Phenotypic Analysis

Microorganisms have the right to be divide on the basis of cell structure, to move metabolism, or on distinctions in cabinet components.

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Learning Objectives

Distinguish in between phenotypic attributes for Bacteria, Archaea and also Eukaryotes

Key Takeaways

Key PointsThe relationship in between the three domains ( Bacteria, Archaea, and also Eukaryota) is of main importance for knowledge the beginning of life. Many of the metabolic pathways room common between Archaea and also Bacteria, while many genes connected in genome expression space common between Archaea and also Eukarya.Microorganisms are very diverse. They encompass bacteria, fungi, algae, and also protozoa; microscope plants, and animals. Single-celled microorganisms were the an initial forms of life to construct on earth, roughly 3 billion–4 billion years ago.The Gram stain characterizes bacteria based upon the structural attributes of your cell walls. By combine morphology and also Gram-staining, most bacteria have the right to be classified together belonging to among 4 teams (Gram-positive cocci, Gram-positive bacilli, Gram-negative cocci, and Gram-negative bacilli).There are some basic differences between Bacteria, Archaea, and also Eukaryotes in cabinet morphology and structure which assist in phenotypic classification and identification.Key TermsGram stain: A method of differentiating bacterial types into two huge groups (Gram-positive and Gram-negative).microorganism: one organism that is too tiny to be checked out by the unaided eye, specifically a single-celled organism, such together a bacterium.domain: In the three-domain system, among three taxa at the rank: Bacteria, Archaea, or Eukaryota.

Microorganisms are really diverse. They encompass bacteria, fungi, algae, and also protozoa; microscopic plants (green algae); and animals such as rotifers and planarians. Most microorganisms room unicellular (single-celled), but this is no universal.

Single-celled microorganisms were the an initial forms of life to construct on earth, roughly 3 billion–4 billion year ago. Further evolution was slow, and for around 3 billion years in the Precambrian eon, every organisms to be microscopic. So, for most of the background of life on earth the only forms of life to be microorganisms. Bacteria, algae, and fungi have actually been figured out in amber the is 220 million years old, which shows that the morphology of microorganisms has changed tiny since the Triassic period. When at the end of the 19th century information started to accumulate around the diversity in ~ the bacter world, scientists started to encompass the bacteria in phylogenetic schemes to define how life on earth may have developed. Several of the at an early stage phylogenetic trees of the prokaryote civilization were morphology-based. Rather were based on the then-current ideas on the presumed conditions on our world at the time that life an initial developed.

Microorganisms have tendency to have a reasonably rapid evolution. Most microorganisms deserve to reproduce rapidly, and also microbes such as bacteria can also freely exchange genes with conjugation, transformation, and transduction, even between widely-divergent species. This horizontal gene transfer, coupled with a high mutation rate and also many other means of hereditary variation, permits microorganisms to rapidly evolve (via herbal selection) to survive in new environments and respond to environmental stresses.

The relationship in between the three domains (Bacteria, Archaea, and Eukaryota) is of main importance for knowledge the origin of life. Many of the metabolic pathways, which make up the bulk of one organism’s genes, room common between Archaea and Bacteria, while most genes connected in genome expression room common between Archaea and also Eukarya. In ~ prokaryotes, archaeal cell framework is most similar to the of Gram-positive bacteria.

Phenotypic techniques of Classifying and also Identifying Microorganisms

Classification seeks to explain the diversity the bacterial types by naming and grouping organisms based upon similarities. Microorganisms have the right to be share on the basis of cabinet structure, moving metabolism, or on distinctions in cell components such as DNA, fat acids, pigments, antigens, and quinones.


Bacterial Morphology: simple morphological differences in between bacteria. The many often discovered forms and their associations.

There room some basic differences between Bacteria, Archaea, and also Eukaryotes in cabinet morphology and structure which assist in phenotypic classification and also identification:


The family member sizes of prokaryotes cells: loved one scales the eukaryotes, prokaryotes, viruses, proteins and also atoms (logarithmic scale).

Bacteria: lack membrane -bound organelles and can duty and reproduce as individual cells, yet often accumulation in multicell colonies. Your genome is generally a single loop that DNA, although lock can likewise harbor little pieces the DNA referred to as plasmids. These plasmids deserve to be transferred between cells v bacterial conjugation. Bacteria room surrounded by a cabinet wall, which provides strength and also rigidity to their cells.Archaea: In the past, the differences between bacteria and also archaea were no recognized and also archaea were classified v bacteria as component of the kingdom Monera. Archaea are also single-celled biology that absence nuclei. Archaea in truth differ from bacteria in both your genetics and also biochemistry. If bacterial cabinet membranes space made from phosphoglycerides through ester bonds, archaean membranes space made of ether lipids.Eukaryotes: unequal bacteria and archaea, standard scale contain organelles such as the cabinet nucleus, the Golgi apparatus, and also mitochondria in your cells. Prefer bacteria, plant cells have cell walls and also contain organelles such as chloroplasts in enhancement to the oribel in other eukaryotes.

The Gram stain, occurred in 1884 through Hans Christian Gram, characterizes bacteria based on the structural qualities of your cell walls. The special layers of peptidoglycan in the “Gram-positive” cell wall surface stain purple, while the slim “Gram-negative” cell wall appears pink. By combining morphology and also Gram-staining, most bacteria have the right to be classified as belonging come one of four groups (Gram-positive cocci, Gram-positive bacilli, Gram-negative cocci, and Gram-negative bacilli). Part organisms are finest identified by stains other than the Gram stain, particularly mycobacteria or Nocardia, which show acid-fastness on Ziehl–Neelsen or comparable stains. Other organisms might need to be established by their growth in distinct media, or by other techniques, such together serology.

Gram-positive bacteria: Streptococcus mutans visualized with a Gram stain.

While this schemes permitted the identification and classification of bacter strains, it was unclear whether these distinctions represented variation in between distinct types or in between strains the the very same species. This suspicion was due to the absence of unique structures in many bacteria, and lateral gene transfer between unrelated species. Due to lateral gene transfer, some very closely related bacteria can have an extremely different morphologies and also metabolisms. To overcome this uncertainty, modern-day bacterial classification emphasizes molecular systematics, using genetic techniques such as guanine cytosine ratio determination, genome-genome hybridization, as well as sequencing genes that have not undergone considerable lateral gene transfer, such as the rRNA gene.

Classification that Prokaryotes

Prokaryotic organisms to be the very first living things on earth and also still inhabit every environment, no matter exactly how extreme.

Key Takeaways

Key PointsAll living things can be classified into three main groups referred to as domains; these include the Archaea, the Bacteria, and also the Eukarya.Prokaryotes occurred during the Precambrian duration 3.5 come 3.8 billion years ago.Prokaryotic organisms have the right to live in every kind of atmosphere on Earth, from very hot, to an extremely cold, to super haline, to very acidic.The domain names Bacteria and Archaea room the ones containing prokaryotes organisms.The Archaea room prokaryotes the inhabit too much environments, such as inside the volcanoes, when Bacteria are more common organisms, such together E. Coli.Key Termsprokaryote: an biology whose cell (or cells) are identified by the lack of a nucleus or any kind of other membrane-bound organellesdomain: in the three-domain system, the highest rank in the category of organisms, over kingdom: Bacteria, Archaea, and also Eukaryaarchaea: a taxonomic domain that single-celled organisms doing not have nuclei, formerly called archaebacteria, yet now known to differ basically from bacteria

Evolution the Prokaryotes

In the recent past, scientists grouped living things into 5 kingdoms (animals, plants, fungi, protists, and also prokaryotes) based upon several criteria such as: the lack or existence of a nucleus and other membrane-bound organelles, the absence or visibility of cabinet walls, multicellularity, etc. In the late 20th century, the pioneering work of Carl Woese and also others contrasted sequences that small-subunit ribosom RNA (SSU rRNA) which brought about a more fundamental way to group organisms on earth. Based upon differences in the structure of cabinet membranes and also in rRNA, Woese and his partner proposed that all life on earth evolved along 3 lineages, referred to as domains. The domain Bacteria comprises every organisms in the kingdom Bacteria, the domain Archaea comprises the remainder of the prokaryotes, and also the domain Eukarya comprises every eukaryotes, including organisms in the kingdoms Animalia, Plantae, Fungi, and Protista.

The present model of the evolution of the first, life organisms is that these were some type of prokaryotes, which might have developed out the protobionts. In general, the eukaryotes are thought to have evolved later in the background of life. However, part authors have actually questioned this conclusion, arguing that the current set of prokaryotic varieties may have advanced from more complicated eukaryotic ancestors with a procedure of simplification. Others have argued that the three domain names of life arose simultaneously, native a set of differed cells that formed a solitary gene pool.

Two of the 3 domains, Bacteria and Archaea, space prokaryotic. Based on fossil evidence, prokaryotes to be the first inhabitants ~ above Earth, showing up 3.5 come 3.8 billion years back during the Precambrian Period. These organisms room abundant and ubiquitous; that is, they are existing everywhere. In enhancement to inhabiting middle environments, they are found in excessive conditions: native boiling springs come permanently frozen atmospheres in Antarctica; native salty environments like the Dead Sea to environments under remarkable pressure, such as the depths of the ocean; and also from locations without oxygen, such as a waste monitoring plant, come radioactively-contaminated regions, such as Chernobyl. Prokaryotes reside in the person digestive system and also on the skin, are responsible for certain illnesses, and also serve an important role in the preparation of many foods.

Prokaryotes in excessive environments: specific prokaryotes deserve to live in extreme environments such as the Morning Glory pool, a hot spring in Yellowstone national Park. The spring’s lively blue color is native the prokaryotes that thrive in its very hot waters.

Key Takeaways

Key PointsThe function of phylogenetic analysis is to recognize the past evolutionary course of organisms. early to technical innovation in contemporary molecular biology and the rapid advance in computational science, accurate inference the the phylogeny of a gene or organism seems possible in the near future.The developing an innovation of nucleic acid sequencing, along with the recognition that order of building blocks in informational macromolecules can be used as ‘molecular clocks’ that contain historical information, led to the breakthrough of the three- domain model ( Archaea – Bacteria -Eucaryota).As more genome sequences become available, researchers have discovered that determining these relationship is complex by the ubiquity of lateral gene transfer amongst archaea and bacteria.Even using enhanced DNA-based identification methods, the total number of bacterial species is not known and cannot also be approximated with any type of certainty. Currently, there room a tiny less than 9,300 known types of prokaryotes.Key TermsLateral gene transfer: Horizontal gene transfer (HGT), likewise lateral gene carry (LGT) or transposition describes the move of genetic material in between organisms various other than upright gene transfer. Vertical deliver occurs once there is gene exchange indigenous the parental generation come the offspring. LGT is then a mechanism of gene exchange that happens individually of reproduction.microbial phylogenetics: The research of the evolution relatedness amongst various teams of microorganisms.

Microbial phylogenetics is the examine of the evolutionary relatedness amongst various groups of microorganisms. The molecular technique to microbial phylogenetic analysis revolutionized our thinking around evolution in the microbial world. The objective of phylogenetic evaluation is to know the past evolutionary course of organisms. Also though we will never know for specific the true phylogeny of any type of organism, phylogenetic evaluation provides best assumptions, thereby providing a structure for various disciplines in microbiology. Because of the technological innovation of modern molecular biology and the rapid advance in computational science, specific inference the the phylogeny of a gene or biology seems feasible in the close to future.

Gene sequences have the right to be offered to reconstruct the bacter phylogeny. This studies suggest that bacteria diverged an initial from the archaeal/eukaryotic lineage. The term “bacteria” was traditionally applied to all microscopic, single-cell prokaryotes. However, molecular systematics showed prokaryotic life to consist that two separate domains, originally called Eubacteria and also Archaebacteria, but now dubbed Bacteria and also Archaea that advanced independently from an old common ancestor. The archaea and also eukaryotes are more closely related to each various other than to the bacteria. Due to the reasonably recent advent of molecule systematics and also a rapid boost in the number of genome sequences that are available, bacterial category remains a an altering and expanding field. For example, a few biologists argue the the Archaea and also Eukaryotes developed from Gram-positive bacteria.

While morphological or metabolic differences allowed the identification and also classification of bacterial strains, it was unclear whether these differences represented variation between distinct species or in between strains of the very same species. This suspicion was because of the absence of distinctive frameworks in many bacteria, as well as lateral gene transfer between unrelated species. The developing modern technology of nucleic mountain sequencing, along with the recognition that sequences of building blocks in informational macromolecules can be provided as ‘molecular clocks’ the contain historical information, led to the advancement of the three-domain design (Archaea – Bacteria – Eucaryota) in the so late 1970’s, primarily based on tiny subunit ribosom RNA sequence comparisons pioneered by Carl Woese and also George Fox.

Evolutionary tree showing the common ancestry of every three domain names of life: A very resolved Tree of Life, based on completely sequenced genomes. Bacteria room colored blue, eukaryotes red, and also archaea green. Loved one positions of some phyla room shown about the tree.

As more genome sequences end up being available, scientists have found that determining these relationship is complicated by the ubiquity of lateral gene transport (LGT) among archaea and also bacteria. Due to lateral gene transfer, some very closely related bacteria deserve to have very different morphologies and metabolisms. To get over this uncertainty, modern bacterial classification emphasizes molecule systematics, using hereditary techniques such as guanine cytosine ratio determination, genome-genome hybridization, and sequencing gene that have not undergone comprehensive lateral gene transfer, such as the rRNA gene.

As with bacterial classification, identification of microbe is progressively using molecule methods. Diagnostics making use of such DNA-based tools, such together polymerase chain reaction, are increasingly popular due to their specificity and also speed, contrasted to culture-based methods. However, even using these boosted methods, the total variety of bacterial species is no known and cannot also be estimated with any kind of certainty. Following existing classification, there space a little less 보다 9,300 known species of prokaryotes, which includes bacteria and also archaea. But attempts to calculation the true level of bacterial diversity have actually ranged from 107 come 109 total species – and even these diverse estimates might be off by numerous orders the magnitude.

There are 4 steps in general phylogenetic analysis of molecular sequences: (i) an option of a suitable molecule or molecule (phylogenetic marker), (ii) salvation of molecular sequences, (iii) multiple succession alignment (MSA), and (iv) phylogenetic treeing and evaluation.

Multilocus sequence analysis (MLSA) represents the novel traditional in microbial molecule systematics. In this context, MLSA is enforced in a reasonably straightforward way, consisting essentially in the concatenation of several sequence partitions because that the same collection of organisms, causing a “supermatrix” which is provided to infer a phylogeny by method of distance-matrix or optimality criterion-based methods. This strategy is expected to have an raised resolving power due to the big number of characters analyzed and also a reduced sensitivity come the affect of conflicting signal (i.e. Phylogenetic incongruence) that an outcome from ultimate horizontal gene carry events. The strategies supplied to attend to multiple partitions deserve to be group in three broad categories: the total evidence, separate analysis, and combination approaches. The concatenation technique that dominates MLSAs in the microbial molecule systematics literary works is recognized to systematists working v plants and animals as the “total molecular evidence” approach. It has been supplied to solve an overwhelming phylogenetic questions such as the relationships amongst the significant groups of cetaceans, that of microsporidia and fungi, or the phylogeny of major plant lineages. The total molecular evidence approach has to be criticized due to the fact that by straight concatenating all obtainable sequence alignments. The proof of conflict phylogenetic signal in the various data partitions is lost together with the possibility to i found it the evolutionary processes that gave rise come such inconsistent signals.

Nongenetic Categories because that Medicine and also Ecology

In medicine, microbe are identified by morphology, physiology, and other attributes; in ecology by habitat, energy, and also carbon source.

Learning Objectives

Outline the traits supplied to classify: bacteria, viruses and also microrganisms in ecology

Key Takeaways

Key PointsA pathogen causes disease in its host. In medicine, there are several broad varieties of pathogens: viruses, bacteria, fungi, eukaryotic bio parasites, and also prions.When identify bacteria in the laboratory, the following qualities are used: Gram staining, shape, existence of a capsule, bonding tendency, motility, respiration, development medium, and whether that is intra- or extracellular.Viruses are mostly classified by phenotypic characteristics, such together morphology, nucleic acid type, setting of replication, organize organisms, and also the form of an illness they cause.In ecology, microorganisms are classified by the form of habitat they require, or trophic level, energy resource and carbon source.Biologists have uncovered that microbial life has actually an amazing versatility for surviving in extreme environments that would be fully inhospitable to facility organisms; these are dubbed extremophiles and also many kinds exist.Different varieties of microorganisms usage a mix of various sources of energy and carbon. These may be alternations in between photo- and chemotrophy, between litho- and organotrophy, between auto- and heterotrophy or a combination of them.Key Termsobligate: Able to exist or survive just in a details environment or by assuming a specific role: one obligate parasite; one obligate anaerobe.pathogen: any organism or substance, specifically a microorganism, qualified of resulting in disease, such together bacteria, viruses, protozoa, or fungi. Microorganisms are not considered to be pathogenic till they have actually reached a population size that is big enough to reason disease.extremophile: An biology that lives under extreme problems of temperature, salinity, and so on. They space commercially essential as a resource of enzyme that operate under similar conditions.

Classifying microbe in medicine

A virus (colloquially well-known as a germ) is an transmittable agent the causes an illness in its host. In medicine, there are number of broad species of pathogens: viruses, bacteria, fungi, eukaryotic bio parasites, and prions.


Although most bacteria space harmless, even beneficial, quite a couple of are pathogenic. Each pathogenic species has a characteristic spectrum the interactions through its human hosts.

Conditionally, pathogenic bacteria are just pathogenic under specific conditions; such together a wound that enables for entry into the blood, or a decrease in immune function. Bacter infections can additionally be divide by place in the body, because that example, the vagina, lungs, skin, spinal cord and also brain, and also urinary tract.

When identify bacteria in the laboratory, the following chatacteristics space used: Gram staining, shape, existence of a capsule, bonding tendency (singly or in pairs), motility, respiration, expansion medium, and whether the is intra- or extracellular.

Culture techniques are designed to grow and identify certain bacteria, if restricting the development of the rather in the sample. Regularly these techniques are design for certain specimens: because that example, a sputum sample will certainly be treated to identify organisms that reason pneumonia. When a pathogenic organism has actually been isolated, it deserve to be further characterised by the morphology, development patterns (aerobic or anaerobic), fads of hemolysis, and staining.


Similar come the classification systems used for moving organisms, virus group is the subject of ongoing dispute due to your pseudo-living nature. Essentially, they room non-living particles with some chemistry characteristics similar to those that life; thus, they execute not right neatly into an established biological classification system.

Viruses are mostly classified by phenotypic characteristics,such as:

morphologynucleic mountain typemode of replicationhost organismstype of disease they cause

Currently there space two main schemes offered for the category of viruses: (1) the international Committee on Taxonomy that Viruses (ICTV) system; and (2) the Baltimore category system, which areas viruses right into one of seven groups. Come date, 6 orders have actually been established by the ICTV:


These orders expectancy viruses through varying host ranges, only some of i beg your pardon infect person hosts.

Baltimore category is a mechanism that areas viruses into one of 7 groups depending on a combination of:

their nucleic acid (DNA or RNA)strandedness (single or double)sensemethod of replication

Other classifications are established by the disease caused by the virus or the morphology, no of i m sorry is satisfactory as different viruses have the right to either reason the same an illness or look really similar. In addition, famous structures space often complicated to recognize under the microscope. Classifying viruses according to your genome means that those in a given classification will every behave in a comparable fashion, offering some indication of exactly how to continue with further research.

Other organisms invariably cause disease in humans, such as obligate intracellular parasites that room able come grow and reproduce only within the cell of other organisms.


In ecology, microorganisms are classified by the form of habitat castle require, or trophic level, energy resource and carbon source.

Habitat Type

Biologists have found that microbial life has actually an amazing flexibility for making it through in extreme environments that would be totally inhospitable to complicated organisms. Some also concluded that life may have started on earth in hydrothermal vents much under the ocean’s surface.

An extremophile is one organism that thrives in physically or geochemically excessive conditions, detrimental to most life ~ above Earth. Most known extremophiles room microbes. The domain Archaea contains renowned examples, yet extremophiles are present in numerous and also diverse genetic lineages of both bacteria and also archaeans. In contrast, organisms the live in an ext moderate atmospheres may be termed mesophiles or neutrophiles.

There are plenty of different class of extremophiles, each matching to the method its environmental niche differs from mesophilic conditions. Countless extremophiles fall under multiple categories and also are termed polyextremophiles. Some examples of varieties of extremophiles:

Acidophile: one organism through optimal growth at level of pH 3 or belowXerophile: an organism that can prosper in exceptionally dry, desiccating conditions; exemplified through the soil microbes of the Atacama DesertHalophile: an organism requiring at the very least 0.2M concentrations of salt (NaCl) because that growthThermophile: one organism that can grow at temperatures between 45–122 °C

Trophic level, energy resource and carbon source

The nutritional settings of an organism: A flowchart to identify if a types is autotroph, heterotroph, or a subtype.

Phototrophs: lug out photon catch to acquire energy. They use the energy from light to bring out miscellaneous cellular metabolic processes. They room not obligatorily photosynthetic. Many of the well-recognized phototrophs are autotrophs, likewise known together photoautotrophs, and can resolve carbon.Photoheterotrophs: create ATP v photophosphorylation however use environmentally-obtained essential compounds to develop structures and other bio- molecules.Photolithoautotroph: one autotrophic organism that provides light energy, and also an not natural electron donor (e.g., H2O, H2, H2S), and also CO2 as its carbon source.Chemotrophs: acquire their energy by the oxidation of electron donors in your environments.Chemoorganotrophs: organisms which oxidation the chemical bonds in essential compounds together their energy source and achieve the carbon molecules they need for cellular function. This oxidized necessary compounds include sugars, fats and proteins.Chemoorganoheterotrophs (or organotrophs) manipulate reduced-carbon compound as power sources, such together carbohydrates, fats, and proteins indigenous plants and animals. Chemolithoheterotrophs (or lithotrophic heterotrophs) utilize inorganic substances to create ATP, consisting of hydrogen sulfide and also elemental sulfur.Lithoautotroph: derives power from reduced compounds of mineral origin. May additionally be referred to as chemolithoautotrophs, showing their autotrophic metabolic pathways. Lithoautotrophs are specifically microbes and most space bacteria. For lithoautotrophic bacteria, only inorganic molecules deserve to be used as energy sources.Mixotroph: deserve to use a mix of various sources that energy and carbon. These might be alternations in between photo- and chemotrophy, in between litho- and also organotrophy, between auto- and also heterotrophy or a combination of them. Have the right to be either eukaryotic or prokaryotic.

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Differing morphology in various Herpes viruses: miscellaneous viruses from the Herpesviridae family members seen using an electron micrograph. Among these members is varicella-zoster (Chickenpox), and herpes simplex type 1 and 2 (HSV-1, HSV-2).