of the prokaryotes can now bacteria. Extremophiles 2: 289—295.
be experimentally determined. Microbiologists no
'^T' ^J:^;
&
""t'^II^"..^^^^^^^
A. Trincone, K. Kristjansson K. 0. Stetter. 1991.
J.
longer have propose bacterial phylogenies based
to
Methanopynis kandleri, gen. and sp. nov. represents a
on speculation or "educated guesses" of what type
novel group of hyperthermophilic methanogens, growing
nrC. 239-247.
of microbe likely preceded another; the phylogenies at Arch. Microbiol. 156:
1
R &
l^denstein, G.Antranikian. 1998. Proteins from
themselves are etched in the sequences of mole-
perlhcrmophiles: Stability and enzymatic catalysis close
and one has do read them. Moreover,
cules, all to is
Advances Biochem. En-
the boiling point of water.
to
the application of molecular phylogenetic methods
38—85.
gin./Biotechnol. 61:
&
to natural environments (Bams et al., 1994; Hu- Madigan, M. T. B. L. Marrs. 1997. Extremophiles. Sci.
Amer. 276: 82-87.
genholtz 1998) has given us the exciting
et al.,
&
A. Oren. 1999. Thermophilic and halophilic
news that the diversity of the microbial world is
— 265—269.
extremophiles. Curr. Opin. Microbiol. 2:
enormous indeed beyond our wildest expec- &
it is M. Martinko Parker. 2000. Brock Biology
, J. J.
tations. Thus, in the final analysis bacterial diver- of Microorganisms, 9th ed. Prentice Hall, Upper Saddle
New
River, Jersey.
sity will likely dwarf that of all of the rest of biology,
Murray, R. G. E. 1992. fhe family Deinococcaceae. Pp.
perhaps by several orders of magnitude. But only
3732-3744
in A. Balows, H. G. M. Dworkin,
Triipier,
continued and expanded research into the diversity &
W. Harder K-H. Schleifer (editors), The Prokaryotes,
A
of microbial life in all environments, extreme and 2nd ed., Handbook on the Biology of Bacteria: Eco-
Annals
12 the
of
Garden
Missouri Botanical
and
physiology, Isolalion, Identification, Applications. 1999. Volcanoes, hydrothermal venting, the
.
&
New
Springer- Verlag, York. origin of In Marti G. Ernest (editors), Vol-
lif*\ J. J.
Orcn, A. (editor). 1999. Microbiology and Biogeoohenustry canoes an(\ the Environment. Cambridge Univ. Press,
CRC
of Hypersaline Environments. Press, Bo<a Raton, ('ambridge, England (in press).
&
mod-
Florida. Ventosa, A., Nielo A. Oren. 1998. Biology of
J. J.
& &
Pereira, S. L. N. Reeve. 1998. Hislones and nucle- erately halophilic aerobic bacteria. Microbiol. Molec.
J.
A
osomes in archaea and eukarya: comparative analy- Biol. Rev. 62: 504-544.
&
Extremophiles 141-148. Vossenberg, C. M. van de, A. M. Driessen W.
sis, 2: L.
J. J.
&
R
Raven, H. G. B. Johnson. 1999. Biology, 5th ed. N. Konings. 199oa. The essence of being extremophilic:
WCB/McGraw-Hill, Dubuque, Iowa. The role of the unique archael membrane Extre-
li[)ids.
&
R. F. Evert S. E. Eichhorn. 1999. Biology of mophiles 2: 163-170.
,
&
New
Plants, 6th ed. W, Freeman, York. W. Zillig W. N. Konings. 1998b. Bio-
II.
,
,
C, membrane
Scldeper, G. Puhler, Holz, A. Gamhacorta. D. Ja- energctics and cytoplasmic stability of the
I.
&
nekovic, U. Santarius, H-P. Klenk W. Zillig. 1995. extremely acido[)lulic, thermophilic archaeon, Picrophi-
67-74.
Picrophilus gen. nov., fani. nov., a novel aerobic hetero- lus oshimac. Extremo[)hilcs 2:
&
trophic, thermoacidophilic genus and family composing Wiegel, M. W. W. Adams 1998. Thermo-
(Editors).
—J.
archaea ea{)able of growth around j)H 0. Bacteriol. philes The Keys to Molecular Evolution and the Ori-
J.
177: 7050-7059. gin Fife? Taylor and Francis, London.
(tf
Stetter, K. 0. 1996. Hyperthennophilic prokaryotes. Woese, C. R. 1987. Bacterial evolution. Microbiol. Rev.
FEMS
149-158. 221-271.
Microbiol. Rev. 18: 51: