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Taxonomy: Life's Filing System - Crash Course Biology #19

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Hank tells us the background story and explains the importance of the science of classifying living things, also known as taxonomy. Crash Course Biology is now available on DVD!

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Further work has revealed additional surprises, which you can read about on the other pages of this exhibit. It is true that most archaeans don't look that different from bacteria under the microscope, and that the extreme conditions under which many species live has made them difficult to culture, so their unique place among living organisms long went unrecognized.

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A brief explanation on how to classify living things into domains and kingdoms. There are 3 Domains: Bacteria, Archaea, and Eukarya. This video helps characterize organisms into the following kingdoms: Bacteria, Archaea, Plantae, Animalia, Fungi, and Protista.

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1. Are archaea unicellular or multicellular?
2. Describe the characteristics of Archaea.
3. Where do you usually find Archaea?
4. What is archaea's relationship with viruses?
5. How do they reproduce?
6. Are they asexual or sexual?
7. Prokaryote or Eukaryote?
8. Define extremophiles, and give examples of extremophiles:
halophiles, methanogens, and thermophiles
9. How do Archaea get energy and food?

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Archaea - Horizon: Why Do Viruses Kill? - BBC

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"In the 1970s, scientists discovered archaea, a single cell life form that lives in hot springs. Research shows that they are full of viruses, proving that viruses are much older than previously thought. Informative clip from the BBC documentary series Horizon: 'Why do viruses kill?"

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bacteria, singular bacterium, any of a group of microscopic single-celled organisms that live in enormous numbers in almost every environment on Earth, from deep-sea vents to deep below Earth's surface to the digestive tracts of humans.

Bacteria lack a membrane-bound nucleus and other internal structures and are therefore ranked among the unicellular life-forms called prokaryotes. Prokaryotes are the dominant living creatures on Earth, having been present for perhaps three-quarters of Earth history and having adapted to almost all available ecological habitats. As a group, they display exceedingly diverse metabolic capabilities and can use almost any organic compound, and some inorganic compounds, as a food source. Some bacteria can cause diseases in humans, animals, or plants, but most are harmless and are beneficial ecological agents whose metabolic activities sustain higher life-forms. Other bacteria are symbionts of plants and invertebrates, where they carry out important functions for the host, such as nitrogen fixation and cellulose degradation. Without prokaryotes, soil would not be fertile, and dead organic material would decay much more slowly. Some bacteria are widely used in the preparation of foods, chemicals, and antibiotics. Studies of the relationships between different groups of bacteria continue to yield new insights into the origin of life on Earth and mechanisms of evolution.

All living organisms on Earth are made up of one of two basic types of cells: eukaryotic cells, in which the genetic material is enclosed within a nuclear membrane, or prokaryotic cells, in which the genetic material is not separated from the rest of the cell. Traditionally, all prokaryotic cells were called bacteria and were classified in the prokaryotic kingdom Monera. However, their classification as Monera, equivalent in taxonomy to the other kingdoms-Plantae, Animalia, Fungi, and Protista-understated the remarkable genetic and metabolic diversity exhibited by prokaryotic cells relative to eukaryotic cells. In the late 1970s American microbiologist Carl Woese pioneered a major change in classification by placing all organisms into three domains-Eukarya, Bacteria (originally called Eubacteria), and Archaea (originally called Archaebacteria)-to reflect the three ancient lines of evolution. The prokaryotic organisms that were formerly known as bacteria were then divided into two of these domains, Bacteria and Archaea. Bacteria and Archaea are superficially similar; for example, they do not have intracellular organelles, and they have circular DNA. However, they are fundamentally distinct, and their separation is based on the genetic evidence for their ancient and separate evolutionary lineages, as well as fundamental differences in their chemistry and physiology. Members of these two prokaryotic domains are as different from one another as they are from eukaryotic cells.

Prokaryotic cells (i.e., Bacteria and Archaea) are fundamentally different from the eukaryotic cells that constitute other forms of life. Prokaryotic cells are defined by a much simpler design than is found in eukaryotic cells. The most-apparent simplification is the lack of intracellular organelles, which are features characteristic of eukaryotic cells. Organelles are discrete membrane-enclosed structures that are contained in the cytoplasm and include the nucleus, where genetic information is retained, copied, and expressed; the mitochondria and chloroplasts, where chemical or light energy is converted into metabolic energy; the lysosome, where ingested proteins are digested and other nutrients are made available; and the endoplasmic reticulum and the Golgi apparatus, where the proteins that are synthesized by and released from the cell are assembled, modified, and exported. All of the activities performed by organelles also take place in bacteria, but they are not carried out by specialized structures. In addition, prokaryotic cells are usually much smaller than eukaryotic cells. The small size, simple design, and broad metabolic capabilities of bacteria allow them to grow and divide very rapidly and to inhabit and flourish in almost any environment.

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Prokaryotic and eukaryotic cells differ in many other ways, including lipid composition, structure of key metabolic enzymes, responses to antibiotics and toxins, and the mechanism of expression of genetic information. Eukaryotic organisms contain multiple linear chromosomes with genes that are much larger than they need to be to encode the synthesis of proteins. Substantial portions of the ribonucleic acid ( RNA) copy of the genetic information (deoxyribonucleic acid, or DNA) are discarded, and the remaining messenger RNA (mRNA) is substantially modified before it is translated into protein. In contrast, bacteria have one circular chromosome that contains all of their genetic information, and their mRNAs are exact copies of their genes and are not modified.

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bacteria | Cell, Evolution, & Classification

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bacteria, singular bacterium, any of a group of microscopic single-celled organisms that live in enormous numbers in almost every environment on Earth, from deep-sea vents to deep below Earth's surface to the digestive tracts of humans. Bacteria lack a membrane-bound nucleus and other internal structures and are therefore ranked among the unicellular life-forms called prokaryotes.

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(OLD VIDEO) Bacteria: The Good, The Bad, The Kinda Gross

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A brief explanation on how to classify living things into domains and kingdoms. There are 3 Domains: Bacteria, Archaea, and Eukarya. This video helps characterize organisms into the following kingdoms: Bacteria, Archaea, Plantae, Animalia, Fungi, and Protista.

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The beneficial bacteria that make delicious food - Erez Garty

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1. Are bacteria unicellular or multicellular?
2. Prokaryote or Eukaryote?
3. ASexual or Sexual Reproduction?
4. What is binary fission?
5. What are some examples of "bad" bacteria? How do you treat them?
6. What are some examples of "good" bacteria? Describe what makes them "good"
7. How do bacteria get food and energy?

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Paul Andersen discusses the defining characteristics of the members of Domain Eukarya. He starts with a brief description of the phylogeny of life on earth. He then discusses the major characteristics of eukaryotic cells. He explains how eukaryotic cells evolved from prokaryotic cells using endosymbiosis and infolding.

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A brief explanation on how to classify living things into domains and kingdoms. There are 3 Domains: Bacteria, Archaea, and Eukarya. This video helps characterize organisms into the following kingdoms: Bacteria, Archaea, Plantae, Animalia, Fungi, and Protista.

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1. Explain what a Eukarya is?
2. Describe the characteristics of Eukarya cells?
3. What makes Eukarya different than bacteria and archaea?
4. How do they reproduce? Give examples of each type, and when it is used?
5. What are the 4 Kingdoms included in this domain?

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Fundamental Statements for this Learning Object:

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.

LEARNING OBJECTIVES FOR THIS SECTION
The Earth is 4.6 billion years old and microbial life is thought to have first appeared between 3.8 and 3.9 billion years ago; in fact, 80% of Earth's history was exclusively microbial life. Microbial life is still the dominant life form on Earth. It has been estimated that the total number of microbial cells on Earth on the order of 2.5 X 10 ³⁰ cells, making it the major fraction of biomass on the planet.

Phylogeny refers to the evolutionary relationships between organisms. The Three Domain System, proposed by Woese and others, is an evolutionary model of phylogeny based on differences in the sequences of nucleotides in the cell's ribosomal RNAs (rRNA), as well as the cell's membrane lipid structure and its sensitivity to antibiotics.

Comparing rRNA structure is especially useful. Because rRNA molecules throughout nature carry out the same function, their structure changes very little over time. Therefore similarities and dissimilarities in rRNA nucleotide sequences are a good indication of how related or unrelated different cells and organisms are.

There are various hypotheses as to the origin of prokaryotic and eukaryotic cells. Because all cells are similar in nature, it is generally thought that all cells came from a common ancestor cell termed the last universal common ancestor (LUCA). These LUCAs eventually evolved into three different cell types, each representing a domain. The three domains are the Archaea, the Bacteria, and the Eukarya.

More recently various fusion hypotheses have begun to dominate the literature. One proposes that the diploid or 2N nature of the eukaryotic genome occurred after the fusion of two haploid or 1N prokaryotic cells. Others propose that the domains Archaea and Eukarya emerged from a common archaeal-eukaryotic ancestor that itself emerged from a member of the domain Bacteria. Some of the evidence behind this hypothesis is based on a "superphylum" of bacteria called PVC, members of which share some characteristics with both archaea and eukaryotes. There is growing evidence that eukaryotes may have originated within a subset of archaea.

In any event, it is accepted today that there are three distinct domains of organisms in nature: Bacteria, Archaea, and Eukarya. A description of the three domains follows:

The Archaea possess the following characteristics:

b . 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(see Fig. 1).

c. The cell walls of Archaea contain no peptidoglycan.

d. Archaea are not sensitive to some antibiotics that affect the Bacteria, but are sensitive to some antibiotics that affect the Eukarya.

e. 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.

One reason for this is that the ether-containing linkages in the Archaea often live in extreme environments and include methanogens, extreme halophiles, and hyperthermophiles. 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 possess the following characteristics:

b. Like the Eukarya, they have membranes composed of unbranched fatty acid chains attached to glycerol by ester linkages (see Fig. 1).

c. The cell walls of Bacteria, unlike the Archaea and the Eukarya, contain peptidoglycan.

d. Bacteria are sensitive to traditional antibacterial antibiotics but are resistant to most antibiotics that affect Eukarya.

e. 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 (also spelled Eucarya) possess the following characteristics:

b. Like the Bacteria, they have membranes composed of unbranched fatty acid chains attached to glycerol by ester linkages (see Fig. 1).

c. Not all Eukarya possess cells with a cell wall, but for those Eukarya having a cell wall, that wall contains no peptidoglycan.

d. Eukarya are resistant to traditional antibacterial antibiotics but are sensitive to most antibiotics that affect eukaryotic cells.

e. 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 kingdoms:

a. Protista Kingdom
Protista are simple, predominately unicellular eukaryotic organisms. Examples includes slime molds, euglenoids, algae, and protozoans.

b. 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.

c. 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.

d. 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 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 .

© Gary E. Kaiser Doc Kaiser's Microbiology Home Page
Copyright
All Rights Reserved
Updated: April, 2014
Please send comments and inquiries to Dr. Gary Kaiser

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Fundamental Statements for this Learning Object: 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.