Extremophile term come from the combination of Latin and Greek words. Extreme come from Latin words extermus and the “phile” comes from the Greek word “philos” which is meant love.Macelroy proposed and starts the name of extremophile when he found the certain of the bacteria that can able to populate the hostile environment or the organism which is also can survive in intermediate environment. There are many interpretation of the extremophile. In Brock Biology of Microorganism 12th edition, define extremophile as “an organism that that is grows optimally under one or more chemical or physical extreme”. In Henderson's Dictionary of Biological Terms,define extremophile as ” prokaryotic microorganism that grows in extreme condition that other microorganisms cannot survive in”. Although the classification or characterization of extremophile looks straightforward, but those definitions above, is unclear or inexact. It need to be discuss more deepen scientifically, to make it precise and clear, what the extremophile meant for?
Philosophical issue of Extremophile
Three main philosophical issues of extremophile need further discussion. Firstly, what is extreme meant? Term extreme in extremophile is including two different extreme conditions that are physical extremes and geochemical extremes. Physical extreme is including temperature, radiation and pressure while the geochemical extreme is including desiccation, salinity pH,oxygen species or redox potential.Organism which thriving in biological extreme such as nutritional extremes and extreme of population density can still disputed, if they were include in the extremophile or not. There are two prospects that are reliable scientifically to describe extreme, firstly looking the extremophile in the evolutionary perspective. The earliest environment for the life defines what is ‘normal'. For example,a model for the origin of cellular life of Bacteria and Archaea, come from the hydrothermal springs on the ocean floor, which have temperature between 90˚C to 100˚C, so any environment that deviates from the temperature is ‘extreme' by definition of the evolutionary aspects. Secondly, definition of extremophile by looking on its physical definition of the extremophile. There were many different interpretation of the extreme word for the extremophile. Satyanarayana, Raghukumar and Shivaji interpreted extreme as ‘any environmental condition that can be perceive as beyond the normal acceptable range ‘. They conclude that the moderate environmental is pH between normal,temperature between 20˚C and 40˚C,air pressure 1 atm. Kristiánsson and Hreggvidsson concluded that ‘extremophile considered to be an organisms that can survive outside of the normal range although their optimal growth conditions are found outside of normal environment'. They assume normal environment is at 4˚C to 40˚C,pH 5 to 8.5 has salinity between seawater and fresh water. From this two examples, the physical definition of the extremophile is not definite, but it following the colloquial definition of the extreme by put the exception for the definition of extreme that there are making by putting their opinion of the normal environment to support the definition.
The second philosophical issue of the extremophile is ecological.Do the extremophile actually want to live in such extreme conditions. Or else, the extremophile actually tolerate the extreme conditions to survive? These questions were answered in the early of twentieth century by many discovery of the extremophile, which is live in the extreme condition. The famous example is the discovery of the extremophile by the Thomas D Brock and Hudson Freeze from the Indiana University.They found the bacteria when they spent their summer in spring 1966 at Yellowstone during their finding in the pink bacteria. They isolate the Thermus Aquaticus, which is widely used in the polymerase chain reaction (PCR).In the certain extend; there is also extremophile that is tolerate to environmental extreme. For example there are certain barophillic or barotolerant bacteria were isolated from the deep sea mud sample several palaces at Japan waters.For example Ryukyu Trench,Suruga Bay and many more. They isolated several barophillic bacteria, which is able to grow under higher hydrostatic pressure than under atmospheric pressure (1atm). By practical,it look easier to determine experimentally,but by looking into deepen into biology and linguistic term,its look complicated and hard to define.
Third philosophical issue of the extremophile is doing the extremophile need to be extremophile during all stages and under all pressures? For example, Deinococcous radiodurans the bacteria which is able to withstand the ionizing radiation which is up to 20 kGy of gamma radition. The bacteria also can withstand the UV radiation up to 1000 J.The bacteria mainly resist the extreme to desiccation which probably a reason why it can withstand in other extraordinary resistant as describe above.The Deinococcous radiodurans is one example of the extremophile which is can change their resistance characteristic. Their resistance to radiation can diminished in stationary compared with logarithmic phase growth under increased concentration of with freezing of desiccation and under nutrient limited conditions. This really shows that bacteria do not need to be extremophile under all condition.
Phylogenetic microbial diversity
Extremophile is one of major part of the microbial world. For example,the hyperthermophile, extreme acidophiles and extreme halophile among the major parts of the of Archaea. In studies of the diversity of the extremophile by phylogenetic, the main target is to discover the new extremophile and characterizing its functions according evolutionary history and line of descent of a species or the higher taxonomic group. Phylogeny indirectly related to nucleotide sequences data. Because the evolution is one of the process inherited nucleotide sequence change, analyzing DNA sequence differences among bacteria allows to reconstructed phylogenetic history. Nowadays, there were many new sequencing techniques tools in discovering and characterizing the microbial diversity. Typically, the studies of genes is included the laborious techniques by cloning the DNA into the vector, inserting them into the host, screening and Sanger sequencing.
However, with new sequencing technique, provide methods, which are cheaper, faster, and simpler.454 pyrosequencing is one of the sequencing technique that using the emulsion of PCR to amplify the clonal sequencing feature . The breaking of the emulsion,is followed by treating the 28µm beads with denaturant.This is to removed to unbound stands.Then it will be treated by hybridization-based enrichment to produced amplicon bearing beads. This technique is very valuable in determining the region, which is technically difficult to determine. For example,the soil microbial diversity which is estimated between2000 and 8.3 million presumably impractical to test by amplification and sequencing.But it is have been determine by the 454 pycrosequencing by a group scientist in 2007.
The Helicos sequencer which is applied to sequencing the single molecule, with ability to read as long as 10kb, have given a major advantages to the microbiologist in characterizing the microbial diversity. It was using the highly sensitive fluorescence detection system to determine the single molecule via sequencing by synthesis. For each cycle,the DNA polymerase and a single species of fluorescence labelled nucleotide are added, resulting in template-dependent extension of the surface –immobilized primer template duplexes refer figure below .The Helicos techniques,very useful to sequencing the shorter sequence. This implicated in small RNAs analysis, transcriptomes, and in comparisons of the nearly related strains and variants of the bacteria.
The Solexa,or known as Illumina Genome Analyzer ,is the generated sequence from the bridge PCR. From figure below, the production of in vitro constructed adapted linked shotgun library.The primer is densely coat at the surface of the solid substrate will be link to the 5 end by the flexible linker.Amplification product will be based on the any given member of template library ,near to the point of the origin . Concentration of the template library is crucial to increase the cluster density to avoiding overcrowding.The application of the Solexa in the sequencing the Microbe genetics is wide nowadays. For example, Sainsbury Laboratory in Norwich has generated draft genome from several plant pathogenic bacteria using the Solexa GA platform.One more famous example is to resequence the occurring strains the model plant Arabidopsis thaliana by the plant.
One of the major methods to assessed the phylogenetic microbial diversity is by using the phylogenetic tree.It has own advantages and disadvantages and the efficiencies of the methods in determine the phylogenetics by the tree are still controversial. The main problem of the studying the efficiencies is that the true tree is usually unknown for any set of real DNA sequences or real organism. As a result,it is difficult to judge which tree is the correct one. The DNA sequence analysis is a alternative way to support the analysis, but the work is tedious and take a long time in analysed the phylogenetic microbial diversity. With new technology nowadays, it helps to solve this problem by using the computer simulation with support by the DNA sequences. There are many types of the computer simulation for the sequence analysis or the tree building,such as FastGroup2,Geneious and UniFrac.In this essay,I will discuss about UniFrac.
UniFrac, the online tools that allows the several phylogenetic tests for differences among the communities easily applied and interpreted.The technique is using the phylogenetics information and multivariate techniques to determine find differences. The scientists from University of Colarado demonstrate that the UniFrac able to cluster the multiple environment and test the environment that have major different. They analyzed the bacterial communities that is already publicised, which is studies of communities at the Columbia River, estuary and adjacent costal ocean The UniFrac analysis have solved several unclear initial analysis. The UniFrac have its new version, which is can quickly analyze and Meta –analyzed the large number of samples using the available technique such as PhyloTrac and Blast. The most significant advantage of UniFrac and its new version is able to speed up the time to phylogenetic analysis which is will be helping or enhance the studies of of microbial diversity.
Thermophile and Hyperthermophile
Life at the high temperature is described either thermophile or the hyperthermophile. Thermophile is the organism that lives in the optimal temperature between 50˚C to 80˚C while the hyperthermophile grow over 80˚C.The thermophile and hyperthermophile is limited for the bacteria and archaea.(figure below) They found in wide range of the environment such as at the hyperthermophillic vent, coal refuse and many more. In the phylogenetic tree of the bacteria, there are three groups of the hyperthermophillic bacteria, which are Thermotoga, Thermosulfobacterium and Aquifex. In the phylogenetic tree of the Archaea, the hyperthermophile is mostly at the Crenarchaeota and there is some Euryarchaeota.
It has two type of genera,which is Thermotoga and Thermodesulfobacterium. Thermotoga is the rod shape,and growth in 90˚C.It is anaerobic bacteria and fermentative chemoorganotroph.The Thermotoga martima ,the most studied member,has roughly 7% of the predicted genome to metabolism of the monosaccharide and polysaccharides.The Thermotoga martima sequencing project has found that the evolutionary relationship of this hyperthermophile with the Archaea by lateral gene transfer(LGT). At about 24% of the Thermotoga martima gene is came from the archaea by comparing it by BLAST score. The thermophilic characteristic of Thermotoga were presumably taken by LGT from the Archaea.It was support by the periodicity of the genome to the another bacteria and archaea.
Thermosulfobacterium is a thermophilc sulphate reducing bacterium ,and it was positioned between Thermotoga and Aquifex.It is not truly extremophile,the optimum growth of the bacteria in around 70˚C.It was also the strict anaerobe that is use sulphate as electron acceptor ,from sulphate to sulphide. It contain lipids that same with Ammonifex bacterium, the gram-positive bacteria that grows anaerobicly. Thus,it is more common among the bacteria than archaea assumption.
Aquifex has two key genera in it class, which is aquifex and Thermocrinis.For the aqifex,it obligately known as chemolithorphic and autotrophic hyperthermophile.The most significant aspect of the aquifex was,the a pyrophillus and a aeolicus are the most thermophilic bacteria known.From the research of the A,aeoliceus,the autrophy in Aquifex is supported. The bacteria gain all the necessary carbon by the CO2 from the environment.The assay of the A.pyrophillus for the activity of the citric acid cycle concluded that in vitro activities for each proposed reaction. The a.aeolicus also has several genes encoding enzyme of the reverse of the citric acids cycle for example fumartte reductase, which can constitute the citric acid cycle pathway.The aquifex placement in phylogenetic tree is the one of the earliest divergences in the eubacterial tree,that provide the anchesteral eubacterial phenotype and the thermophilic nature of the first bacteria.
Most of the hyperthermophile is come from the archaea.The highest temperature that hyperthermophile can withstand is 113˚C by the Pyrolobus fumarii. There were many adaptation of the archaea that make them can survive high temperature such as stability of monomers, protein folding,chaperonins,solutes and Reveres gyrase and so on. The relationship between archaea and bacteria as we discuss above showed by the comparative analysis. This close relationship is more to the example of the evolutionary convergence although,the SSU rRNA GC base pair showed the high percentage. The research on the LGT reveal the similarity of the Archaea and bacteria,but its cannot indicates the overall organism evolution.
In nature,there are certain habitat that its effects by the osmotic factor.For example, the seawater which is have high concentration of salts.The seawater ,having at about 3% NaCl plus small amount of various mineral.Halophile is the organism which is have specific requirement for NaCl in addition to growing optimally on seawater or other extreme condition. The halophile may be found in three domain of life,Archaea,Bacteria and Eukarya.In archaea,the halophile is among the species in Eurayachaeota group and there are aerobes. There are at about 27 recognized genera of the halophilic Archaea. The haloarchaea is among the main component of microbial biomass such as Dead Sea,Israel,Lake Magadi,Kenya and Adriatic solar saltern as several example in the worldwide.As they we suites at the soda lake habitat,the haloarchaea can grow in very low Calcium ion and Magnesium ion concentration and very high pH.In eukarya,the halophile is scattered. Among the famous eukarya is the green alga Dunaliella.It was the main primary producer in Dead Sea and other hypersaline lakes.It is halotolarent than truly halophillic,make its can grows in much wider salt concentration. The bacteria domain contains a huge number of types of halophillic and halotolarent microorganism.There is a close relationship of non –halophilic bacteria with the in the branching of proteobacteria that is containg halophilic representative.In the cyanobacteria,the halophile is found between flavobacterium -cytophaga branch,spirochectes and also the actinomyctes. There is aerobic and anaerobic bacteria organism were also included in halophilic bacteria .For aerobic halophillic bacteria include the organism such as Deleya/Halomonas group and actinomyctes Micrococcus halobius.While among the anaerobic halophlic bacteria is fermentative bacteria Haloanaerobiaceae and phototrophic sulphur oxidizing family ectotthiorhodospiraceae
Acidophile is the living organism that are active in the extremely acidic environment.It tend to be in specialized form which is makes them unable to grow in neutral pH environment. Most of the acidophile is prokaryotes organism,but the are also diversity in Bacteria and Archaea. The first isolated and characterized acidophilic microorganism is Acidthiobacillus thiooxidans in 1921 and referred to Thiobacillus thiooxidans.This well studied organism,is autotrophic chemolithotroph that they use inorganic electron as donor, fixed carbon dioxide,and used the inorganic electron donor .