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22.1A: Classification of Prokaryotes - Biology

22.1A: Classification of Prokaryotes - Biology


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Prokaryotic organisms were the first living things on earth and still inhabit every environment, no matter how extreme.

Learning Objectives

  • Discuss the origins of prokaryotic organisms in terms of the geologic timeline

Key Points

  • All living things can be classified into three main groups called domains; these include the Archaea, the Bacteria, and the Eukarya.
  • Prokaryotes arose during the Precambrian Period 3.5 to 3.8 billion years ago.
  • Prokaryotic organisms can live in every type of environment on Earth, from very hot, to very cold, to super haline, to very acidic.
  • The domains Bacteria and Archaea are the ones containing prokaryotic organisms.
  • The Archaea are prokaryotes that inhabit extreme environments, such as inside of volcanoes, while Bacteria are more common organisms, such as E. coli.

Key Terms

  • prokaryote: an organism whose cell (or cells) are characterized by the absence of a nucleus or any other membrane-bound organelles
  • domain: in the three-domain system, the highest rank in the classification of organisms, above kingdom: Bacteria, Archaea, and Eukarya
  • archaea: a taxonomic domain of single-celled organisms lacking nuclei, formerly called archaebacteria, but now known to differ fundamentally from bacteria

Evolution of Prokaryotes

In the recent past, scientists grouped living things into five kingdoms (animals, plants, fungi, protists, and prokaryotes) based on several criteria such as: the absence or presence of a nucleus and other membrane-bound organelles, the absence or presence of cell walls, multicellularity, etc. In the late 20th century, the pioneering work of Carl Woese and others compared sequences of small-subunit ribosomal RNA (SSU rRNA) which resulted in a more fundamental way to group organisms on earth. Based on differences in the structure of cell membranes and in rRNA, Woese and his colleagues proposed that all life on earth evolved along three lineages, called domains. The domain Bacteria comprises all organisms in the kingdom Bacteria, the domain Archaea comprises the rest of the prokaryotes, and the domain Eukarya comprises all eukaryotes, including organisms in the kingdoms Animalia, Plantae, Fungi, and Protista.

The current model of the evolution of the first, living organisms is that these were some form of prokaryotes, which may have evolved out of protobionts. In general, the eukaryotes are thought to have evolved later in the history of life. However, some authors have questioned this conclusion, arguing that the current set of prokaryotic species may have evolved from more complex eukaryotic ancestors through a process of simplification. Others have argued that the three domains of life arose simultaneously, from a set of varied cells that formed a single gene pool.

Two of the three domains, Bacteria and Archaea, are prokaryotic. Based on fossil evidence, prokaryotes were the first inhabitants on Earth, appearing 3.5 to 3.8 billion years ago during the Precambrian Period. These organisms are abundant and ubiquitous; that is, they are present everywhere. In addition to inhabiting moderate environments, they are found in extreme conditions: from boiling springs to permanently frozen environments in Antarctica; from salty environments like the Dead Sea to environments under tremendous pressure, such as the depths of the ocean; and from areas without oxygen, such as a waste management plant, to radioactively-contaminated regions, such as Chernobyl. Prokaryotes reside in the human digestive system and on the skin, are responsible for certain illnesses, and serve an important role in the preparation of many foods.


22.1A: Classification of Prokaryotes - Biology

Introduction to Prokaryotes
Prokaryotes are usually single-celled organisms, it has been around for billions of years and it can be found in air, water and soil. Some can cause serious diseases. They can thrive in habitats not suitable for any eukaryotes &ndashExtreme heat, cold, acidity, salinity. Prokaryotes have plasma membrane surrounding the cell but no membrane bound organelles such as the mitochondria, nucleus or Golgi bodies.

Bacteria Cell Wall
Bacteria cell wall is a layered structure which surrounds the protoplasm of the cell to protect cells from the environment. The lipid bilayer cell membrane of most of the Gram-positive bacteria is covered by a porous peptidoglycan layer which does not exclude most antimicrobial agents. Gram-negative bacteria are surrounded by two membranes. The outer membrane functions as an efficient permeability barrier because it contains lipopolysaccharides and proteins. Bacteria cell wall is made up of a unique peptidoglycan (a polymer of disaccharide which is cross linked to amino acids) called Murein. Its basic structure is a carbohydrate backbone of alternating units of N-acetyl glucosamine and N-acetyl muramic acid. Bacteria lacking a cell wall are called mycoplasma, which usually inhabit osmotically protected environments and have sterol like compounds in their membranes.

Organelles and Inclusions
Cytoplasm contains chromosomes and ribosomes. A chromosome is usually a circular DNA molecule. Enzymes are attached to the plasma membrane. Often distinct granules are found in cytoplasm for storage of fat, glycogen and enzymes. Ribosomes are the only cytoplasmic organelles in prokaryotes.

Mobility , Response to Stimuli and Reproduction
Bacteria have rotating rings that gives it propeller movement to allow move to different environments. Some bacteria have short hair like structures to help the bacteria to adhere to each other and to surfaces. A special pilli are involved in bacterial reproduction &ndash Sex Pilli.

Prokaryotes have the ability to move toward environmental stimuli. They can also respond to light, oxygen and magnets. Prokaryotes reproduce asexually by Binary fission, or sexually by conjugation.

Classification of Prokaryotes
Classification can be based on oxygen requirement, Nutrition, Photosynthetic Capacity, Chemosynthetic Capacity, Feeding of Organic Matter, Staining and Shape. Based on nutrition, bacteria can be classified as heterotrophs, chemosynthetic and photosynthetic bacteria. Archaea is also called Archaebacteria they are more closely related to eukaryotes than prokaryotes. In a 3-dimensional system, it contains Archaea, bacteria and eukaryotes.

Protists
Protists are all eukaryotes and therefore all have cell organelles, most of them are single-celled but multi-celled form exists. Protists contain three groups: algae, slime molds (fungi) and protozoa. Algae include three groups: red algae, brown algae and green algae. Protozoa have contractile vacuoles which collect excess water and pump it outside the cell body. Amoeba is a typical protozoa. Protozoa can reproduce via sexual and asexual pathway. They can form cysts during harsh conditions.

Prokaryotes are usually single-celled organisms. They have plasma membrane surrounding the cell but no membrane bound organelles such as the mitochondria, nucleus or Golgi bodies. Their only cytoplasm organelle is ribosome, the metabolism enzymes are attached to the plasma membrane which encompasses the cell. Bacteria have cell walls to protect them from the environment. They have rotating rings that gives it propeller movements to allow move to different environments. Some bacteria have short hair like structures to help the bacteria to adhere to each other and to surfaces. Bacteria classification can be based on oxygen requirement, Nutrition, Photosynthetic Capacity, Chemosynthetic Capacity, Feeding of Organic Matter, Staining and Shape. Protists are all eukaryotes and therefore all have cell organelles, most of them are single-celled but multi-celled form exists. Protists contain three groups: algae, slime molds (fungi) and protozoa. Protozoa can reproduce via sexual and asexual pathway. They can form cysts during harsh conditions.

  • Colorful text boxes for explicit demonstration of concepts
  • Elegant drawing and graphics for vivid explanation and classification
  • Schematic presentation for easy understanding
  • Flow chart and tables are used for summarization
  • Importance of Cell Wall
  • Cell Wall of Gram Positive and Negative Bacteria
  • Chemical Composition
  • Biopolymer
  • Mycoplasma

Inclusions and Organelles

  • Cytoplasm of Prokaryotes
  • Location of Enzymes
  • Inclusion Organelles
  • Ribosomes

Classification of Bacteria

  • Oxygen Requirements
  • Nutrition
  • Photosynthetic Capacity
  • Chemosynthetic Capacity
  • Feeding of Organic Matter
  • Staining
  • Shape
  • Characteristics
  • Features
  • Evolution of Protists
  • Heterotrophs: Algae, Water Molds, Slime Molds, Protozoa, Fungi
  • Adaptations
  • Disease Causing Protists
  • Symbiotic Relationship

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Needs of Prokaryotes

The diverse environments and ecosystems on Earth have a wide range of conditions in terms of temperature, available nutrients, acidity, salinity, and energy sources. Prokaryotes are very well equipped to make their living out of a vast array of nutrients and conditions. To live, prokaryotes need a source of energy, a source of carbon, and some additional nutrients.

Macronutrients

Cells are essentially a well-organized assemblage of macromolecules and water. Recall that macromolecules are produced by the polymerization of smaller units called monomers. For cells to build all of the molecules required to sustain life, they need certain substances, collectively called nutrients. When prokaryotes grow in nature, they obtain their nutrients from the environment. Nutrients that are required in large amounts are called macronutrients, whereas those required in smaller or trace amounts are called micronutrients. Just a handful of elements are considered macronutrients—carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur. (A mnemonic for remembering these elements is the acronym CHONPS.)

Why are these macronutrients needed in large amounts? They are the components of organic compounds in cells, including water. Carbon is the major element in all macromolecules: carbohydrates, proteins, nucleic acids, lipids, and many other compounds. Carbon accounts for about 50 percent of the composition of the cell. Nitrogen represents 12 percent of the total dry weight of a typical cell and is a component of proteins, nucleic acids, and other cell constituents. Most of the nitrogen available in nature is either atmospheric nitrogen (N2) or another inorganic form. Diatomic (N2) nitrogen, however, can be converted into an organic form only by certain organisms, called nitrogen-fixing organisms. Both hydrogen and oxygen are part of many organic compounds and of water. Phosphorus is required by all organisms for the synthesis of nucleotides and phospholipids. Sulfur is part of the structure of some amino acids such as cysteine and methionine, and is also present in several vitamins and coenzymes. Other important macronutrients are potassium (K), magnesium (Mg), calcium (Ca), and sodium (Na). Although these elements are required in smaller amounts, they are very important for the structure and function of the prokaryotic cell.

Micronutrients

In addition to these macronutrients, prokaryotes require various metallic elements in small amounts. These are referred to as micronutrients or trace elements. For example, iron is necessary for the function of the cytochromes involved in electron-transport reactions. Some prokaryotes require other elements—such as boron (B), chromium (Cr), and manganese (Mn)—primarily as enzyme cofactors.

Practice Question

The substances needed to sustain life are _____.


History, Discovery, and Classification of lncRNAs

The RNA World Hypothesis suggests that prebiotic life revolved around RNA instead of DNA and proteins. Although modern cells have changed significantly in 4 billion years, RNA has maintained its central role in cell biology. Since the discovery of DNA at the end of the nineteenth century, RNA has been extensively studied. Many discoveries such as housekeeping RNAs (rRNA, tRNA, etc.) supported the messenger RNA model that is the pillar of the central dogma of molecular biology, which was first devised in the late 1950s. Thirty years later, the first regulatory non-coding RNAs (ncRNAs) were initially identified in bacteria and then in most eukaryotic organisms. A few long ncRNAs (lncRNAs) such as H19 and Xist were characterized in the pre-genomic era but remained exceptions until the early 2000s. Indeed, when the sequence of the human genome was published in 2001, studies showed that only about 1.2% encodes proteins, the rest being deemed "non-coding." It was later shown that the genome is pervasively transcribed into many ncRNAs, but their functionality remained controversial. Since then, regulatory lncRNAs have been characterized in many species and were shown to be involved in processes such as development and pathologies, revealing a new layer of regulation in eukaryotic cells. This newly found focus on lncRNAs, together with the advent of high-throughput sequencing, was accompanied by the rapid discovery of many novel transcripts which were further characterized and classified according to specific transcript traits.In this review, we will discuss the many discoveries that led to the study of lncRNAs, from Friedrich Miescher's "nuclein" in 1869 to the elucidation of the human genome and transcriptome in the early 2000s. We will then focus on the biological relevance during lncRNA evolution and describe their basic features as genes and transcripts. Finally, we will present a non-exhaustive catalogue of lncRNA classes, thus illustrating the vast complexity of eukaryotic transcriptomes.

Keywords: Central dogma Classification Non-coding RNA RNA World.


22.1A: Classification of Prokaryotes - Biology

The kingdom of Prokaryotes is made up of the domains, Archaea and Bacteria.

The domain bacteria are prokaryotes, single-celled organisms that have no membrane-bound organelles and make up a large proportion of living organisms. The domain bacteria contains five major groups: proteobacteria, chlamydias, spirochetes, cyanobacteria, and gram-positive bacteria. Mostly, those from the domain bacteria are what we encounter every day. Some are symbiotic with plants, others live in hot vents deep under the sea, others are pathogens and cause human diseases, some are photosynthesizers, and several are both harmless bacteria and harmful ones.

Archaea are also classed as prokaryotes. These are single-celled organisms that are visually similar to bacteria but contain genes and several metabolic pathways that are more similar to eukaryotes than to bacteria. They are prokaryotes that inhabit extreme environments (high salt, temperature, or chemicals). So far, no archaea that are human pathogens have yet been discovered. Archaea do live in our bodies and seem to be neither harmless or beneficial.

Domains of life: Bacteria and Archaea are both prokaryotes but differ enough to be placed in separate domains. An ancestor of modern Archaea is believed to have given rise to Eukarya, the third domain of life.


Practice Questions

Khan Academy

MCAT Official Prep (AAMC)

Sample Test B/B Section Passage 1 Question 5

Sample Test B/B Section Question 44

• The domain prokaryote contains two classes: Archaea and Bacteria

• Bacteria are the most common prokaryote organisms that we encounter every day, ranging from harmful to beneficial ones.

• Archaea are prokaryotes that inhabit extreme environments, such as inside of volcanoes Their ancestor is believed to have given rise to Eukarya, the third domain of life.

Prokaryote: an organism whose cell (or cells) are characterized by the absence of a nucleus or any other membrane-bound organelles

Domain: in the three-domain system, the highest rank in the classification of organisms, above kingdom: Bacteria, Archaea, and Eukarya

Archaea: a taxonomic domain of single-celled organisms lacking nuclei, formerly called archaebacteria, but now known to differ fundamentally from bacteria

Symbiotic: a mutually beneficial relationship between two organisms

Pathogens: a microorganism that causes disease

Photosynthesizer: Any organism that uses photosynthesis to generate carbohydrates

Bacteria: single-celled organisms

Eukaryote: an organism with genetic material within a distinct nucleus


Exercise B: Classification of Hardware

In this exercise, you will practice the process of classifying different pieces of hardware in a process similar to how Linnaeus classified organisms of the natural world during the 18 th century. Linnaeus grouped organisms based on physical similarities. Such morphological similarities are known as synapomorphies . He hypothesized that organisms which looked more similar, are more closely related. This principle of logic is known as parsimony , and is still used as the primary classification tool. After determining how different types of organisms are evolutionarily related, scientists create a phylogenetic tree (Fig. 9).

These phylogenetic trees are visualizations of ancestor-descendent relationships through time. The fewer linkages that exist between taxa on a phylogenetic tree, the more closely related they are. In the example in Figure 9, taxa B and C are more closely related than taxa A is to taxa B or taxa C .

Creating a Hardware Phylogeny

You will create a phylogenetic tree using parsimony to classify ten (10) pieces of hardware in a hierarchal fashion based on synapomorphies (similar to Fig 10) .


Classification [back to top]

There are some 10 million species of living organisms (mostly insects), and many more extinct ones, so they need to be classified in a systematic way. In 1753 the Swede Carolus Linnaeus introduced the binomial nomenclature for naming organisms. This consists of two parts: a generic name (with a capital letter) and a specific name (with a small letter), e.g. Panthera leo (lion) and Panthera tigris (tiger). This system replaced non-standard common names, and is still in use today.

A group of similar organisms is called a taxon, and the science of classification is called taxonomy. In taxonomy groups are based on similar physical or molecular properties, and groups are contained within larger composite groups with no overlap. The smallest group of similar organisms is the species closely related species are grouped into genera (singular genus), genera into families, families into orders, orders into classes, classes into phyla (singular phylum), and phyla into kingdoms. So you need to remember KPCOFGS.

This shows how the seven taxons are used to classify humans. As we go through the taxon hierarchy from kingdom to species, the groups get smaller and the animals are more closely related.


Amoeba Characteristics

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The Amoeba (plural Amoebae or Amoebas) is found in terrestrial as well as aquatic habitats. In fact, it can thrive in nearly all types of habitat. Some are parasitic in nature, thereby causing harm in humans and animals. As of date, six parasitic species are identified which cause mild to severe ailments in humans. Hence, this unicellular eukaryotic organism is widely studied in microbiology. Let’s discuss in brief about the characteristic features of the Amoeba.

A cell membrane encloses the cytoplasm and cell organelles of Amoeba. Since there is no cell wall, its cellular structure is not definite. It can exhibit in any form, based on the surrounding condition. It possesses pseudopodia for locomotion and feeding purposes. The pseudopods are extensions of the cytoplasm. Amoeba engulfs food by means of phagocytosis, meaning it encircles bacteria or other smaller protists, and secretes digestive enzymes into the vacuole. Digestion of food particles takes place in the vacuole with the help of enzymatic actions.

An Amoeba can have more than two nuclei in the cell. Similar to other protozoans, it reproduces asexually either by mitosis or cytokinesis. Under forceful division of Amoeba, the portion that contains nucleus survives, while the portions without nucleus die. When the organism is exposed to lethal environment, it turns into a dormant form, known as the Amoebic cyst. It continues to remain in the cyst form until it encounters normal environmental conditions.


The Revised Classification of Eukaryotes

Correponding Author: Sina M. Adl, Department of Soil Science, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada–Telephone number: +306 966 6866 FAX number: +306 966 6881 e-mail: [email protected] Search for more papers by this author

Department of Biology, Dalhousie University, Halifax, NS, B3H 4R2 Canada

Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, 02881 USA

Biology Center and Faculty of Sciences, Institute of Parasitology, University of South Bohemia, České Budějovice, Czech Republic

Zoology Department, Natural History Museum, London, SW7 5BD United Kingdom

Wadsworth Center, New York State Department of Health, Albany, New York, 12201 USA

Department of Biochemistry, Dalhousie University, Halifax, NS, B3H 4R2 Canada

Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4 Canada

Department of Ecology, University of Kaiserslautern, 67663 Kaiserslautern, Germany

Department of Parasitology, Charles University, Prague, 128 43 Praha 2, Czech Republic

Department of Biology, Dalhousie University, Halifax, NS, B3H 4R2 Canada

Forschungsinstitut Senckenberg, DZMB – Deutsches Zentrum für Marine Biodiversitätsforschung, D-26382 Wilhelmshaven, Germany

Institute of Biology, University of Neuchâtel, Neuchâtel, CH-2009 Switzerland

Muséum National d'Histoire Naturellem, UMR 7138 Systématique, Adaptation et Evolution, Paris, 75231 Cedex Paris 05, France

Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1 Canada

Department of Biological Sciences, LeMoyne College, Syracuse, New York, 13214 USA

Institute of Biology, University of Neuchâtel, Neuchâtel, CH-2009 Switzerland

Department of Biology, Middle Georgia College, Cochran, Georgia, 31014 USA

Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, 80309 USA

Department of Genetics and Evolution, University of Geneva, 1211 Geneva 4, Switzerland

School of Life, Sport and Social Sciences, Edinburgh Napier University, Edinburgh, EH11 4BN United Kingdom

Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, 72701 USA

GenBank taxonomy, NIH/NLM/NCBI, Bethesda, Maryland, 20892-6510 USA

Department of Invertebrate Zoology, St.Petersburg State University, St. Petersburg, 199034 Russia

Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, 72701 USA

Department of Soil Science, University of Saskatchewan, Saskatoon, SK, S7N 5A8 Canada

Department of Biology, Dalhousie University, Halifax, NS, B3H 4R2 Canada

Correponding Author: Sina M. Adl, Department of Soil Science, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada–Telephone number: +306 966 6866 FAX number: +306 966 6881 e-mail: [email protected] Search for more papers by this author

Department of Biology, Dalhousie University, Halifax, NS, B3H 4R2 Canada

Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, 02881 USA

Biology Center and Faculty of Sciences, Institute of Parasitology, University of South Bohemia, České Budějovice, Czech Republic

Zoology Department, Natural History Museum, London, SW7 5BD United Kingdom

Wadsworth Center, New York State Department of Health, Albany, New York, 12201 USA

Department of Biochemistry, Dalhousie University, Halifax, NS, B3H 4R2 Canada

Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4 Canada

Department of Ecology, University of Kaiserslautern, 67663 Kaiserslautern, Germany

Department of Parasitology, Charles University, Prague, 128 43 Praha 2, Czech Republic

Department of Biology, Dalhousie University, Halifax, NS, B3H 4R2 Canada

Forschungsinstitut Senckenberg, DZMB – Deutsches Zentrum für Marine Biodiversitätsforschung, D-26382 Wilhelmshaven, Germany

Institute of Biology, University of Neuchâtel, Neuchâtel, CH-2009 Switzerland

Muséum National d'Histoire Naturellem, UMR 7138 Systématique, Adaptation et Evolution, Paris, 75231 Cedex Paris 05, France

Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1 Canada

Department of Biological Sciences, LeMoyne College, Syracuse, New York, 13214 USA

Institute of Biology, University of Neuchâtel, Neuchâtel, CH-2009 Switzerland

Department of Biology, Middle Georgia College, Cochran, Georgia, 31014 USA

Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, 80309 USA

Department of Genetics and Evolution, University of Geneva, 1211 Geneva 4, Switzerland

School of Life, Sport and Social Sciences, Edinburgh Napier University, Edinburgh, EH11 4BN United Kingdom

Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, 72701 USA

GenBank taxonomy, NIH/NLM/NCBI, Bethesda, Maryland, 20892-6510 USA

Department of Invertebrate Zoology, St.Petersburg State University, St. Petersburg, 199034 Russia

Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, 72701 USA

Abstract

This revision of the classification of eukaryotes, which updates that of Adl et al. [J. Eukaryot. Microbiol. 52 (2005) 399], retains an emphasis on the protists and incorporates changes since 2005 that have resolved nodes and branches in phylogenetic trees. Whereas the previous revision was successful in re-introducing name stability to the classification, this revision provides a classification for lineages that were then still unresolved. The supergroups have withstood phylogenetic hypothesis testing with some modifications, but despite some progress, problematic nodes at the base of the eukaryotic tree still remain to be statistically resolved. Looking forward, subsequent transformations to our understanding of the diversity of life will be from the discovery of novel lineages in previously under-sampled areas and from environmental genomic information.


CHAPTER SUMMARY

22.1 Prokaryotic Diversity

Prokaryotes existed for billions of years before plants and animals appeared. Hot springs and hydrothermal vents may have been the environments in which life began. Microbial mats are thought to represent the earliest forms of life on Earth, and there is fossil evidence of their presence about 3.5 billion years ago. A microbial mat is a multi-layered sheet of prokaryotes that grows at interfaces between different types of material, mostly on moist surfaces. During the first 2 billion years, the atmosphere was anoxic and only anaerobic organisms were able to live. Cyanobacteria evolved from early phototrophs and began the oxygenation of the atmosphere. The increase in oxygen concentration allowed the evolution of other life forms. Fossilized microbial mats are called stromatolites and consist of laminated organo-sedimentary structures formed by precipitation of minerals by prokaryotes. They represent the earliest fossil record of life on Earth.

Bacteria and archaea grow in virtually every environment. Those that survive under extreme conditions are called extremophiles (extreme lovers). Some prokaryotes cannot grow in a laboratory setting, but they are not dead. They are in the viable-but-non-culturable (VBNC) state. The VBNC state occurs when prokaryotes enter a dormant state in response to environmental stressors. Most prokaryotes are social and prefer to live in communities where interactions take place. A biofilm is a microbial community held together in a gummy-textured matrix.

22.2 Structure of Prokaryotes

Prokaryotes (domains Archaea and Bacteria) are single-celled organisms lacking a nucleus. They have a single piece of circular DNA in the nucleoid area of the cell. Most prokaryotes have a cell wall that lies outside the boundary of the plasma membrane. Some prokaryotes may have additional structures such as a capsule, flagella, and pili. Bacteria and Archaea differ in the lipid composition of their cell membranes and the characteristics of the cell wall. In archaeal membranes, phytanyl units, rather than fatty acids, are linked to glycerol. Some archaeal membranes are lipid monolayers instead of bilayers.

The cell wall is located outside the cell membrane and prevents osmotic lysis. The chemical composition of cell walls varies between species. Bacterial cell walls contain peptidoglycan. Archaean cell walls do not have peptidoglycan, but they may have pseudopeptidoglycan, polysaccharides, glycoproteins, or protein-based cell walls. Bacteria can be divided into two major groups: Gram positive and Gram negative, based on the Gram stain reaction. Gram-positive organisms have a thick cell wall, together with teichoic acids. Gram-negative organisms have a thin cell wall and an outer envelope containing lipopolysaccharides and lipoproteins.

22.3 Prokaryotic Metabolism

Prokaryotes are the most metabolically diverse organisms they flourish in many different environments with various carbon energy and carbon sources, variable temperature, pH, pressure, and water availability. Nutrients required in large amounts are called macronutrients, whereas those required in trace amounts are called micronutrients or trace elements. Macronutrients include C, H, O, N, P, S, K, Mg, Ca, and Na. In addition to these macronutrients, prokaryotes require various metallic elements for growth and enzyme function. Prokaryotes use different sources of energy to assemble macromolecules from smaller molecules. Phototrophs obtain their energy from sunlight, whereas chemotrophs obtain energy from chemical compounds.

Prokaryotes play roles in the carbon and nitrogen cycles. Carbon is returned to the atmosphere by the respiration of animals and other chemoorganotrophic organisms. Consumers use organic compounds generated by producers and release carbon dioxide into the atmosphere. The most important contributor of carbon dioxide to the atmosphere is microbial decomposition of dead material. Nitrogen is recycled in nature from organic compounds to ammonia, ammonium ions, nitrite, nitrate, and nitrogen gas. Gaseous nitrogen is transformed into ammonia through nitrogen fixation. Ammonia is anaerobically catabolized by some prokaryotes, yielding N2 as the final product. Nitrification is the conversion of ammonium into nitrite. Nitrification in soils is carried out by bacteria. Denitrification is also performed by bacteria and transforms nitrate from soils into gaseous nitrogen compounds, such as N2O, NO, and N2.

22.4 Bacterial Diseases in Humans

Devastating diseases and plagues have been among us since early times. There are records about microbial diseases as far back as 3000 B.C. Infectious diseases remain among the leading causes of death worldwide. Emerging diseases are those rapidly increasing in incidence or geographic range. They can be new or re-emerging diseases (previously under control). Many emerging diseases affecting humans, such as brucellosis, are zoonoses. The WHO has identified a group of diseases whose re-emergence should be monitored: Those caused by bacteria include bubonic plague, diphtheria, and cholera.

Biofilms are considered responsible for diseases such as bacterial infections in patients with cystic fibrosis, Legionnaires’ disease, and otitis media. They produce dental plaque colonize catheters, prostheses, transcutaneous, and orthopedic devices and infect contact lenses, open wounds, and burned tissue. Biofilms also produce foodborne diseases because they colonize the surfaces of food and food-processing equipment. Biofilms are resistant to most of the methods used to control microbial growth. The excessive use of antibiotics has resulted in a major global problem, since resistant forms of bacteria have been selected over time. A very dangerous strain, methicillin-resistant Staphylococcus aureus (MRSA), has wreaked havoc recently. Foodborne diseases result from the consumption of contaminated food, pathogenic bacteria, viruses, or parasites that contaminate food.

22.5 Beneficial Prokaryotes

Pathogens are only a small percentage of all prokaryotes. In fact, our life would not be possible without prokaryotes. Nitrogen is usually the most limiting element in terrestrial ecosystems atmospheric nitrogen, the largest pool of available nitrogen, is unavailable to eukaryotes. Nitrogen can be “fixed,” or converted into ammonia (NH3) either biologically or abiotically. Biological nitrogen fixation (BNF) is exclusively carried out by prokaryotes. After photosynthesis, BNF is the second most important biological process on Earth. The most important source of BNF is the symbiotic interaction between soil bacteria and legume plants.

Microbial bioremediation is the use of microbial metabolism to remove pollutants. Bioremediation has been used to remove agricultural chemicals that leach from soil into groundwater and the subsurface. Toxic metals and oxides, such as selenium and arsenic compounds, can also be removed by bioremediation. Probably one of the most useful and interesting examples of the use of prokaryotes for bioremediation purposes is the cleanup of oil spills.

Human life is only possible due to the action of microbes, both those in the environment and those species that call us home. Internally, they help us digest our food, produce crucial nutrients for us, protect us from pathogenic microbes, and help train our immune systems to function correctly.

Footnotes

1. [1] Bodaker, I, Itai, S, Suzuki, MT, Feingersch, R, Rosenberg, M, Maguire, ME, Shimshon, B, and others. Comparative community genomics in the Dead Sea: An increasingly extreme environment. The ISME Journal 4 (2010): 399–407,doi:10.1038/ ismej.2009.141. published online 24 December 2009.

2. [2] Battistuzzi, FU, Feijao, A, and Hedges, SB. A genomic timescale of prokaryote evolution: Insights into the origin of methanogenesis, phototrophy, and the colonization of land. BioMed Central: Evolutionary Biology 4 (2004): 44, doi:10.1186/ 1471-2148-4-44.

3. [3] Papagrigorakis MJ,Synodinos PN, andYapijakis C. Ancient typhoid epidemic reveals possible ancestral strain of Salmonella entericaserovar Typhi.Infect Genet Evol 7 (2007): 126–7, Epub 2006 Jun.

4. [4] Naimi, TS, LeDell, KH, Como-Sabetti, K, et al. Comparison of community- and health care-associated methicillin-resistant Staphylococcus aureus infection.JAMA290 (2003): 2976–84,doi: 10.1001/jama.290.22.2976.