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Biogeography represents a branch of biological science that studies biogeographical division of plant, animal as well as biological diversity. It explains how the patterns of these evolve after a while (Ganderton and Coker, 2005). In recent years, whereas biogeography has conventionally concentrated on multicellulare organisms, biologists have discussed and analysed various biogeographical questions and they have been recently interested in unicellular organisms (microorganisms) (Ramette and Tiedje, 2007). With the development of biotechnological tools and computer programming, microbiologists take more opportunity for studying natural microbial communities in the environment. At present, there are a considerable number of different Sequences available to compare and classify of microbial communities ,as a result of these, there are several microbial taxa designed to display changes and evolutions of biogeaographical microbes. Therefore, genetic changes and evolutions make Microbial communities are not homogenous in the environmental-types. Moreover, the diversity of microorganisms form a single position to another cannot resemble. If this branch of science did not present, there could be not locative heterogeneity in microbial groups. Furthermore, microbial evolutions in microbial variety would be anticipated by surveying the microbial group in a single area at one specific position in time. It seems obvious that microbial biogeography is not only involving microorganisms and macroorganisms communities but also including plant communities. Thus, microbiologists do not understand completely why and how the diversity of microorganisms evolves and alters across period and location.
How analysis of ribosomal RNA differes from Protein sequence data
There are several important steps to purify and amplify the ribosomal RNA. First of all, after extracting the rRNA sequences in the microbial species, Polymerase Chain Reaction (PCR) was used to amplify and clean the ribosomal sequences. Sequence Analysis software, which are called eletropherograms, were used to find and check erroneous positions.like rRNA analysis, there are different methods to analyse proteins. Spectroscopy and Edman degradation reactions are used for protein anlaysis. However, The ribosomal RNA sequences were then gathered and at least more than one strands were also utilised to construct the final consensus sequence for each bacterial species. Therefore, the rRNA data have been used to respond far too many questions linking to the origins of life and the divergence of ancient populations. It is clear that the communities of microbes are significantly divers and they can be detected in individual natural samples and even found in a single sample. The ribosomal rRNA enables scientists to find out microbial evolutions and biogeography of microbes. Although taking and preparing of the rRNA samples are computationally difficult and costly, Present of rRNA make scientists less focused on protein sequences to classify microbial diversity (Gans etal., 2005). One of the differences of rRNA with protein are short sequence and nucleotide number. Currently, scientists are quantify rRNA sequence data for identifying and classifying of microbial communities as well as microbial diversity. A considerable number of surveys concerning biogeography often compares microbial patterns by assembling rRNA sequence data into single OTUs (operational taxonomic units). This platform can be used to detect the range of different nucleotides between different rRNA sequences.
The ribosomal RNA strands have been widely focusing for microbial phlogentic since they are present in all microbes in comparison with proteins. First of all, number, structure and function of the ribosomal RNA are dissimilar with the proteins. To compare protein sequences, user can use the Fold Function Assignment system (FFAS) and FASTA but BLAST can be used to compare rRNA sequences. wherease, multiple alignment rRNA are compared via four nucleotides to make phylogenetic tree and identification , multiple protein sequences are via about 20 amino acids. Biologists are, therefore, depended on these to find and classify novel microbes. In this investigation, the ribosomal RNA sequences data are used for phylogentic analysis. They include forty fife bacterial sequences in twenty two globally freshwater positions. Analysis of the ribosomal RNA sequences is not similar to Protein analysis.
However, Protein sequences are difficult to compare with each other because each sequence composes of more than twenty amino acids. Most proteins have the same structure but different functions because mutation and change rates occur less than protein sequences. However, the rate of mutations and evolutions make most of the microbial species are significantly different. (book). There are many approaches obtainable for introducing a phylogentic tree from data sample.
Do microbes have biogeography? And can microbial communities be so surprisingly diverse?
In the past, although there were not enough advanced technologies and well experiences concerning studying microbial environments and diversity, there were some experts stated that microbial communities have in everywhere. However, according to Baas-Becking 1934 (as cited in de Wit and Bouvier, 2006) â€œeverything is everywhere, but, the environment selectsâ€Â. This means that they have biogeography and also there is actually no criticism and no question that microbial communities are surprisingly diverse (Baker and Banfield, 2003). Currently, it is very easy to detected that the microbial diversity and their communities can be found in extreme locations because they have been observed in single natural samples. Although the science of biogeography is not modern, microbiologists have a wide range of suitable accurate techniques and methodologies available to study a large rest of the diversity of microorganisms in many parts of the world. Thus, the science of microbial biogeography is ready for most important evolutions in proving this hypothesis. To support this above statement, molecular markers and microscopy played an important role in this area. It appears clearly that the term of microbe include a wide range of taxa. For example, archaea and prokaryote those are significantly phlogenetically different as well as different with the regards of their physiologies, histories and morphologies
Interpretation concerning Phylogenetic analysis
Phylogentetic tree is a biological tree introducing the biogeographical and evolutionary relationships among the microbes, plants and animals. This tree has various shapes (penny et al, 1992). In this investigation, BLAST platform is performed to compare forty five different sequence alignments. BLAST (abbreviated to Basic Local Alignment Search Tool) is a powerful programme to compare any molecular data with original databases available in GeneBank. However, maximum-likelihood is a method applied to construct and introduce a phylogenetic tree. For this purpose, there are two software programs available to design a graphical multiple sequence alignment. For example, SeaView program, which are capable of writing and reading multiple ready sequence alignment, is utilised to design the maximum-likelihood tree. Both Seaview and PAUP tool are significantly efficient and sophisticated to carry out phylogentic tree. Each includes several accurate steps to align all preparing sequence data. Firstly, the Muscle option is selected to align all of the sequence data (Edgar, 2004). Secondly, Create set within site option is selected to organise multiple sequence alignments and also remove gaps among sequences. Thirdly, Maximum likelihood (ML), which is leading model of the evolutionary sequence, can integrate underlying information about distinct possibilities of various mutations and unusual changes of sequence nucleotides.
Mutations basically include transitions occurred between adenine and guanine or cytosine and thymine and also transversions occurred between purine and pryimidine groups. The incorporating information about distinct mutations has played a predominant role in building various evolutionary trees because these different mutations can extremely create two resembling species, which have the same geographical location but have different positions in the phylogenetic tree. However, transversion and transition rates have underlying effect branch lengths, in other word; branch lengths in the evolutionary trees have numerical relationships with the mutation ratios. If the changed ratios in microbial species 16s rRNA sequences are very high, they will have long branches and also will have separate group. The Maximum- likelihood model is able to find the most potential phylogentic tree provided the incorporating information.
As shown in this root tree, according to biogeography, microbial species scatter nearly into two groups but one of the two is out-group. The biggest group can be found in three different areas Such as, America, Europe, and Mixed. Most species are from America. The second group is from Europe and another is mixed. As a result of mutation and evolutionary changes, most species are significantly different with each other. For example, Mesodinium _rubrum and Mesodinium_sp. are significantly different because the mutation rate in Mesodinium sp ribosomal rRNA sequence was very high. However, Mesodinium chamaeleon, Pulex and major are very similar since there were no any mutation occurred in the rRNA sequence. Some species are very similar but they have different locations. In comparison with other species, Mesodinium _sp takes the longest branch this means that mutation rate was significantly high in rRNA sequence. Although, most of those species identified in Europe, their rRNA sequence alignments are very similar to each other, those species found in America, the mutation rates in their sequence alignments are significantly high. In comparison with Europe and American groups, mixed group has high mutation rate in ribosomal sequences
Mesodinium and Myrionecta represent the Litosmatea (Lynn and Small 2000). Krainer and foissner noticed that Mesodinium major and Mesodinium pulex are significantly different from other species. Litostomes is a big class that diverged from the ancestral stock. Litostomes is divided into several branches. To design phylogenetic tree, forty fife ribosomal rRNA sequences are used. It is obvious that our phylogenetic tree is quite poor because there is not high different between the species of Mesodinium ,except that Mesodinium rubrum and Mesodinium sp have much higher substitution rates since they suffer from too much mutation(Van de peer and Wachter 1997). It was explained that there is a significant correlation between mutation and evolutionary changes. Change in ribosomal RNA sequence alignment can create novel species. There are many environmental variable influences that cause change in sequence alignments; as a result, novel species is created. Mutations are one of the leading factors that lead to produce several microbial communities. Furthermore evolutionary changes can play a predominate role in spreading microbes. They can scatter the same species.
The investigation of microbial biogeography will assist microbiologists to construct a expected understanding of unicellular diversity. It will help them to know the impact of factors on microbial communities and their diversity. The microbiologists might be able to utilise pre-existing ideas in biogeography to know microbial systems. They may examine biogeographical concepts that are very complex to test with organism communities. However, with the help of phylogenetic tree, we will get nearer to understanding the complete breadth of microbial diversity on earth.