question-2 : The tree of life was produced by comparing Genetic Sequence Data, and can you make a tree of life with the domain of bacteria, archaea, and eukarya.

Question- 2 :  The tree of life was produced by comparing Genetic Sequence Data, and can you make a                             tree of life with the domain of bacteria, archaea, and eukarya.

answer       :

The three-domain system is a biological classification introduced by Carl Woese, Otto Kandler, and Mark Wheelis in 1990 that divides cellular life forms into three domains, namely Archaea, Bacteria, and Eukaryote or Eukarya. The key difference from earlier classifications such as the two-empire system and the five-kingdom classification is the splitting of archaea from bacteria as completely different organism. It has been challenged by the two-domain system that divides organisms into Bacteria and Archaea only, as eukaryotes are considered as one group of archaea.

background story :

Woese argued, on the basis of differences in 16S rRNA genes, that bacteria, archaea, and eukaryotes each arose separately from an ancestor with poorly developed genetic machinery, often called a progenote. To reflect these primary lines of descent, he treated each as a domain, divided into several different kingdoms. Originally his split of the prokaryotes was into Eubacteria (now Bacteria) and Archaebacteria (now Archaea). Woese initially used the term "kingdom" to refer to the three primary phylogenic groupings, and this nomenclature was widely used until the term "domain" was adopted in 1990.^[1]

Acceptance of the validity of Woese's phylogenetically valid classification was a slow process. Prominent biologists including Salvador Luria and Ernst Mayr objected to his division of the prokaryotes. Not all criticism of him was restricted to the scientific level. A decade of labor-intensive oligonucleotide cataloging left him with a reputation as "a crank," and Woese would go on to be dubbed "Microbiology's Scarred Revolutionary" by a news article printed in the journal Science in 1997.The growing amount of supporting data led the scientific community to accept the Archaea by the mid-1980s. Today, very few scientists still accept the concept of a unified Prokarya.

classification :

The three-domain system adds a level of classification (the domains) "above" the kingdoms present in the previously used five- or six-kingdom systems. This classification system recognizes the fundamental divide between the two prokaryotic groups, insofar as Archaea appear to be more closely related to Eukaryotes than they are to other prokaryotes – bacteria-like organisms with no cell nucleus. The three-domain system sorts the previously known kingdoms into these three domains: Archaea, Bacteria, and Eukarya.

The Archaea (archaebacteria)

The Archaea possess the following characteristics:

1. Archaea are prokaryotic cells.
2. Unlike the Bacteria and the Eukarya, the Archaea have membranes composed of branched hydrocarbon chains (many also containing rings within the hydrocarbon chains) attached to glycerol by ether linkages (Figure 1.3.3$\mathrm{1.3.}3$).
3. The cell walls of Archaea contain no peptidoglycan.
4. Archaea are not sensitive to some antibiotics that affect the Bacteria, but are sensitive to some antibiotics that affect the Eukarya.
5. Archaea contain rRNA that is unique to the Archaea as indicated by the presence molecular regions distinctly different from the rRNA of Bacteria and Eukarya.

Figure 1.3.3$\mathrm{1.3.}3$: Membrane Lipids of Archaea, Bacteria, and Eukarya. The Bacteria and the Eukarya have membranes composed of unbranched fatty acid chains attached to glycerol by ester linkages. The Archaea have membranes composed of branched hydrocarbon chains attached to glycerol by ether linkages.

Archaea often live in extreme environments and include methanogens, extreme halophiles, and hyperthermophiles. One reason for this is that the ether-containing linkages in the Archaea membranes is more stabile than the ester-containing linkages in the Bacteria and Eukarya and are better able to withstand higher temperatures and stronger acid concentrations.

The Bacteria (eubacteria)

Bacteria (also known as eubacteria or "true bacteria") are prokaryotic cells that are common in human daily life, encounter many more times than the archaebacteria. Eubacteria can be found almost everywhere and kill thousands upon thousands of people each year, but also serve as antibiotics producers and food digesters in our stomachs. The Bacteria possess the following characteristics:

1. Bacteria are prokaryotic cells.
2. Like the Eukarya, they have membranes composed of unbranched fatty acid chains attached to glycerol by ester linkages (Figure 1.3.3$\mathrm{1.3.}3$).
3. The cell walls of Bacteria, unlike the Archaea and the Eukarya, contain peptidoglycan.
4. Bacteria are sensitive to traditional antibacterial antibiotics but are resistant to most antibiotics that affect Eukarya.
5. Bacteria contain rRNA that is unique to the Bacteria as indicated by the presence molecular regions distinctly different from the rRNA of Archaea and Eukarya.

Bacteria include mycoplasmas, cyanobacteria, Gram-positive bacteria, and Gram-negative bacteria.

The Eukarya (eukaryotes)

The Eukarya (also spelled Eucarya) possess the following characteristics:

1. Eukarya have eukaryotic cells.
2. Like the Bacteria, they have membranes composed of unbranched fatty acid chains attached to glycerol by ester linkages (Figure 1.3.3$\mathrm{1.3.}3$).
3. Not all Eukarya possess cells with a cell wall, but for those Eukarya having a cell wall, that wall contains no peptidoglycan.
4. Eukarya are resistant to traditional antibacterial antibiotics but are sensitive to most antibiotics that affect eukaryotic cells.
5. Eukarya contain rRNA that is unique to the Eukarya as indicated by the presence molecular regions distinctly different from the rRNA of Archaea and Bacteria.

The Eukarya are subdivided into the following four kingdoms:

1. Protista Kingdom: Protista are simple, predominately unicellular eukaryotic organisms. Examples includes slime molds, euglenoids, algae, and protozoans.
2. Fungi Kingdom: Fungi are unicellular or multicellular organisms with eukaryotic cell types. The cells have cell walls but are not organized into tissues. They do not carry out photosynthesis and obtain nutrients through absorption. Examples include sac fungi, club fungi, yeasts, and molds.
3. Plantae Kingdom: Plants are multicellular organisms composed of eukaryotic cells. The cells are organized into tissues and have cell walls. They obtain nutrients by photosynthesis and absorption. Examples include mosses, ferns, conifers, and flowering plants.
4. Animalia Kingdom: Animals are multicellular organisms composed of eukaryotic cells. The cells are organized into tissues and lack cell walls. They do not carry out photosynthesis and obtain nutrients primarily by ingestion. Examples include sponges, worms, insects, and vertebrates.

It used to be thought that the changes that allow microorganisms to adapt to new environments or alter their virulence capabilities was a relatively slow process occurring within an organism primarily through mutations, chromosomal rearrangements, gene deletions and gene duplications. Those changes would then be passed on to that microbe's progeny and natural selection would occur. This gene transfer from a parent organism to its offspring is called vertical gene transmission.

It is now known that microbial genes are transferred not only vertically from a parent organism to its progeny, but also horizontally to relatives that are only distantly related, e.g., other species and other genera. This latter process is known as horizontal gene transfer. Through mechanisms such as transformation, transduction, and conjugation, genetic elements such as plasmids, transposons, integrons, and even chromosomal DNA can readily be spread from one microorganism to another. As a result, the old three-branched "tree of life" in regard to microorganisms (Figure 1.3.1$\mathrm{1.3.}1$) now appears to be more of a "net of life."

Microbes are known to live in remarkably diverse environments, many of which are extremely harsh. This amazing and rapid adaptability is a result of their ability to quickly modify their repertoire of protein functions by modifying, gaining, or losing their genes. This gene expansion predominantly takes place by horizontal transfer.

Summary

1. Phylogeny refers to the evolutionary relationships between organisms.
2. Organisms can be classified into one of three domains based on differences in the sequences of nucleotides in the cell's ribosomal RNAs (rRNA), the cell's membrane lipid structure, and its sensitivity to antibiotics.
3. The three domains are the Archaea, the Bacteria, and the Eukarya.
4. Prokaryotic organisms belong either to the domain Archaea or the domain Bacteria; organisms with eukaryotic cells belong to the domain Eukarya.
5. Microorganism transfer genes to other microorganisms through horizontal gene transfer - the transfer of DNA to an organism that is not its offspring.

 The three domains are the Archaea, the Bacteria, and the Eukarya.

Figure 1.3.1$\mathrm{1.3.}1$: A phylogenetic tree based on rRNA data, showing the separation of bacteria, archaea, and eukaryota domains.

Diversity Of Life Forms - Bacteria & Archaea 

 

[sir ppt points]

• Bacteria and Archaea represent two of the three largest branches on the tree of life 

• Virtually all bacteria and archaea are unicellular, and are prokaryotes meaning they lack a membrane-bound nucleus 

• The third major branch consisting of eukaryotes is called the Eukarya referring to organisms having cells with a membrane-bound nucleus

 • Although both bacteria and archaea have a relatively simple morphology, they are very different at the molecular level 

• There are key differences in the types of molecules that make up their plasma membranes and cell walls

 • In addition, the machinery that bacteria and archaea use to process genetic information is strikingly different 

 • The proteins and ribosomes found in archaea are more similar to those found in eukaryotes than to those found in bacteria

 • These differences have practical consequences, i.e., antibiotics that poison bacterial ribosomes do not affect the ribosomes of archaea or eukaryotes

 • If all ribosomes were identical, these antibiotics would kill our body cells along with the bacterial species that they were supposed to target

 • Prokaryotes are found almost everywhere; they live in environments as unusual as oxygen-free mud, hot springs, and salt flats

 • Bacteria or archaea that live in high-salt, high-temperature, low-temperature, or high-pressure habitats are extremophiles.