Phenotypic Analysis

Microorganisms deserve to be classified on the communication of cabinet structure, to move metabolism, or on distinctions in cell components.

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Learning Objectives

Distinguish between phenotypic qualities for Bacteria, Archaea and Eukaryotes

Key Takeaways

Key PointsThe relationship between the three domain names ( Bacteria, Archaea, and Eukaryota) is of main importance for understanding the origin of life. Most of the metabolic pathways are common in between Archaea and also Bacteria, while many genes associated in genome expression room common between Archaea and also Eukarya.Microorganisms are very diverse. They encompass bacteria, fungi, algae, and protozoa; microscopic plants, and animals. Single-celled microorganisms were the very first forms of life to build on earth, around 3 billion–4 billion year ago.The Gram stain characterizes bacteria based upon the structural features of their cell walls. By combining morphology and Gram-staining, many bacteria deserve to be classified together belonging to one of 4 teams (Gram-positive cocci, Gram-positive bacilli, Gram-negative cocci, and also Gram-negative bacilli).There space some simple differences between Bacteria, Archaea, and also Eukaryotes in cell morphology and structure which help in phenotypic classification and identification.Key TermsGram stain: A method of distinguishing bacterial species into two big groups (Gram-positive and Gram-negative).microorganism: an organism the is too small to be seen by the unaided eye, particularly a single-celled organism, such as 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 protozoa; microscopic tree (green algae); and animals such as rotifers and planarians. Many microorganisms are unicellular (single-celled), but this is not universal.

Single-celled microorganisms were the very first forms that life to develop on earth, around 3 billion–4 billion years ago. Further advancement was slow, and for around 3 billion year in the Precambrian eon, every organisms to be microscopic. So, for most of the background of life on earth the only develops of life were microorganisms. Bacteria, algae, and fungi have been identified in amber the is 220 million year old, which shows that the morphology of microorganisms has actually changed tiny since the Triassic period. As soon as at the end of the 19th century information began to accumulate around the diversity within the bacter world, researchers started to encompass the bacteria in phylogenetic schemes to explain how life on planet may have actually developed. Few of the early phylogenetic trees of the prokaryote human being were morphology-based. Rather were based upon the then-current principles on the presumed problems on our world at the moment that life first developed.

Microorganisms have tendency to have actually a fairly rapid evolution. Most microorganisms have the right to reproduce rapidly, and also microbes such together bacteria can also freely exchange genes through conjugation, transformation, and transduction, even in between widely-divergent species. This horizontal gene transfer, coupled v a high mutation rate and many other means of hereditary variation, enables microorganisms to promptly evolve (via herbal selection) to endure in new environments and also respond to eco-friendly stresses.

The relationship in between the three domain names (Bacteria, Archaea, and Eukaryota) is of central importance for expertise the beginning of life. Most of the metabolic pathways, which comprise the bulk of an organism’s genes, are common between Archaea and also Bacteria, while many genes associated in genome expression room common between Archaea and also Eukarya. Within prokaryotes, archaeal cell structure is most similar to the of Gram-positive bacteria.

Phenotypic methods of Classifying and Identifying Microorganisms

Classification seeks to define the diversity of bacterial varieties by naming and grouping organisms based on similarities. Microorganisms have the right to be classified on the communication of cabinet structure, cellular metabolism, or on differences in cell components such as DNA, fatty acids, pigments, antigens, and quinones.


Bacterial Morphology: an easy morphological differences between bacteria. The many often uncovered forms and also their associations.

There are some straightforward differences in between Bacteria, Archaea, and Eukaryotes in cabinet morphology and also structure which help in phenotypic classification and identification:


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

Bacteria: absence membrane -bound organelles and can role and reproduce together individual cells, however often aggregate in multicellular colonies. Their genome is generally a single loop the DNA, although castle can likewise harbor little pieces of DNA called plasmids. This plasmids can be transferred in between cells with bacterial conjugation. Bacteria are surrounded by a cell wall, which offers strength and rigidity to their cells.Archaea: In the past, the differences between bacteria and also archaea were not recognized and archaea to be classified v bacteria as component of the kingdom Monera. Archaea are also single-celled organisms that absence nuclei. Archaea in reality differ native bacteria in both your genetics and biochemistry. While bacterial cell membranes room made indigenous phosphoglycerides v ester bonds, archaean membranes room made of ether lipids.Eukaryotes: unlike bacteria and archaea, standard scale contain organelles such together the cell nucleus, the Golgi apparatus, and mitochondria in their cells. Favor bacteria, tree cells have cell walls and also contain organelles such as chloroplasts in addition to the organelles in various other eukaryotes.

The Gram stain, developed in 1884 by Hans Christian Gram, characterizes bacteria based upon the structural characteristics of their cell walls. The special layers that peptidoglycan in the “Gram-positive” cell wall stain purple, while the slim “Gram-negative” cell wall appears pink. By combining morphology and Gram-staining, most bacteria can be classified as belonging come one of 4 groups (Gram-positive cocci, Gram-positive bacilli, Gram-negative cocci, and Gram-negative bacilli). Part organisms are finest identified through stains other than the Gram stain, an especially mycobacteria or Nocardia, which show acid-fastness ~ above Ziehl–Neelsen or comparable stains. Other organisms might need come be figured out by their growth in distinct media, or by various other techniques, such together serology.

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

While this schemes allowed the identification and also classification of bacterial strains, it was unclear whether these differences represented variation between distinct species or in between strains the the very same species. This uncertainty was because of the absence of unique structures in most bacteria, as well as lateral gene transfer in between unrelated species. As result of lateral gene transfer, some carefully related bacteria can have very different morphologies and metabolisms. To get over this uncertainty, modern bacterial category emphasizes molecule systematics, using genetic techniques such as guanine cytosine ratio determination, genome-genome hybridization, and sequencing gene that have not undergone substantial lateral gene transfer, such as the rRNA gene.

Classification the Prokaryotes

Prokaryotic organisms were the an initial living points on earth and still inhabit every environment, no matter how extreme.

Key Takeaways

Key PointsAll living things deserve to be classified into three key groups called domains; these include the Archaea, the Bacteria, and the Eukarya.Prokaryotes emerged during the Precambrian duration 3.5 come 3.8 billion year ago.Prokaryotic organisms deserve to live in every type of environment on Earth, from really hot, to very cold, to super haline, to very acidic.The domain names Bacteria and also Archaea room the ones containing prokaryotic organisms.The Archaea space prokaryotes that inhabit excessive environments, such together inside that volcanoes, while Bacteria are an ext common organisms, such together E. Coli.Key Termsprokaryote: an organism whose cell (or cells) are characterized by the lack of a cell core or any other membrane-bound organellesdomain: in the three-domain system, the greatest rank in the category of organisms, above kingdom: Bacteria, Archaea, and Eukaryaarchaea: a taxonomic domain of single-celled organisms lacking nuclei, formerly called archaebacteria, yet now well-known to differ basically from bacteria

Evolution of Prokaryotes

In the recent past, scientists grouped living points into 5 kingdoms (animals, plants, fungi, protists, and also prokaryotes) based on several criteria together as: the lack or visibility of a nucleus and other membrane-bound organelles, the absence or existence of cabinet walls, multicellularity, etc. In the so late 20th century, the pioneering occupational of Carl Woese and also others compared sequences the small-subunit ribosome RNA (SSU rRNA) which led to a more basic way to team organisms top top earth. Based on differences in the framework of cell membranes and in rRNA, Woese and his partner proposed the all life on planet evolved along three lineages, called domains. The domain Bacteria comprises all organisms in the kingdom Bacteria, the domain Archaea comprises the remainder of the prokaryotes, and also the domain Eukarya comprises all eukaryotes, including organisms in the kingdoms Animalia, Plantae, Fungi, and also Protista.

The present model the the evolution of the first, living organisms is the these to be some type of prokaryotes, which might have advanced out that protobionts. In general, the eukaryotes space thought to have progressed later in the history of life. However, part authors have questioned this conclusion, suggesting that the current collection of prokaryotic varieties may have advanced from more complex eukaryotic ancestors through a procedure of simplification. Others have argued that the three domain names of life occurred simultaneously, from a set of varied cells that formed a single gene pool.

Two that the 3 domains, Bacteria and Archaea, space prokaryotic. Based on fossil evidence, prokaryotes to be the an initial inhabitants ~ above Earth, appearing 3.5 to 3.8 billion years ago during the Precambrian Period. These organisms space abundant and ubiquitous; that is, lock are existing everywhere. In enhancement to inhabiting moderate environments, lock are discovered in too much conditions: indigenous boiling springs come permanently frozen atmospheres in Antarctica; indigenous salty environments like the Dead Sea to environments under remarkable pressure, such together the depths of the ocean; and from areas without oxygen, such as a waste monitoring plant, come radioactively-contaminated regions, such as Chernobyl. Prokaryotes reside in the human digestive system and on the skin, space responsible for specific illnesses, and serve vital role in the ready of countless foods.

Prokaryotes in excessive environments: certain prokaryotes can live in extreme settings such together the Morning Glory pool, a hot spring in Yellowstone nationwide Park. The spring’s lively blue color is from the prokaryotes that flourish in its very hot waters.

Key Takeaways

Key PointsThe function of phylogenetic analysis is to recognize the past evolutionary path of organisms. early out to technological innovation in modern molecular biology and the rapid breakthrough in computational science, specific inference of the phylogeny of a gene or biology seems feasible in the near future.The developing technology of nucleic acid sequencing, along with the acknowledgment that assignment of building blocks in informational macromolecules deserve to be provided as ‘molecular clocks’ that contain historic information, led to the breakthrough of the three- domain design ( Archaea – Bacteria -Eucaryota).As an ext genome sequences come to be available, scientists have uncovered that identify these relationships is complicated by the ubiquity of lateral gene transfer among archaea and also bacteria.Even using boosted DNA-based to know methods, the total number of bacterial varieties is not known and also cannot also be estimated with any certainty. Currently, there room a small less 보다 9,300 known types of prokaryotes.Key TermsLateral gene transfer: Horizontal gene transfer (HGT), also lateral gene transfer (LGT) or transposition describes the carry of hereditary material between organisms various other than upright gene transfer. Vertical transfer occurs once there is gene exchange indigenous the parental generation come the offspring. LGT is then a device of gene exchange the happens individually of reproduction.microbial phylogenetics: The research of the evolution relatedness among various groups of microorganisms.

Microbial phylogenetics is the study of the evolution relatedness among various teams of microorganisms. The molecular technique to microbial phylogenetic analysis revolutionized our thinking about evolution in the microbial world. The purpose of phylogenetic analysis is to understand the previous evolutionary path of organisms. Also though we will certainly never understand for certain the true phylogeny of any kind of organism, phylogenetic analysis provides ideal assumptions, thereby providing a structure for various disciplines in microbiology. Due to the technical innovation of modern molecular biology and the rapid advancement in computational science, precise inference of the phylogeny the a gene or biology seems feasible in the close to future.

Gene sequences have the right to be offered to reconstruct the bacterial phylogeny. This studies show that bacteria diverged first from the archaeal/eukaryotic lineage. The term “bacteria” to be traditionally applied to all microscopic, single-cell prokaryotes. However, molecular systematics confirmed prokaryotic life to consist of two separate domains, originally dubbed Eubacteria and Archaebacteria, however now dubbed Bacteria and Archaea that progressed independently from an ancient common ancestor. The archaea and eukaryotes are an ext closely concerned each other than to the bacteria. As result of the fairly recent arrival of molecular systematics and a rapid rise in the number of genome order that are available, bacterial category remains a transforming and broadening field. Because that example, a couple of biologists argue the the Archaea and 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 distinctions represented variation between distinct species or in between strains that the exact same species. This suspicion was because of the absence of distinctive frameworks in most bacteria, and also lateral gene transfer between unrelated species. The developing technology of nucleic acid sequencing, together with the acknowledgment that assignment of building blocks in informational macromolecules can be supplied as ‘molecular clocks’ that contain historic information, brought about the development of the three-domain design (Archaea – Bacteria – Eucaryota) in the so late 1970’s, primarily based on small subunit ribosome RNA sequence comparisons pioneered by Carl Woese and George Fox.

Evolutionary tree reflecting the common ancestry of all three domain names of life: A very resolved Tree of Life, based on totally sequenced genomes. Bacteria are colored blue, standard scale red, and also archaea green. Relative positions of part phyla are shown roughly the tree.

As more genome sequences come to be available, researchers have found that determining these relationships is complex by the prevalence of lateral gene move (LGT) amongst archaea and bacteria. As result of lateral gene transfer, some very closely related bacteria can have really different morphologies and metabolisms. To get rid of this uncertainty, modern bacterial category emphasizes molecular systematics, using genetic techniques such as guanine cytosine ratio determination, genome-genome hybridization, as well as sequencing genes that have not undergone extensive lateral gene transfer, such together the rRNA gene.

As v bacterial classification, to know of microbe is significantly using molecule methods. Diagnostics utilizing such DNA-based tools, such as polymerase chain reaction, are significantly popular due to their specificity and also speed, compared to culture-based methods. However, also using these improved methods, the total number of bacterial species is not known and cannot also be estimated with any kind of certainty. Following present classification, there room a tiny less 보다 9,300 known varieties of prokaryotes, which contains bacteria and also archaea. Yet attempts to calculation the true level of bacterial diversity have ranged from 107 to 109 total species – and even these varied estimates may be turn off by countless orders the magnitude.

There are 4 steps in basic phylogenetic analysis of molecule sequences: (i) selection of a perfect molecule or molecules (phylogenetic marker), (ii) acquisition of molecular sequences, (iii) multiple succession alignment (MSA), and also (iv) phylogenetic treeing and also evaluation.

Multilocus sequence analysis (MLSA) represents the novel typical in microbial molecule systematics. In this context, MLSA is implemented in a relatively straightforward way, consisting essentially in the concatenation of number of sequence partitions for the same collection of organisms, leading to a “supermatrix” i beg your pardon is offered to infer a phylogeny by way of distance-matrix or optimality criterion-based methods. This strategy is expected to have actually an enhanced resolving power as result of the big number of personalities analyzed and a reduced sensitivity to the affect of conflicting signal (i.e. Phylogenetic incongruence) that result from eventual horizontal gene transport events. The strategies used to address multiple partitions have the right to be group in three broad categories: the complete evidence, different analysis, and mix approaches. The concatenation technique that restrict MLSAs in the microbial molecule systematics literary works is known to systematists working with plants and animals together the “total molecule evidence” approach. It has been provided to solve challenging phylogenetic questions such as the relationships among the major groups the cetaceans, that of microsporidia and also fungi, or the phylogeny of major plant lineages. The full molecular evidence strategy has to be criticized because by directly concatenating all accessible sequence alignments. The proof of conflict phylogenetic signals in the different data partitions is lost along with the opportunity to i found it the evolutionary processes that provided rise come such inconsistent signals.

Nongenetic Categories because that Medicine and Ecology

In medicine, microorganisms are figured out by morphology, physiology, and other attributes; in ecology by habitat, energy, and carbon source.

Learning Objectives

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

Key Takeaways

Key PointsA pathogen causes an illness in that is host. In medicine, there are several broad varieties of pathogens: viruses, bacteria, fungi, eukaryotic bio parasites, and prions.When identify bacteria in the laboratory, the following characteristics are used: Gram staining, shape, visibility of a capsule, bonding tendency, motility, respiration, development medium, and whether that is intra- or extracellular.Viruses are greatly classified by phenotypic characteristics, such together morphology, nucleic mountain type, mode of replication, host organisms, and the type of an illness they cause.In ecology, microorganisms room classified by the form of habitat castle require, or trophic level, energy resource and carbon source.Biologists have discovered that microbial life has actually an amazing flexibility for enduring in extreme atmospheres that would certainly be totally inhospitable to complex organisms; these are called extremophiles and many kinds exist.Different species of microorganisms usage a mix of various sources that energy and carbon. These may be alternations between photo- and chemotrophy, between litho- and organotrophy, in between auto- and also heterotrophy or a combination of them.Key Termsobligate: Able to exist or survive just in a details environment or by suspect a particular role: one obligate parasite; an obligate anaerobe.pathogen: any organism or substance, particularly a microorganism, qualified of causing disease, such together bacteria, viruses, protozoa, or fungi. Microorganisms room not thought about to it is in pathogenic until they have reached a population size the is huge enough to cause disease.extremophile: An biology that stays under extreme conditions of temperature, salinity, and so on. They space commercially crucial as a resource of enzymes that run under comparable conditions.

Classifying microorganisms in medicine

A virus (colloquially recognized as a germ) is an contagious agent that causes condition in its host. In medicine, over there are several broad varieties of pathogens: viruses, bacteria, fungi, eukaryotic bio parasites, and also prions.


Although many bacteria space harmless, even beneficial, quite a few are pathogenic. Each pathogenic types has a characteristic spectrum the interactions with its human hosts.

Conditionally, pathogenic bacteria are just pathogenic under certain conditions; such as a wound that enables for entry into the blood, or a diminish in immune function. Bacter infections can also be divide by location 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, development medium, and whether it is intra- or extracellular.

Culture techniques are designed to grow and identify details bacteria, while restricting the development of the rather in the sample. Often these techniques are design for details specimens: for example, a sputum sample will be cure to identify organisms that cause pneumonia. When a pathogenic organism has been isolated, it deserve to be further qualified by that is morphology, growth patterns (aerobic or anaerobic), patterns of hemolysis, and also staining.


Similar come the classification systems provided for moving organisms, virus group is the subject of ongoing controversy due to their pseudo-living nature. Essentially, they are non-living particles through some chemical characteristics comparable to those of life; thus, they carry out not to the right neatly into an established organic classification system.

Viruses are largely classified by phenotypic characteristics,such as:

morphologynucleic acid typemode the replicationhost organismstype of condition they cause

Currently there are two key schemes offered for the classification of viruses: (1) the global Committee ~ above Taxonomy the Viruses (ICTV) system; and (2) the Baltimore classification system, which locations viruses right into one of seven groups. To date, 6 orders have actually been created by the ICTV:


These orders expectations viruses v varying hold ranges, only some of i m sorry infect person hosts.

Baltimore category is a mechanism that places viruses right into one of seven groups depending upon a combination of:

their nucleic mountain (DNA or RNA)strandedness (single or double)sensemethod the replication

Other classifications are figured out by the disease caused by the virus or the morphology, neither of which is satisfactory as various viruses have the right to either reason the same condition or look very similar. In addition, viral structures room often daunting to determine under the microscope. Classifying viruses follow to your genome way that those in a given group will every behave in a similar fashion, giving some indication of exactly how to proceed with additional research.

Other organisms invariably cause an illness in humans, such together obligate intracellular helminth that space able come grow and also reproduce just within the cells of other organisms.


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

Habitat Type

Biologists have uncovered that microbial life has an amazing adaptability for making it through in extreme environments that would certainly be totally inhospitable to facility organisms. Some also concluded the life might have begun on earth in hydrothermal vents far under the ocean’s surface.

An extremophile is an organism that thrives in physical or geochemically too much conditions, detrimental to many life on Earth. Most known extremophiles space microbes. The domain Archaea consists of renowned examples, however extremophiles are present in numerous and also diverse genetic lineages the both bacteria and also archaeans. In contrast, organisms that live in more moderate environments may be termed mesophiles or neutrophiles.

There are many different great of extremophiles, each equivalent to the means its eco-friendly niche differs from mesophilic conditions. Many extremophiles fall under multiple categories and are termed polyextremophiles. Some instances of types of extremophiles:

Acidophile: one organism through optimal development at level of pH 3 or belowXerophile: an organism that can thrive in very dry, desiccating conditions; exemplified by the floor microbes that the Atacama DesertHalophile: an biology requiring at the very least 0.2M concentration of salt (NaCl) for growthThermophile: one organism that can flourish at temperatures in between 45–122 °C

Trophic level, energy resource and carbon source

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

Phototrophs: bring out photon record to get energy. They use the energy from irradiate to bring out miscellaneous cellular metabolic processes. They room not obligatorily photosynthetic. Many of the well-recognized phototrophs are autotrophs, also known as photoautotrophs, and also can deal with carbon.Photoheterotrophs: create ATP with photophosphorylation but use environmentally-obtained organic compounds to develop structures and also other bio- molecules.Photolithoautotroph: one autotrophic biology that supplies light energy, and also an inorganic electron donor (e.g., H2O, H2, H2S), and CO2 as its carbon source.Chemotrophs: attain their energy by the oxidation that electron donors in your environments.Chemoorganotrophs: organisms which oxidization the chemistry bonds in essential compounds together their energy resource and attain the carbon molecules they need for to move function. This oxidized essential compounds incorporate sugars, fats and also proteins.Chemoorganoheterotrophs (or organotrophs) make use of reduced-carbon compound as power sources, such together carbohydrates, fats, and proteins indigenous plants and animals. Chemolithoheterotrophs (or lithotrophic heterotrophs) utilize inorganic substances to develop ATP, including hydrogen sulfide and also elemental sulfur.Lithoautotroph: derives power from reduced compounds that mineral origin. May also be referred to as chemolithoautotrophs, showing their autotrophic metabolic pathways. Lithoautotrophs are solely microbes and also most room bacteria. For lithoautotrophic bacteria, only not natural molecules can be used as power sources.Mixotroph: can use a mix of different sources the energy and also carbon. These might be alternations in between photo- and chemotrophy, between litho- and organotrophy, in between auto- and heterotrophy or a mix of them. Can be either eukaryotic bio or prokaryotic.

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Differing morphology in different Herpes viruses: various viruses from the Herpesviridae household seen making use of an electron micrograph. Amongst these members is varicella-zoster (Chickenpox), and also herpes simplex form 1 and also 2 (HSV-1, HSV-2).