Extreme Environments and Extremophiles

From an ecological view, the whole Earth system encompasses numerous niches with unique environmental settings and each of them has its own biota that consists of functional related consortia of organism. For not only survival but also prosperous growth and reproduction, moderate environments of comparatively less evolutionary stress are preferred by vast majority of life.

The criteria for moderate conditions are somehow anthropocentric, referred to those adequate physical and chemical property that are close to the range favored by human beings: pH value around neutral, temperatures between 20 to 40°C, air pressure about 1 atm, with sufficient water activity (better higher than 0.7) and nutrients accessibility, suitable concentration of salts (between normal fresh water and sea water), without excessive exposure to radiation (compared with the average amount that is received on the surface of the Earth), and lower levels of heavy metal or toxic compounds (such as organic solvents). In contrast, those harsh environments which are featured by unusual physicochemical conditions, such as high acidity and alkalinity, extreme temperatures, high pressure or vacuum state, low water activity, low amount of nutrition, high salinity, intensive radiation, and places with high concentration of heavy metal or toxic substance, are defined as extreme environments (Rothschild and Mancinelli, 2001; Wilson and Brimble, 2009).

Survival and reproduction are the most important goals to achieve for all kinds of life. In order to adapt to the dynamic material surroundings, organisms are usually capable of tolerating a certain degree of physical and chemical fluctuations in environments. However, a state of tolerating is different from optimal growth; thus, organisms which can survive in extreme environments are sometimes just extremotolerant instead of extremophilicɡthe latter describes the characteristics that an organism has its optimal growth under extreme conditions, and the organism per se is called an extremophile

(Macelroy, 1974; Kristjansson and Hreggvidsson, 1995; Wilson and Brimble, 2009). Accordingly, extremophiles thriving in environments with multiple harsh properties are grouped as “polyextremophiles”.

Increasing interest and efforts in researches relevant to extreme environments and organisms started around the 1950’s. Biotopes such as deep sea,

hypersaline environments, hot springs, deserts, ice, permafrost and atmosphere are the most focused regions for studying and all of them have various

combinations of geochemical backgrounds. For instance, general features of deep sea environment are low temperature around 1 to 2°C, anoxic and lack of photosynthesis. However, at some specific locations, when hydrothermal vents or ancient evaporite beddings exist, environmental conditions would then be a mixture of its original geochemical context plus individual variables:

hydrothermal vents heat up surrounding sea water and provide an additional chemical source, and dissolution of evaporite beddings would greatly increase

the local salinity. The same is true for other locales: environmental conditions are results of interplays of regional backgrounds and local variables.

In the conventional classification of extremophiles, the main categories are divided based on physical and chemical conditions optimal for growth. Those commonly mentioned are thermophiles (high-temperature-loving),

psychrophiles (low-temperature-loving), acidophiles (low-pH-loving), alkaliphiles (high-pH-loving), halophiles (high-salinity-loving), xerophiles (low-water-activity-loving) and barophiles (pressure-loving, also called piezophiles). In some cases, those being able to resist particular stringent environmental factors are included into extremophiles, such as radioresistant and endolithic (living in cracks or pores of rocks or minerals) organisms, although this is somehow incongruent with the definition of extremophiles.

To view extremophiles as a whole, interest of research are of three categories:

(1) evolution and earth history, (2) astrobiology and extraterrestrial trace of life and (3) biotechnological applications (Wilson and Brimble, 2009). From the formation of the planet Earth to the existence of life, the

proto-environments are regarded to be analogous to some current extreme biotopes, which are generally anaerobic with extreme high temperature, low organic matters, and sparse nutrients. Through the expansion of knowledge on extreme biogeochemical systems, mechanisms of evolution, and biodiversity, the paleoclimatic change along the geological time could be better deduced. In

a broader scale, the current search for extraterrestrial life within the solar system is supported by knowledge from studying environment analogues on the Earth. In practical aspects, extremozymes (Hough and Danson, 1999) produced by extremophiles with distinct functions have tremendous potential for the biotechnology industry, bioremediation, chemistry and pharmacyɡ the well-known Taq polymerase isolated from Thermus aquaticus (Brock and Freeze, 1969) used in polymerase chain reaction has served as a remarkable example.

1.1.2 The Underexplored Microbial Extreme Ecosystems

Microbial ecosystems, compared with other ecosystems of macro-organisms, are still poorly understood. Microscopic size made them inconspicuous for human eyes, therefore receiving less than sufficient attention. Furthermore, their almost-universal existence, difficulties in cultivation and technical constraints (although great progression has been made molecularly and bioinformatically, abundance and diversity of microorganism are not

completely assessable within a short period of time) have made the discovery and in-depth understanding of microorganisms in a slower process than their significance deserved. The same situation occurs in the exploration of microbial extreme ecosystems.

Extreme biotopes, located only in limited geographic regions with unusual physical and chemical characteristics, usually harbor a significantly lower

amount of cells compared to normal niches and thus make it more laborious to collect sufficient amount of samples (Ferrer et al., 2009) for adequate analyses.

In the study of extreme ecosystems, prokaryotic organisms have long been the major target of interest because of their higher abundance and diversity over other multicellular or eukaryotic life in extreme environments. Prokaryotic microorganisms, which consist of members from bacteria and archaea

domains, are thought to be the most wide-spread form of life on Earth and the number of prokaryotes was about 10³⁰ cells in total (Turnbaugh and Gordon, 2008). As inhabitants and decomposers in ecosystems, their remarkable physiological functions are closely connected to the biogeochemical cycles of the Earth.

As progress of microbiology started from traditional culture-based methods into a culture-independent era and by the aid of extensive global explorations, rapid analysis and large amount of sequence data also revealed the

underestimation of prokaryotic diversity in extreme environments (Hugenholtz et al., 1998; Reysenbach et al., 2000; Takai et al., 2001b; Huber et al., 2002b;

Satyanarayana et al., 2005; Sogin et al., 2006; Yim et al., 2006; Huber et al., 2007; Wilson et al., 2008; Kato et al., 2011). Cultivation had identified 10 or 12 divisions in Bacteria domain and 2 or 3 divisions in Archaea domain (Woese, 1987). However, more than 40 divisions in bacteria (Pace, 1997) and more than 12 divisions in archaea (DeLong and Pace, 2001) are now

discovered through culture-independent approaches and the total number of

genospecies approximates 10⁶ to 10⁸ (Sleator et al., 2008) with 1316 complete prokaryotic genomes available in online databases (updated in October 2012).

According to statistics, in recent prokaryotic sequencing projects only c.a. 4%

of them belong to extremophiles (Ferrer et al., 2007), which strongly indicates that there is still room and needs in the field of extreme ecosystem

explorations.