By Kamel Ghaddar (K.G.)
external image Lake-Camargue-490x225.jpg(2)


halophile archaea.jpeg(8) (JLev)


external image halophiles_191203.jpg (TM)

Table of Contents
1.Classification/Diagnostic characteristics
2. Relationship to humans
3. Habitat and niche
4. Predator avoidance
5. Nutrient acquisition
6.Reproduction and life cycle
7.Growth and development
8.Integument
9.Movement
10.Sensing the environment
11.Gas exchange
12.Waste removal
13.Environmental physiology (temperature, water and salt regulation)
14.Internal circulation
15.Chemical control (i.e. endocrine system)
16. Sources






1.Classification/Diagnostic characteristics
Archaea are a separate domain from Bacteria and Eukarya. Biologists separated them after sequencing archaeal genomes and finding 1,738 genes with many that were unlike those found in the other domains. They are single celled prokaryotes, like bacteria, but their metabolism and other processes are so different that they may have separated into distinct evolutionary lineages very early. Prokaryotes do not have membrane bound nuclei and typically do not have membrane-bound internal compartments either, so they do not have mitochondria, golgi apparati, or other membrane bound organelles. Genetic studies indicate that all three life domains may have had a single common ancestor at the beginning. There is evidence to show Eukaryotes, which are complex cells, are like a fusion of archaea and bacteria: they have some genes that more closely resemble archaea and some that resemble bacteria.
Archaea are divided into four groups: Crenarchaeota and Euryarchaeota and the lesser known Korarchaeota and Nanoarchaeota.
Halophiles belong to the group Euryarchaeota and are, as their name implies, salt-lovers. They live in very salty environments and those that live in areas with very extreme salinity are known as extreme halophiles.
Halophiles, like all archaea are single celled prokaryotes. They contain pink carotenoid pigments, causing the waters they occupy to turn redish-pinkish and making their presence in the water more obvious.
Halopiles, like many archaea/prokaryotes, are so small they can only be seen with advanced microscopes. It is mostly because of their small size that little is known archaea. Some archaea have not even been seen with microscopes but are discovered from samples of DNA found in the environment.
But species of archae whose morphologies (shapes) are known include cocci (spherical), bacilli (rod shaped), and even triangular and square-shaped species.
halobacterium.jpeg
Halobacterium salinarium, an example of Halophile Archaea
(3) (SJ)





2. Relationship to humans
Most humans probably share space with archaea at some point in the day, but do not notice them from their extremely small size. Humans are only likely to be near halophiles, which live in salted areas, at seas and oceans. Halophiles are probably an annoyance to workers of commercial seawater evaporating ponds, such as in San Francisco Bay, home to extreme halophiles. Because Halophiles' carotenoid pigments cause the ponds to appear a rich red color rather than clear, it may make it harder for workers to check on the pond water quality.

Halophiles are used to clean places with pollution and help clean polluted water with high concentrations of salt. They also help ferment( turn carbohydrates to alcohol or carbon dioxide to acid) food such as soy sauce and other sauces that are used for fish and fish that has rubbed with salt.(11)(NC)

Halophilic archaea are in the preliminary stages of being used for industrial production of certain chemicals. Halophilic Archaeas unique ability to endure extremely high concentrations of salt makes them an ideal organism to work with when bacterias and other organisms are incapable of surviving the environment The proteins and other chemicals produced by halophilic archaea are uniquely resistant to high salinity solutions and will not denature because of this. (14) (DA)

Actinidic archaea have been related to the pathogenesis of schizophrenia, malignancy, metabolic syndrome x, autoimmune disease and neuronal degeneration. These bacteria can use cholestreol as a energy source. Archaeal cholesterol catabolism can generate porphyrins which in turn can cause the above diseases. (15)(BS)





3. Habitat and niche
Archaea are well known for thriving in extreme habitats in which other organisms could not even survive. Extremophiles (type of archaea that can live in extreme areas) can live in environments such as those with very high salinity (salt content), low oxygen levels, extreme temperatures, and very high or low pH. Halophiles live in salty oceans and seas, while extreme halophiles live in areas of extreme saltiness, such as the dead sea. Few organisms can survive in these areas because their cells would literally shrivel up from their water flowing out by diffusion into the highly hypertonic (more salty outside of cells) environment. Extreme halophiles have been found in areas with 11.5 pH, the most alkaline environment inhibited by living organisms.
But not all archaea are extremophiles, some live in moderate areas, such as soil, but so far, most archaea have been found to live in ocean depths. Archaea also live in the digestive tracts of animals.
Halophiles live together in bodies of water similar to how algae do, and can even colonize on fish, leading to observable red spots on fishes' bodies.

Halophiles can turn the water they live in a red or pinkish color. This is due to the cells(most typically mitochondria and chloroplasts) of halophiles containing high levels of carotenoid pigments, possibly used for UV protection. They require salt concentrations in excess of about 10% to grow, and optimal growth usually occurs at much higher concentrations, typically 20–25%. However, Haloarchaea can grow up to about 37% salts.(13) (Shwetha)


Grand Prismatic Spring (Yellowstone National Park) [Source: Wikipedia Public Domain] (DM)
Grand Prismatic Spring (Yellowstone National Park) [Source: Wikipedia Public Domain] (DM)









4. Predator avoidance
Since extremophiles live in such harsh environments, very few organisms would survive living alongside them since their cell's would shrivel up as water diffused out into the hypertonic environment. Therefore extremophiles (archaea that live in extreme environments) do not have any natural predators. Other archaea (including unextreme halophiles) that do not live in extreme environments are so small they are not noticeable by many animals, other than how they turn the waters they occupy into different colors due to their pink carotenoid pigments.




5. Nutrient acquisition
Some halophiles have a unique system for trapping light energy and using it to form ATP (adenosine triphosphate), without using any form of chlorophyll. When oxygen is in short supply, they use a pigment called retinal (the same pigment found in eyes) and special proteins to form light absorbing molecules called microbial rhodopsin. This molecule then absorbs energy which can travel through chemical reactions and eventually aid in forming ATP. Halophiles take in nutrients from their environment by endocytosis, where the halophile's cell membrane pinches in and surrounds the food, bringing it into the cell. Some archaea do not require the same nutrients that other organisms require and some of those nutrients would not be present in extreme environments, so those archaea obtain those nutrients they need that are present in the environment and use them in special ways, distinct from other organisms. Some prokaryotes (group to which archaea belong) obtain nutrients from biofilms formed by the community.Biofilms are polysaccharide matrices that trap cells, protecting them and allowing for sharing of nutrients. Prokaryotes including archaea and bacteria) can be photoautotrophs (perform photosynthesis), photoheterotrophs (use light as energy source but obtain organic compounds made by other organisms), chemoautotrophs (oxidize inorganic substances and use that energy to fix carbon by various methods), and chemoheterotrophs (obtain energy and carbon from complex organic compounds that have been made by other organisms). Most archaea are chemoheterotrophs, and many are chemoautotrophs.

[1] (FZ)
This video shows how bacteriorhodopsin functions.


6.Reproduction and life cycle
Halophiles are archaea and reproduce not by mitosis but by binary fission. Cells grow until a certain size and then split into two daughter cells which then grow and then split and so on, adding to the colony.

Binary Fission.jpg
Figure 5. Binary Fission: The Reproduction Process of Halophile Archaea [12] (AY)

The archaea genome is held in one chromosome. At the beginning of binary fission, the DNA is replicated with the help of an enzyme called DNA polymerase. The two identical DNA copies then move to opposite sides of the cell (the process by which this occurs is not yet determined). The cell then divides in two through a process called furrowing. One chromosome ends up in each daughter cell, producing two exactly identical cells. Archaea have no means of sexual reproduction. (9) (AA)



7.Growth and development
Halophile cells take in nutrients and grow until a certain size and then split into daughter cells, which then grow larger and then split. No other development occurs due to the simplicity of organism.

Hadophile archaea grow by converting light to ATP through a distinct system, thus adapting to their extreme environments. Through the retinal pigment, which will combine with a protein, archaea develop a light-absorbing molecule, called the microbial rhodopsin. (AWC)[2]



8.Integument
All archaea (including halophiles) are unique in that they do not have peptidoglycan in their cell walls, and some have a distinctive lipid composition in their cell membranes, found not in bacteria or eukaryotes. Most eukaryotes and bacteria contain unbranched (unconnected) long-chain fatty acids connected to glycerol molecules by ester linkages (chemical compounds consisting of a carbonyl group adjacent to an ether linkage). Some archaea have long-chain hydrocarbons connected to glycerol molecules by ether linkages (a class of organic compounds that contain an ether group, an oxygen bound to two alkyl or aryl groups (contain only hydrogen and carbon and single bonded ).Also these long-chain hydrocarbons are branched (connected). One class of archaeal lipids contain glycerol at both ends of the hydrocarbons, forming a lipid monolayer membrane rather than a lipid bilayer. But both lipid bilayers and monolayers are found in archaea. The effects of these distinct features on some archaeal membranes is unknown. Other than these differences however, membranes are similar between bacteria, archaea, and eukaryotes.
prokaryote.jpg
Simple Cell Structure (MC)



Halophiles are coated with a special protein covering, which allows only specific amounts of saline/salt into the cell. The protein covering helps to seal in water with the right level of saline and uses the process of diffuesion to help keep the salt content at the right level. (6) (JF)

They also have NA+ pumps to push NA+ ions out of the cell and K+ pumps to concentrate K+ within the cell. This allows for the balance of osmotic pressure with the concentration of K+ being about 5M and the concentration of NA+ being 4M. (LC) 10





9.Movement
Haloarchaea cells can move backwards and forwards through the rotations of their flagella, and tend to change the direction of their movement depending on the color of the light. Orange light can be converted into energy, so haloarchaea move toward the source, but blue and ultraviolet light causes the organism to move away from the source since these wavelengths have damaging effects. (5)(BB-V)
Although functionally similar to bacterial flagella, archaeal flagella are unique motility structures in terms of their structure and assembly. Assembly of the archaeal flagellum, which lacks the internal channel found in bacterial flagella. (HSC)






10.Sensing the environment

Some prokaryotes (which archaea belong to) form communities and biofilms. Biofilms are polysaccharide matrices that trap cells, protecting them and allowing for sharing of nutrients. Prokaryotes can also release chemical signals to communicate with surrounding cells in these systems.

The immune system of halophilic archaea helps defend themselves against foreign invaders, much like other prokaryotes. One of these strategies consists of the CRISPR/Cas system, which is adaptive and hereditary—it recognizes an invader through an individualized sequence mechanism. In order to identify the invading nucleic acid, a crRNA that matches with the DNA of the invader and a protospacer adjacent motif (PAM) which is a short sequence, are needed (7) (E.S.S.).



11.Gas exchange
Halophiles, and archaea are unicellular, so necessary gases (not all archaea need oxygen) can simply diffuse through the cell membrane itself or through protein transport channels by facilitated diffusion. No other gas exhange mechanisms are necessary due to the simplicity and small size of the organisms. The waste gases travel out of the cell again either by diffusing through the membrane by simple diffusion or through facilitated diffusion through protein channels.
Some prokaryotes (which archaea belong to) can only live by anaerobic (without oxygen) metabolism because oxygen is poisonous to them. These oxygen-sensitive organisms are called obligate anaerobes. Some prokaryotes can shift metabolism between anaerobic and aerobic (using oxygen) and are called facultative anaerobes. Some can alternate between anaerobic metabolism (like fermentation) and cellular respiration. Aerotolerant anaerobes cannot use cellular respiration but are not damaged by the presence of oxygen. Finally, some prokaryotes are obligate aerobes (require oxygen for survival in cellular respiration).



12.Waste removal
Halophiles and archaea remove waste through exocytosis, in which waste is excreted out of the cell membrane in vesicles, which attach and become part of the cell membrane as the waste leaves the cell.
Halophiles



13.Environmental physiology (temperature, water and salt regulation)
Some archaea maintain internal stability in spite of their outside environment being different. This is known as homeostasis.Some archaea just internally tolerate the environment outside, whether pH, salinity, or otherwise.

Many cells would have a lot of water loss under the salty conditions that the Halophile Archea live in, however these archea have a way of dealing with it. To make sure that they do not have too much water loss, the halophiles accumulate high levels of solutes in their cytoplasm. This insures that water will not leave the cell into the outside environment (4) (WSS)

Halophiles use the relationship of fluids on the inside and outside of the cell, or osmotic pressure, as well as chemical substances like sugars, alcohols, and amino acids to help control the amount of salt inside the cell. Healthy cells successfully keep the pressure the same on both the inside and outside of the cells. (6) (JF)





14.Internal circulation
Halophiles and archaea are unicellular, therefore they do not need an internal circulatory system.




15.Chemical control (i.e. endocrine system)




Review Questions
1. By which method does Halophile Archaea reproduce, and explain that process. (BH)
2. What makes the Halophile Archaea's movement unique from the common organism's movement? (JLau)
3. How does the integument of archaea differ from that of bacteria and eukaryotes? (SM)
4. Explain how the archea's production of ATP differs from the way a plant captures light and produces ATP (PS)
5) How does Halophile Archaea grow through light? Explain the process and system (ES)

16. Sources
  1. ^ http://www.youtube.com/watch?v=c4wI4XnjjhE
  2. ^ http://www.ncbi.nlm.nih.gov/pubmed/9878396

1. Hillis, David M. Principles of Life. Sunderland, MA: Sinauer Associates, 2012. Print.
2. Picture source: "Deep Red Sea." Greenlimbs. N.p., 14 Aug. 2012. Web. 04 Dec. 2012. <http://greenlimbs.com/deep-red-sea/>.
3. http://plantphys.info/organismal/lechtml/archaea.shtml
4. http://halo.umbi.umd.edu/~dassarma/halophiles.pdf
5. http://wwwmosi.informatik.uni-rostock.de/cmsb08/pdfs/talk_oesterheldt.pdf
6. http://library.thinkquest.org/CR0212089/halo.htm
7. Maier, Lisa-Katharina. "Landes Bioscience Journals: Mobile Genetic Elements." Mobile Genetic Elements. Landes Bioscience, 2012. Web. 13 Dec. 2012.
8. http://biology-forums.com/index.php?action=gallery;sa=view&id=746
9. http://plantphys.info/organismal/lechtml/archaea.shtml
10.http://serc.carleton.edu/microbelife/extreme/hypersaline/index.html
11. http://simple.wikipedia.org/wiki/Halophile
12. Addison Wesley Longman Inc. <http://www.uic.edu/classes/bios/bios100/lecturesf04am/binfission.jpg>\
13.http://en.wikipedia.org/wiki/Haloarchaea
14. http://www.saltscience.or.jp/p_summary/07B3-E.pdf
15. http://journaldatabase.org/articles/archaeal_porphyrins_regulation_cell.html






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