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Marine prokaryotes are marine
bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were am ...
and marine
archaea Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaeba ...
. They are defined by their habitat as
prokaryote A prokaryote () is a single-celled organism that lacks a nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek πρό (, 'before') and κάρυον (, 'nut' or 'kernel').Campbell, N. "Biology:Concepts & Con ...
s that live in
marine environments Marine habitats are habitats that support marine life. Marine life depends in some way on the saltwater that is in the sea (the term ''marine'' comes from the Latin ''mare'', meaning sea or ocean). A habitat is an ecological or environmental a ...
, that is, in the
saltwater Saline water (more commonly known as salt water) is water that contains a high concentration of dissolved salts (mainly sodium chloride). On the United States Geological Survey (USGS) salinity scale, saline water is saltier than brackish water, ...
of seas or oceans or the
brackish Brackish water, sometimes termed brack water, is water occurring in a natural environment that has more salinity than freshwater, but not as much as seawater. It may result from mixing seawater (salt water) and fresh water together, as in estua ...
water of coastal
estuaries An estuary is a partially enclosed coastal body of brackish water with one or more rivers or streams flowing into it, and with a free connection to the open sea. Estuaries form a transition zone between river environments and maritime environme ...
. All cellular life forms can be divided into prokaryotes and eukaryotes.
Eukaryote Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bacter ...
s are
organism In biology, an organism () is any living system that functions as an individual entity. All organisms are composed of cells ( cell theory). Organisms are classified by taxonomy into groups such as multicellular animals, plants, and fu ...
s whose cells have a
nucleus Nucleus ( : nuclei) is a Latin word for the seed inside a fruit. It most often refers to: * Atomic nucleus, the very dense central region of an atom *Cell nucleus, a central organelle of a eukaryotic cell, containing most of the cell's DNA Nucl ...
enclosed within
membranes A membrane is a selective barrier; it allows some things to pass through but stops others. Such things may be molecules, ions, or other small particles. Membranes can be generally classified into synthetic membranes and biological membranes. Bi ...
, whereas prokaryotes are the organisms that do not have a nucleus enclosed within a membrane. The
three-domain system The three-domain system is a biological classification introduced by Carl Woese, Otto Kandler, and Mark Wheelis in 1990 that divides cellular life forms into three domains, namely Archaea, Bacteria, and Eukaryota or Eukarya. The key difference ...
of classifying life adds another division: the prokaryotes are divided into two domains of life, the microscopic bacteria and the microscopic archaea, while everything else, the eukaryotes, become the third domain. Prokaryotes play important roles in
ecosystem An ecosystem (or ecological system) consists of all the organisms and the physical environment with which they interact. These biotic and abiotic components are linked together through nutrient cycles and energy flows. Energy enters the syst ...
s as decomposers recycling nutrients. Some prokaryotes are
pathogen In biology, a pathogen ( el, πάθος, "suffering", "passion" and , "producer of") in the oldest and broadest sense, is any organism or agent that can produce disease. A pathogen may also be referred to as an infectious agent, or simply a g ...
ic, causing disease and even death in plants and animals.2002 WHO mortality data
Accessed 20 January 2007
Marine prokaryotes are responsible for significant levels of the
photosynthesis Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that, through cellular respiration, can later be released to fuel the organism's activities. Some of this chemical energy is stored in ...
that occurs in the ocean, as well as significant cycling of
carbon Carbon () is a chemical element with the symbol C and atomic number 6. It is nonmetallic and tetravalent—its atom making four electrons available to form covalent chemical bonds. It belongs to group 14 of the periodic table. Carbon ma ...
and other
nutrients A nutrient is a substance used by an organism to survive, grow, and reproduce. The requirement for dietary nutrient intake applies to animals, plants, fungi, and protists. Nutrients can be incorporated into cells for metabolic purposes or excr ...
. Prokaryotes live throughout the
biosphere The biosphere (from Greek βίος ''bíos'' "life" and σφαῖρα ''sphaira'' "sphere"), also known as the ecosphere (from Greek οἶκος ''oîkos'' "environment" and σφαῖρα), is the worldwide sum of all ecosystems. It can also ...
. In 2018 it was estimated the total
biomass Biomass is plant-based material used as a fuel for heat or electricity production. It can be in the form of wood, wood residues, energy crops, agricultural residues, and waste from industry, farms, and households. Some people use the terms bio ...
of all prokaryotes on the planet was equivalent to 77 billion
tonne The tonne ( or ; symbol: t) is a unit of mass equal to 1000  kilograms. It is a non-SI unit accepted for use with SI. It is also referred to as a metric ton to distinguish it from the non-metric units of the short ton ( United State ...
s of carbon (77 Gt C). This is made up of 7 Gt C for archaea and 70 Gt C for bacteria. These figures can be contrasted with the estimate for the total biomass for animals on the planet, which is about 2 Gt C, and the total biomass of humans, which is 0.06 Gt C. This means archaea collectively have over 100 times the collective biomass of humans, and bacteria over 1000 times. There is no clear evidence of life on Earth during the first 600 million years of its existence. When life did arrive, it was dominated for 3,200 million years by the marine prokaryotes. More complex life, in the form of
crown eukaryotes Taking into account the definition of a crown group, crown eukaryotes could be seen as the aggrupation of all lineages descending from LECA (Last Eukarytotic Common Ancestor). This comprises a huge ensemble of taxa that seemingly diverged simult ...
, didn't appear until the
Cambrian explosion The Cambrian explosion, Cambrian radiation, Cambrian diversification, or the Biological Big Bang refers to an interval of time approximately in the Cambrian Period when practically all major animal phyla started appearing in the fossil record. ...
a mere 500 million years ago.


Evolution

The
Earth Earth is the third planet from the Sun and the only astronomical object known to harbor life. While large volumes of water can be found throughout the Solar System, only Earth sustains liquid surface water. About 71% of Earth's sur ...
is about 4.54 billion years old. The earliest undisputed evidence of life on Earth dates from at least 3.5 billion years ago, during the Eoarchean Era after a geological crust started to solidify following the earlier molten
Hadean The Hadean ( ) is a geologic eon of Earth history preceding the Archean. On Earth, the Hadean began with the planet's formation about 4.54 billion years ago (although the start of the Hadean is defined as the age of the oldest solid materia ...
Eon.
Microbial mat A microbial mat is a multi-layered sheet of microorganisms, mainly bacteria and archaea, or bacteria alone. Microbial mats grow at interfaces between different types of material, mostly on submerged or moist surfaces, but a few survive in deserts ...
fossils A fossil (from Classical Latin , ) is any preserved remains, impression, or trace of any once-living thing from a past geological age. Examples include bones, shells, exoskeletons, stone imprints of animals or microbes, objects preserved ...
have been found in 3.48 billion-year-old
sandstone Sandstone is a clastic sedimentary rock composed mainly of sand-sized (0.0625 to 2 mm) silicate grains. Sandstones comprise about 20–25% of all sedimentary rocks. Most sandstone is composed of quartz or feldspar (both silicat ...
in
Western Australia Western Australia (commonly abbreviated as WA) is a state of Australia occupying the western percent of the land area of Australia excluding external territories. It is bounded by the Indian Ocean to the north and west, the Southern Ocean to t ...
. Past species have also left records of their evolutionary history. Fossils, along with the comparative anatomy of present-day organisms, constitute the morphological, or anatomical, record. By comparing the anatomies of both modern and extinct species, paleontologists can infer the lineages of those species. However, this approach is most successful for organisms that had hard body parts, such as shells, bones or teeth. Further, as prokaryotes such as bacteria and archaea share a limited set of common morphologies, their fossils do not provide information on their ancestry. Prokaryotes inhabited the Earth from approximately 3–4 billion years ago. No obvious changes in morphology or cellular organisation occurred in these organisms over the next few billion years. The eukaryotic cells emerged between 1.6 and 2.7 billion years ago. The next major change in cell structure came when bacteria were engulfed by eukaryotic cells, in a cooperative association called
endosymbiosis An ''endosymbiont'' or ''endobiont'' is any organism that lives within the body or cells of another organism most often, though not always, in a mutualistic relationship. (The term endosymbiosis is from the Greek: ἔνδον ''endon'' "within ...
. The engulfed bacteria and the host cell then underwent coevolution, with the bacteria evolving into either mitochondria or
hydrogenosome A hydrogenosome is a membrane-enclosed organelle found in some anaerobic ciliates, flagellates, and fungi. Hydrogenosomes are highly variable organelles that have presumably evolved from protomitochondria to produce molecular hydrogen and ATP i ...
s. Another engulfment of
cyanobacteria Cyanobacteria (), also known as Cyanophyta, are a phylum of gram-negative bacteria that obtain energy via photosynthesis. The name ''cyanobacteria'' refers to their color (), which similarly forms the basis of cyanobacteria's common name, bl ...
l-like organisms led to the formation of chloroplasts in algae and plants. The history of life was that of the unicellular prokaryotes and eukaryotes until about 610 million years ago when multicellular organisms began to appear in the oceans in the
Ediacaran The Ediacaran Period ( ) is a geological period that spans 96 million years from the end of the Cryogenian Period 635 million years ago (Mya), to the beginning of the Cambrian Period 538.8 Mya. It marks the end of the Proterozoic Eon, and t ...
period. The
evolution of multicellularity A multicellular organism is an organism that consists of more than one cell, in contrast to unicellular organism. All species of animals, land plants and most fungi are multicellular, as are many algae, whereas a few organisms are partially uni- ...
occurred in multiple independent events, in organisms as diverse as
sponge Sponges, the members of the phylum Porifera (; meaning 'pore bearer'), are a basal animal clade as a sister of the diploblasts. They are multicellular organisms that have bodies full of pores and channels allowing water to circulate throu ...
s,
brown algae Brown algae (singular: alga), comprising the class Phaeophyceae, are a large group of multicellular algae, including many seaweeds located in colder waters within the Northern Hemisphere. Brown algae are the major seaweeds of the temperate and p ...
,
cyanobacteria Cyanobacteria (), also known as Cyanophyta, are a phylum of gram-negative bacteria that obtain energy via photosynthesis. The name ''cyanobacteria'' refers to their color (), which similarly forms the basis of cyanobacteria's common name, bl ...
, slime moulds and
myxobacteria The myxobacteria ("slime bacteria") are a group of bacteria that predominantly live in the soil and feed on insoluble organic substances. The myxobacteria have very large genomes relative to other bacteria, e.g. 9–10 million nucleotides except ...
. In 2016 scientists reported that, about 800 million years ago, a minor genetic change in a single molecule called GK-PID may have allowed organisms to go from a single cell organism to one of many cells. Soon after the emergence of these first multicellular organisms, a remarkable amount of biological diversity appeared over a span of about 10 million years, in an event called the
Cambrian explosion The Cambrian explosion, Cambrian radiation, Cambrian diversification, or the Biological Big Bang refers to an interval of time approximately in the Cambrian Period when practically all major animal phyla started appearing in the fossil record. ...
. Here, the majority of
types Type may refer to: Science and technology Computing * Typing, producing text via a keyboard, typewriter, etc. * Data type In computer science and computer programming, a data type (or simply type) is a set of possible values and a set of allo ...
of modern animals appeared in the fossil record, as well as unique lineages that subsequently became extinct. Various triggers for the Cambrian explosion have been proposed, including the accumulation of
oxygen Oxygen is the chemical element with the symbol O and atomic number 8. It is a member of the chalcogen group in the periodic table, a highly reactive nonmetal, and an oxidizing agent that readily forms oxides with most elements ...
in the
atmosphere An atmosphere () is a layer of gas or layers of gases that envelop a planet, and is held in place by the gravity of the planetary body. A planet retains an atmosphere when the gravity is great and the temperature of the atmosphere is low. A ...
from photosynthesis.


Background

The words prokaryote and eukaryote come from the Greek where ''pro'' means "before", ''eu'' means "well" or "true", and ''karyon'' means "nut", "kernel" or "nucleus". So etymologically, prokaryote means "before nucleus" and eukaryote means "true nucleus". The division of life forms between prokaryotes and eukaryotes was firmly established by the microbiologists
Roger Stanier Roger Yate Stanier (22 October 1916 – 29 January 1982) was a Canadian microbiologist who was influential in the development of modern microbiology. As a member of the Delft School and former student of C. B. van Niel, he made important contribu ...
and C. B. van Niel in their 1962 paper, ''The concept of a bacterium''. One reason for this classification was so what was then often called ''blue-green algae'' (now called
cyanobacteria Cyanobacteria (), also known as Cyanophyta, are a phylum of gram-negative bacteria that obtain energy via photosynthesis. The name ''cyanobacteria'' refers to their color (), which similarly forms the basis of cyanobacteria's common name, bl ...
) would cease to be classified as plants but grouped with bacteria. In 1990
Carl Woese Carl Richard Woese (; July 15, 1928 – December 30, 2012) was an American microbiologist and biophysicist. Woese is famous for defining the Archaea (a new domain of life) in 1977 through a pioneering phylogenetic taxonomy of 16S ribosomal RNA, ...
''et al.'' introduced the
three-domain system The three-domain system is a biological classification introduced by Carl Woese, Otto Kandler, and Mark Wheelis in 1990 that divides cellular life forms into three domains, namely Archaea, Bacteria, and Eukaryota or Eukarya. The key difference ...
. The prokaryotes were split into two domains, the archaea and the bacteria, while the eukaryotes become a domain in their own right. The key difference from earlier classifications is the splitting of archaea from bacteria. The earliest evidence for life on earth comes from
biogenic A biogenic substance is a product made by or of life forms. While the term originally was specific to metabolite compounds that had toxic effects on other organisms, it has developed to encompass any constituents, secretions, and metabolites of p ...
carbon signatures and
stromatolite Stromatolites () or stromatoliths () are layered sedimentary formations ( microbialite) that are created mainly by photosynthetic microorganisms such as cyanobacteria, sulfate-reducing bacteria, and Pseudomonadota (formerly proteobacteria). T ...
fossils discovered in 3.7 billion-year-old rocks. In 2015, possible "remains of biotic life" were found in 4.1 billion-year-old rocks. In 2017 putative evidence of possibly the oldest forms of life on Earth was reported in the form of fossilized
microorganism A microorganism, or microbe,, ''mikros'', "small") and ''organism'' from the el, ὀργανισμός, ''organismós'', "organism"). It is usually written as a single word but is sometimes hyphenated (''micro-organism''), especially in old ...
s discovered in
hydrothermal vent A hydrothermal vent is a fissure on the seabed from which geothermally heated water discharges. They are commonly found near volcanically active places, areas where tectonic plates are moving apart at mid-ocean ridges, ocean basins, and hotspo ...
precipitates that may have lived as early as 4.28 billion years ago, not long after the oceans formed 4.4 billion years ago, and not long after the
formation of the Earth Earth is the third planet from the Sun and the only astronomical object known to harbor life. While large volumes of water can be found throughout the Solar System, only Earth sustains liquid surface water. About 71% of Earth's surface ...
4.54 billion years ago. Microbial mats of coexisting
bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were am ...
and
archaea Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaeba ...
were the dominant form of life in the early Archean Eon and many of the major steps in early evolution are thought to have taken place in this environment. The evolution of
photosynthesis Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that, through cellular respiration, can later be released to fuel the organism's activities. Some of this chemical energy is stored in ...
around 3.5 Ga resulted in a buildup of its waste product
oxygen Oxygen is the chemical element with the symbol O and atomic number 8. It is a member of the chalcogen group in the periodic table, a highly reactive nonmetal, and an oxidizing agent that readily forms oxides with most elements ...
in the atmosphere, leading to the
great oxygenation event The Great Oxidation Event (GOE), also called the Great Oxygenation Event, the Oxygen Catastrophe, the Oxygen Revolution, the Oxygen Crisis, or the Oxygen Holocaust, was a time interval during the Paleoproterozoic era when the Earth's atmospher ...
beginning around 2.4 Ga. The earliest evidence of eukaryotes dates from 1.85 Ga, and while they may have been present earlier, their diversification accelerated when they started using oxygen in their
metabolism Metabolism (, from el, μεταβολή ''metabolē'', "change") is the set of life-sustaining chemical reactions in organisms. The three main functions of metabolism are: the conversion of the energy in food to energy available to run ...
. Later, around 1.7 Ga,
multicellular organism A multicellular organism is an organism that consists of more than one cell, in contrast to unicellular organism. All species of animals, land plants and most fungi are multicellular, as are many algae, whereas a few organisms are partially uni ...
s began to appear, with differentiated cells performing specialised functions. A stream of airborne microorganisms, including prokaryotes, circles the planet above weather systems but below commercial air lanes. Some peripatetic microorganisms are swept up from terrestrial dust storms, but most originate from marine microorganisms in
sea spray Sea spray are aerosol particles formed from the ocean, mostly by ejection into Earth's atmosphere by bursting bubbles at the air-sea interface. Sea spray contains both organic matter and inorganic salts that form sea salt aerosol (SSA). SSA ha ...
. In 2018, scientists reported that hundreds of millions of viruses and tens of millions of bacteria are deposited daily on every square meter around the planet. Microscopic life undersea is diverse and still poorly understood, such as for the role of
virus A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. Since Dmitri Ivanovsk ...
es in marine ecosystems. Most marine viruses are
bacteriophage A bacteriophage (), also known informally as a ''phage'' (), is a duplodnaviria virus that infects and replicates within bacteria and archaea. The term was derived from "bacteria" and the Greek φαγεῖν ('), meaning "to devour". Bac ...
s, which are harmless to plants and animals, but are essential to the regulation of saltwater and freshwater ecosystems. They infect and destroy bacteria and archaea in aquatic microbial communities, and are the most important mechanism of recycling carbon in the marine environment. The organic molecules released from the dead bacterial cells stimulate fresh bacterial and algal growth. Viral activity may also contribute to the
biological pump The biological pump (or ocean carbon biological pump or marine biological carbon pump) is the ocean's biologically driven sequestration of carbon from the atmosphere and land runoff to the ocean interior and seafloor sediments.Sigman DM & GH ...
, the process whereby
carbon Carbon () is a chemical element with the symbol C and atomic number 6. It is nonmetallic and tetravalent—its atom making four electrons available to form covalent chemical bonds. It belongs to group 14 of the periodic table. Carbon ma ...
is sequestered in the deep ocean.


Marine bacteria

Bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were am ...
constitute a large
domain Domain may refer to: Mathematics *Domain of a function, the set of input values for which the (total) function is defined ** Domain of definition of a partial function ** Natural domain of a partial function **Domain of holomorphy of a function * ...
of prokaryotic
microorganism A microorganism, or microbe,, ''mikros'', "small") and ''organism'' from the el, ὀργανισμός, ''organismós'', "organism"). It is usually written as a single word but is sometimes hyphenated (''micro-organism''), especially in old ...
s. Typically a few
micrometre The micrometre (American and British English spelling differences#-re, -er, international spelling as used by the International Bureau of Weights and Measures; SI symbol: μm) or micrometer (American and British English spelling differences# ...
s in length, bacteria have a number of shapes, ranging from spheres to rods and spirals. Bacteria were among the first life forms to appear on
Earth Earth is the third planet from the Sun and the only astronomical object known to harbor life. While large volumes of water can be found throughout the Solar System, only Earth sustains liquid surface water. About 71% of Earth's sur ...
, and are present in most of its
habitat In ecology, the term habitat summarises the array of resources, physical and biotic factors that are present in an area, such as to support the survival and reproduction of a particular species. A species habitat can be seen as the physical ...
s. Bacteria inhabit soil, water, acidic hot springs,
radioactive waste Radioactive waste is a type of hazardous waste that contains radioactive material. Radioactive waste is a result of many activities, including nuclear medicine, nuclear research, nuclear power generation, rare-earth mining, and nuclear weapon ...
, and the deep portions of
Earth's crust Earth's crust is Earth's thin outer shell of rock, referring to less than 1% of Earth's radius and volume. It is the top component of the lithosphere, a division of Earth's layers that includes the crust and the upper part of the mantle. The ...
. Bacteria also live in
symbiotic Symbiosis (from Greek , , "living together", from , , "together", and , bíōsis, "living") is any type of a close and long-term biological interaction between two different biological organisms, be it mutualistic, commensalistic, or para ...
and
parasitic Parasitism is a close relationship between species, where one organism, the parasite, lives on or inside another organism, the host, causing it some harm, and is adapted structurally to this way of life. The entomologist E. O. Wilson ha ...
relationships with plants and animals. Once regarded as
plant Plants are predominantly photosynthetic eukaryotes of the kingdom Plantae. Historically, the plant kingdom encompassed all living things that were not animals, and included algae and fungi; however, all current definitions of Plantae excl ...
s constituting the class ''Schizomycetes'', bacteria are now classified as
prokaryotes A prokaryote () is a single-celled organism that lacks a nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek πρό (, 'before') and κάρυον (, 'nut' or 'kernel').Campbell, N. "Biology:Concepts & Con ...
. Unlike cells of animals and other
eukaryote Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bacter ...
s, bacterial cells do not contain a
nucleus Nucleus ( : nuclei) is a Latin word for the seed inside a fruit. It most often refers to: * Atomic nucleus, the very dense central region of an atom *Cell nucleus, a central organelle of a eukaryotic cell, containing most of the cell's DNA Nucl ...
and rarely harbour membrane-bound
organelle In cell biology, an organelle is a specialized subunit, usually within a cell, that has a specific function. The name ''organelle'' comes from the idea that these structures are parts of cells, as organs are to the body, hence ''organelle,'' th ...
s. Although the term ''bacteria'' traditionally included all prokaryotes, the
scientific classification Taxonomy is the practice and science of categorization or classification. A taxonomy (or taxonomical classification) is a scheme of classification, especially a hierarchical classification, in which things are organized into groups or types. ...
changed after the discovery in the 1990s that prokaryotes consist of two very different groups of organisms that
evolved Evolution is change in the heritable characteristics of biological populations over successive generations. These characteristics are the expressions of genes, which are passed on from parent to offspring during reproduction. Variati ...
from an ancient common ancestor. These evolutionary domains are called ''Bacteria'' and ''
Archaea Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaeba ...
''. The ancestors of modern bacteria were unicellular microorganisms that were the first forms of life to appear on Earth, about 4 billion years ago. For about 3 billion years, most organisms were microscopic, and bacteria and archaea were the dominant forms of life. Although bacterial
fossil A fossil (from Classical Latin , ) is any preserved remains, impression, or trace of any once-living thing from a past geological age. Examples include bones, shells, exoskeletons, stone imprints of animals or microbes, objects preserved ...
s exist, such as
stromatolite Stromatolites () or stromatoliths () are layered sedimentary formations ( microbialite) that are created mainly by photosynthetic microorganisms such as cyanobacteria, sulfate-reducing bacteria, and Pseudomonadota (formerly proteobacteria). T ...
s, their lack of distinctive morphology prevents them from being used to examine the history of bacterial evolution, or to date the time of origin of a particular bacterial species. However, gene sequences can be used to reconstruct the bacterial
phylogeny A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree showing the evolutionary relationships among various biological s ...
, and these studies indicate that bacteria diverged first from the archaeal/eukaryotic lineage. Bacteria were also involved in the second great evolutionary divergence, that of the archaea and eukaryotes. Here, eukaryotes resulted from the entering of ancient bacteria into
endosymbiotic An ''endosymbiont'' or ''endobiont'' is any organism that lives within the body or cells of another organism most often, though not always, in a mutualistic relationship. (The term endosymbiosis is from the Greek: ἔνδον ''endon'' "within ...
associations with the ancestors of eukaryotic cells, which were themselves possibly related to the
Archaea Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaeba ...
. This involved the engulfment by proto-eukaryotic cells of alphaproteobacterial symbionts to form either
mitochondria A mitochondrion (; ) is an organelle found in the cells of most Eukaryotes, such as animals, plants and fungi. Mitochondria have a double membrane structure and use aerobic respiration to generate adenosine triphosphate (ATP), which is used ...
or
hydrogenosome A hydrogenosome is a membrane-enclosed organelle found in some anaerobic ciliates, flagellates, and fungi. Hydrogenosomes are highly variable organelles that have presumably evolved from protomitochondria to produce molecular hydrogen and ATP i ...
s, which are still found in all known Eukarya. Later on, some eukaryotes that already contained mitochondria also engulfed cyanobacterial-like organisms. This led to the formation of
chloroplast A chloroplast () is a type of membrane-bound organelle known as a plastid that conducts photosynthesis mostly in plant and algal cells. The photosynthetic pigment chlorophyll captures the energy from sunlight, converts it, and stores it i ...
s in algae and plants. There are also some algae that originated from even later endosymbiotic events. Here, eukaryotes engulfed a eukaryotic algae that developed into a "second-generation" plastid. This is known as secondary endosymbiosis. Bacteria grow to a fixed size and then reproduce through
binary fission Binary may refer to: Science and technology Mathematics * Binary number, a representation of numbers using only two digits (0 and 1) * Binary function, a function that takes two arguments * Binary operation, a mathematical operation that ta ...
, a form of
asexual reproduction Asexual reproduction is a type of reproduction that does not involve the fusion of gametes or change in the number of chromosomes. The offspring that arise by asexual reproduction from either unicellular or multicellular organisms inherit the ...
. Under optimal conditions, bacteria can grow and divide extremely rapidly, and bacterial populations can double as quickly as every 9.8 minutes. '' Pelagibacter ubique'' and its relatives may be the most abundant microorganisms in the ocean, and it has been claimed that they are possibly the most abundant bacteria in the world. They make up about 25% of all microbial
plankton Plankton are the diverse collection of organisms found in water (or air) that are unable to propel themselves against a current (or wind). The individual organisms constituting plankton are called plankters. In the ocean, they provide a cruc ...
cells, and in the summer they may account for approximately half the cells present in temperate ocean surface water. The total abundance of ''P. ubique'' and relatives is estimated to be about 2 × 1028 microbes. However, it was reported in ''
Nature Nature, in the broadest sense, is the physical world or universe. "Nature" can refer to the phenomena of the physical world, and also to life in general. The study of nature is a large, if not the only, part of science. Although humans are ...
'' in February 2013 that the
bacteriophage A bacteriophage (), also known informally as a ''phage'' (), is a duplodnaviria virus that infects and replicates within bacteria and archaea. The term was derived from "bacteria" and the Greek φαγεῖν ('), meaning "to devour". Bac ...
HTVC010P, which attacks ''P. ubique'', has been discovered and is probably the most common organism on the planet. '' Roseobacter'' is also one of the most abundant and versatile microorganisms in the ocean. They are diversified across different types of marine habitats, from coastal to open oceans and from sea ice to sea floor, and make up about 25% of coastal marine bacteria. Members of the '' Roseobacter'' genus play important roles in marine biogeochemical cycles and climate change, processing a significant portion of the total carbon in the marine environment. They form symbiotic relationships which allow them to degrade aromatic compounds and uptake trace metals. They are widely used in aquaculture and quorum sensing. During algal blooms, 20-30% of the prokaryotic community are Roseobacter. The largest known bacterium, the marine '' Thiomargarita namibiensis'', can be visible to the naked eye and sometimes attains .


Cyanobacteria

Cyanobacteria Cyanobacteria (), also known as Cyanophyta, are a phylum of gram-negative bacteria that obtain energy via photosynthesis. The name ''cyanobacteria'' refers to their color (), which similarly forms the basis of cyanobacteria's common name, bl ...
were the first organisms to evolve an ability to turn sunlight into chemical energy. They form a phylum (division) of bacteria which range from unicellular to
filamentous The word filament, which is descended from Latin ''filum'' meaning " thread", is used in English for a variety of thread-like structures, including: Astronomy * Galaxy filament, the largest known cosmic structures in the universe * Solar filamen ...
and include colonial species. They are found almost everywhere on earth: in damp soil, in both freshwater and marine environments, and even on Antarctic rocks. In particular, some species occur as drifting cells floating in the ocean, and as such were amongst the first of the
phytoplankton Phytoplankton () are the autotrophic (self-feeding) components of the plankton community and a key part of ocean and freshwater ecosystems. The name comes from the Greek words (), meaning 'plant', and (), meaning 'wanderer' or 'drifter'. ...
. The first primary producers that used photosynthesis were oceanic
cyanobacteria Cyanobacteria (), also known as Cyanophyta, are a phylum of gram-negative bacteria that obtain energy via photosynthesis. The name ''cyanobacteria'' refers to their color (), which similarly forms the basis of cyanobacteria's common name, bl ...
about 2.3 billion years ago. The release of molecular
oxygen Oxygen is the chemical element with the symbol O and atomic number 8. It is a member of the chalcogen group in the periodic table, a highly reactive nonmetal, and an oxidizing agent that readily forms oxides with most elements ...
by
cyanobacteria Cyanobacteria (), also known as Cyanophyta, are a phylum of gram-negative bacteria that obtain energy via photosynthesis. The name ''cyanobacteria'' refers to their color (), which similarly forms the basis of cyanobacteria's common name, bl ...
as a by-product of photosynthesis induced global changes in the Earth's environment. Because oxygen was toxic to most life on Earth at the time, this led to the near-extinction of oxygen-intolerant organisms, a dramatic change which redirected the evolution of the major animal and plant species. File:Trichodesmium_bloom_off_Great_Barrier_Reef_2014-03-07_19-59.jpg, Bloom of the
filamentous The word filament, which is descended from Latin ''filum'' meaning " thread", is used in English for a variety of thread-like structures, including: Astronomy * Galaxy filament, the largest known cosmic structures in the universe * Solar filamen ...
cyanobacteria '' Trichodesmium'' File:Potomac river eutro.jpg,
Cyanobacteria Cyanobacteria (), also known as Cyanophyta, are a phylum of gram-negative bacteria that obtain energy via photosynthesis. The name ''cyanobacteria'' refers to their color (), which similarly forms the basis of cyanobacteria's common name, bl ...
blooms can contain lethal
cyanotoxin Cyanotoxins are toxins produced by cyanobacteria (also known as blue-green algae). Cyanobacteria are found almost everywhere, but particularly in lakes and in the ocean where, under high concentration of phosphorus conditions, they reproduce exp ...
s
File:Synechococcus PCC 7002 DIC.jpg,
Synechococcus ''Synechococcus'' (from the Greek ''synechos'', in succession, and the Greek ''kokkos'', granule) is a unicellular cyanobacterium that is very widespread in the marine environment. Its size varies from 0.8 to 1.5 µm. The photosynthetic c ...
, a widespread marine cyanobacterium within a species of ''
Synechococcus ''Synechococcus'' (from the Greek ''synechos'', in succession, and the Greek ''kokkos'', granule) is a unicellular cyanobacterium that is very widespread in the marine environment. Its size varies from 0.8 to 1.5 µm. The photosynthetic c ...
'' File:Synechococcus elongatus PCC 7942 electron micrograph showing carboxysomes.jpeg, Carboxysomes appearing as polyhedral dark structures within a species of ''
Synechococcus ''Synechococcus'' (from the Greek ''synechos'', in succession, and the Greek ''kokkos'', granule) is a unicellular cyanobacterium that is very widespread in the marine environment. Its size varies from 0.8 to 1.5 µm. The photosynthetic c ...
''
The tiny (0.6
µm The micrometre ( international spelling as used by the International Bureau of Weights and Measures; SI symbol: μm) or micrometer ( American spelling), also commonly known as a micron, is a unit of length in the International System of Uni ...
) marine cyanobacterium ''
Prochlorococcus ''Prochlorococcus'' is a genus of very small (0.6 μm) marine cyanobacteria with an unusual pigmentation ( chlorophyll ''a2'' and ''b2''). These bacteria belong to the photosynthetic picoplankton and are probably the most abundant photosynth ...
'', discovered in 1986, forms today an important part of the base of the ocean
food chain A food chain is a linear network of links in a food web starting from producer organisms (such as grass or algae which produce their own food via photosynthesis) and ending at an apex predator species (like grizzly bears or killer whales), de ...
and accounts for much of the photosynthesis of the open ocean and an estimated 20% of the oxygen in the Earth's atmosphere. It is possibly the most plentiful genus on Earth: a single millilitre of surface seawater may contain 100,000 cells or more. Originally, biologists classified
cyanobacteria Cyanobacteria (), also known as Cyanophyta, are a phylum of gram-negative bacteria that obtain energy via photosynthesis. The name ''cyanobacteria'' refers to their color (), which similarly forms the basis of cyanobacteria's common name, bl ...
as an algae, and referred to it as "blue-green algae". The more recent view is that cyanobacteria are bacteria, and hence are not even in the same Kingdom as algae. Most authorities exclude all
prokaryotes A prokaryote () is a single-celled organism that lacks a nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek πρό (, 'before') and κάρυον (, 'nut' or 'kernel').Campbell, N. "Biology:Concepts & Con ...
, and hence cyanobacteria from the definition of algae.


Other bacteria

Other marine bacteria, apart from cyanobacteria, are ubiquitous or can play important roles in the ocean. These include the opportunistic
copiotroph A copiotroph is an organism found in environments rich in nutrients, particularly carbon. They are the opposite to oligotrophs, which survive in much lower carbon concentrations. Copiotrophic organisms tend to grow in high organic substrate condit ...
, '' Alteromonas macleodii''.


Marine archaea

The
archaea Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaeba ...
(Greek for ''ancient'') constitute a
domain Domain may refer to: Mathematics *Domain of a function, the set of input values for which the (total) function is defined ** Domain of definition of a partial function ** Natural domain of a partial function **Domain of holomorphy of a function * ...
and kingdom of single-celled
microorganism A microorganism, or microbe,, ''mikros'', "small") and ''organism'' from the el, ὀργανισμός, ''organismós'', "organism"). It is usually written as a single word but is sometimes hyphenated (''micro-organism''), especially in old ...
s. These microbes are
prokaryotes A prokaryote () is a single-celled organism that lacks a nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek πρό (, 'before') and κάρυον (, 'nut' or 'kernel').Campbell, N. "Biology:Concepts & Con ...
, meaning they have no
cell nucleus The cell nucleus (pl. nuclei; from Latin or , meaning ''kernel'' or ''seed'') is a membrane-bound organelle found in eukaryotic cells. Eukaryotic cells usually have a single nucleus, but a few cell types, such as mammalian red blood cells, h ...
or any other membrane-bound
organelle In cell biology, an organelle is a specialized subunit, usually within a cell, that has a specific function. The name ''organelle'' comes from the idea that these structures are parts of cells, as organs are to the body, hence ''organelle,'' th ...
s in their cells. Archaea were initially classified as
bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were am ...
, but this classification is outdated. Archaeal cells have unique properties separating them from the other two domains of life,
Bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were am ...
and
Eukaryota Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bacter ...
. The Archaea are further divided into multiple recognized
phyla Phyla, the plural of ''phylum'', may refer to: * Phylum, a biological taxon between Kingdom and Class * by analogy, in linguistics, a large division of possibly related languages, or a major language family which is not subordinate to another Phy ...
. Classification is difficult because the majority have not been isolated in the laboratory and have only been detected by analysis of their
nucleic acid Nucleic acids are biopolymers, macromolecules, essential to all known forms of life. They are composed of nucleotides, which are the monomers made of three components: a 5-carbon sugar, a phosphate group and a nitrogenous base. The two main ...
s in samples from their environment. Bacteria and archaea are generally similar in size and shape, although a few archaea have very strange shapes, such as the flat and square-shaped cells of ''
Haloquadratum walsbyi ''Haloquadratum walsbyi'' is of the genus ''Haloquadratum,'' within the archaea domain known for its square halophilic nature. First discovered in a brine pool in the Sinai peninsula of Egypt, ''H. walsbyi'' is noted for its flat, square-shaped ...
''. Despite this morphological similarity to bacteria, archaea possess
gene In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a b ...
s and several
metabolic pathway In biochemistry, a metabolic pathway is a linked series of chemical reactions occurring within a cell. The reactants, products, and intermediates of an enzymatic reaction are known as metabolites, which are modified by a sequence of chemical ...
s that are more closely related to those of eukaryotes, notably the
enzyme Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as products ...
s involved in transcription and
translation Translation is the communication of the meaning of a source-language text by means of an equivalent target-language text. The English language draws a terminological distinction (which does not exist in every language) between ''transla ...
. Other aspects of archaeal biochemistry are unique, such as their reliance on
ether lipid In organic chemistry, ethers are a class of compounds that contain an ether group—an oxygen atom connected to two alkyl or aryl groups. They have the general formula , where R and R′ represent the alkyl or aryl groups. Ethers can again be ...
s in their
cell membrane The cell membrane (also known as the plasma membrane (PM) or cytoplasmic membrane, and historically referred to as the plasmalemma) is a biological membrane that separates and protects the interior of all cells from the outside environment (t ...
s, such as
archaeol Archaeol is composed of two phytanyl chains linked to the sn-2 and sn-3 positions of glycerol. As its phosphate ester, it is a common component of the membranes of archaea. Structure and contrast with other lipids Archaeol is a diether. The 2 ...
s. Archaea use more energy sources than eukaryotes: these range from
organic compounds In chemistry, organic compounds are generally any chemical compounds that contain carbon-hydrogen or carbon-carbon bonds. Due to carbon's ability to catenate (form chains with other carbon atoms), millions of organic compounds are known. The s ...
, such as sugars, to
ammonia Ammonia is an inorganic compound of nitrogen and hydrogen with the formula . A stable binary hydride, and the simplest pnictogen hydride, ammonia is a colourless gas with a distinct pungent smell. Biologically, it is a common nitrogenous ...
,
metal ions A metal (from Greek μέταλλον ''métallon'', "mine, quarry, metal") is a material that, when freshly prepared, polished, or fractured, shows a lustrous appearance, and conducts electricity and heat relatively well. Metals are typica ...
or even
hydrogen gas Hydrogen is the chemical element with the symbol H and atomic number 1. Hydrogen is the lightest element. At standard conditions hydrogen is a gas of diatomic molecules having the formula . It is colorless, odorless, tasteless, non-toxic, a ...
. Salt-tolerant archaea (the
Haloarchaea Haloarchaea (halophilic archaea, halophilic archaebacteria, halobacteria) are a class of the Euryarchaeota, found in water saturated or nearly saturated with salt. Halobacteria are now recognized as archaea rather than bacteria and are one of t ...
) use sunlight as an energy source, and other species of archaea fix carbon; however, unlike plants and
cyanobacteria Cyanobacteria (), also known as Cyanophyta, are a phylum of gram-negative bacteria that obtain energy via photosynthesis. The name ''cyanobacteria'' refers to their color (), which similarly forms the basis of cyanobacteria's common name, bl ...
, no known species of archaea does both. Archaea
reproduce asexually Asexual reproduction is a type of reproduction that does not involve the fusion of gametes or change in the number of chromosomes. The offspring that arise by asexual reproduction from either unicellular or multicellular organisms inherit the ...
by
binary fission Binary may refer to: Science and technology Mathematics * Binary number, a representation of numbers using only two digits (0 and 1) * Binary function, a function that takes two arguments * Binary operation, a mathematical operation that ta ...
, fragmentation, or
budding Budding or blastogenesis is a type of asexual reproduction in which a new organism develops from an outgrowth or bud due to cell division at one particular site. For example, the small bulb-like projection coming out from the yeast cell is kno ...
; unlike bacteria and eukaryotes, no known species forms
spore In biology, a spore is a unit of sexual or asexual reproduction that may be adapted for dispersal and for survival, often for extended periods of time, in unfavourable conditions. Spores form part of the life cycles of many plants, algae, ...
s. Archaea are particularly numerous in the oceans, and the archaea in
plankton Plankton are the diverse collection of organisms found in water (or air) that are unable to propel themselves against a current (or wind). The individual organisms constituting plankton are called plankters. In the ocean, they provide a cruc ...
may be one of the most abundant groups of organisms on the planet. Archaea are a major part of Earth's life and may play roles in both the
carbon cycle The carbon cycle is the biogeochemical cycle by which carbon is exchanged among the biosphere, pedosphere, geosphere, hydrosphere, and atmosphere of the Earth. Carbon is the main component of biological compounds as well as a major compon ...
and the
nitrogen cycle The nitrogen cycle is the biogeochemical cycle by which nitrogen is converted into multiple chemical forms as it circulates among atmospheric, terrestrial, and marine ecosystems. The conversion of nitrogen can be carried out through both biolo ...
.
Thermoproteota The Thermoproteota (also known as crenarchaea) are archaea that have been classified as a phylum of the Archaea domain. Initially, the Thermoproteota were thought to be sulfur-dependent extremophiles but recent studies have identified characteris ...
(also called Crenarchaeota or eocytes) are a phylum of archaea thought to be very abundant in marine environments and one of the main contributors to the fixation of carbon. File:RT8-4.jpg, Eocytes may be the most abundant of marine archaea File:Halobacteria with scale.jpg,
Halobacteria Haloarchaea (halophilic archaea, halophilic archaebacteria, halobacteria) are a class of the Euryarchaeota, found in water saturated or nearly saturated with salt. Halobacteria are now recognized as archaea rather than bacteria and are one of ...
, found in water near saturated with salt, are now recognised as archaea. File:Haloquadratum walsbyi00.jpg, Flat, square-shaped cells of the archaea ''
Haloquadratum walsbyi ''Haloquadratum walsbyi'' is of the genus ''Haloquadratum,'' within the archaea domain known for its square halophilic nature. First discovered in a brine pool in the Sinai peninsula of Egypt, ''H. walsbyi'' is noted for its flat, square-shaped ...
'' File:Methanosarcina barkeri fusaro.gif, ''
Methanosarcina barkeri '' Methanosarcina barkeri'' is the most fundamental species of the genus '' Methanosarcina'', and their properties apply generally to the genus ''Methanosarcina''. ''Methanosarcina barkeri'' can produce methane anaerobically through different m ...
'', a marine archaea that produces
methane Methane ( , ) is a chemical compound with the chemical formula (one carbon atom bonded to four hydrogen atoms). It is a group-14 hydride, the simplest alkane, and the main constituent of natural gas. The relative abundance of methane ...
File:Thermophile bacteria2.jpg,
Thermophile A thermophile is an organism—a type of extremophile—that thrives at relatively high temperatures, between . Many thermophiles are archaea, though they can be bacteria or fungi. Thermophilic eubacteria are suggested to have been among the earl ...
s, such as '' Pyrolobus fumarii'', survive well over 100 °C
''
Nanoarchaeum equitans ''Nanoarchaeum equitans'' is a species of marine archaea that was discovered in 2002 in a hydrothermal vent off the coast of Iceland on the Kolbeinsey Ridge by Karl Stetter. It has been proposed as the first species in a new phylum. Strains of ...
'' is a species of marine archaea discovered in 2002 in a
hydrothermal vent A hydrothermal vent is a fissure on the seabed from which geothermally heated water discharges. They are commonly found near volcanically active places, areas where tectonic plates are moving apart at mid-ocean ridges, ocean basins, and hotspo ...
. It is a
thermophile A thermophile is an organism—a type of extremophile—that thrives at relatively high temperatures, between . Many thermophiles are archaea, though they can be bacteria or fungi. Thermophilic eubacteria are suggested to have been among the earl ...
that grows in temperatures at about 80 degrees Celsius. ''Nanoarchaeum'' appears to be an
obligate symbiont Symbiosis (from Greek , , "living together", from , , "together", and , bíōsis, "living") is any type of a close and long-term biological interaction between two different biological organisms, be it mutualistic, commensalistic, or parasi ...
on the
archaeon Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaebact ...
''
Ignicoccus ''Ignicoccus'' is a genus of hyperthermophillic Archaea living in marine hydrothermal vents. They were discovered in samples taken at the Kolbeinsey Ridge north of Iceland, as well as at the East Pacific Rise (at 9 degrees N, 104 degrees W) i ...
''. It must stay in contact with the host organism to survive since ''Nanoarchaeum equitans'' cannot synthesize lipids but obtains them from its host. Its cells are only 400 nm in diameter, making it one of the smallest known cellular organisms, and the smallest known archaeon. Marine archaea have been classified as follows:See especially Fig. 4 in * Marine Group I (MG-I or MGI): marine Nitrososphaerota with subgroups Ia (aka I.a) up to Id * Marine Group II (MG-II): marine
Euryarchaeota Euryarchaeota (from Ancient Greek ''εὐρύς'' eurús, "broad, wide") is a phylum of archaea. Euryarchaeota are highly diverse and include methanogens, which produce methane and are often found in intestines, halobacteria, which survive extr ...
, order Poseidoniales with subgroups IIa up to IId (IIa resembling Poseidoniaceae, IIb resembling Thalassarchaceae)
Viruses parasiting MGII are classified as magroviruses * Marine Group III (MG-III): also marine Euryarchaeota, Marine Benthic Group D * Marine Group IV (MG-IV): also marine Euryarchaeota


Trophic mode

Prokaryote metabolism is classified into nutritional groups on the basis of three major criteria: the source of
energy In physics, energy (from Ancient Greek: ἐνέργεια, ''enérgeia'', “activity”) is the quantitative property that is transferred to a body or to a physical system, recognizable in the performance of work and in the form of ...
, the
electron donor In chemistry, an electron donor is a chemical entity that donates electrons to another compound. It is a reducing agent that, by virtue of its donating electrons, is itself oxidized in the process. Typical reducing agents undergo permanent chemi ...
s used, and the source of
carbon Carbon () is a chemical element with the symbol C and atomic number 6. It is nonmetallic and tetravalent—its atom making four electrons available to form covalent chemical bonds. It belongs to group 14 of the periodic table. Carbon ma ...
used for growth. Marine prokaryotes have diversified greatly throughout their long existence. The metabolism of prokaryotes is far more varied than that of eukaryotes, leading to many highly distinct prokaryotic types. For example, in addition to using
photosynthesis Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that, through cellular respiration, can later be released to fuel the organism's activities. Some of this chemical energy is stored in ...
or
organic compound In chemistry, organic compounds are generally any chemical compounds that contain carbon-hydrogen or carbon-carbon bonds. Due to carbon's ability to catenate (form chains with other carbon atoms), millions of organic compounds are known. Th ...
s for energy, as eukaryotes do, marine prokaryotes may obtain energy from
inorganic compound In chemistry, an inorganic compound is typically a chemical compound that lacks carbon–hydrogen bonds, that is, a compound that is not an organic compound. The study of inorganic compounds is a subfield of chemistry known as '' inorganic chemis ...
s such as
hydrogen sulfide Hydrogen sulfide is a chemical compound with the formula . It is a colorless chalcogen-hydride gas, and is poisonous, corrosive, and flammable, with trace amounts in ambient atmosphere having a characteristic foul odor of rotten eggs. The under ...
. This enables marine prokaryotes to thrive as
extremophile An extremophile (from Latin ' meaning "extreme" and Greek ' () meaning "love") is an organism that is able to live (or in some cases thrive) in extreme environments, i.e. environments that make survival challenging such as due to extreme tem ...
s in harsh environments as cold as the ice surface of Antarctica, studied in
cryobiology Cryobiology is the branch of biology that studies the effects of low temperatures on living things within Earth's cryosphere or in science. The word cryobiology is derived from the Greek words κρῧος ryos "cold", βίος ios "life", and λ� ...
, as hot as undersea
hydrothermal vent A hydrothermal vent is a fissure on the seabed from which geothermally heated water discharges. They are commonly found near volcanically active places, areas where tectonic plates are moving apart at mid-ocean ridges, ocean basins, and hotspo ...
s, or in high saline conditions as (
halophile The halophiles, named after the Greek word for "salt-loving", are extremophiles that thrive in high salt concentrations. While most halophiles are classified into the domain Archaea, there are also bacterial halophiles and some eukaryotic species, ...
s). Some marine prokaryotes live
symbiotic Symbiosis (from Greek , , "living together", from , , "together", and , bíōsis, "living") is any type of a close and long-term biological interaction between two different biological organisms, be it mutualistic, commensalistic, or para ...
ally in or on the bodies of other marine organisms. *
Phototrophy Phototrophs () are organisms that carry out photon capture to produce complex organic compounds (e.g. carbohydrates) and acquire energy. They use the energy from light to carry out various cellular metabolic processes. It is a common misconcep ...
is a particularly significant marker that should always play a primary role in bacterial classification. *
Aerobic anoxygenic phototrophic bacteria Aerobic anoxygenic phototrophic bacteria (AAPBs) are Alphaproteobacteria and Gammaproteobacteria that are obligate aerobes that capture energy from light by anoxygenic photosynthesis. Anoxygenic photosynthesis is the phototrophic process where light ...
(AAPBs) are widely distributed marine
plankton Plankton are the diverse collection of organisms found in water (or air) that are unable to propel themselves against a current (or wind). The individual organisms constituting plankton are called plankters. In the ocean, they provide a cruc ...
that may constitute over 10% of the open ocean microbial community. Marine AAPBs are classified in two marine ('' Erythrobacter'' and '' Roseobacter'') genera. They can be particularly abundant in
oligotrophic An oligotroph is an organism that can live in an environment that offers very low levels of nutrients. They may be contrasted with copiotrophs, which prefer nutritionally rich environments. Oligotrophs are characterized by slow growth, low rates o ...
conditions where they were found to be 24% of the community. These are
heterotrophic A heterotroph (; ) is an organism that cannot produce its own food, instead taking nutrition from other sources of organic carbon, mainly plant or animal matter. In the food chain, heterotrophs are primary, secondary and tertiary consumers, but ...
organisms that use light to produce energy, but are unable to utilise carbon dioxide as their primary carbon source. Most are obligately
aerobic Aerobic means "requiring air," in which "air" usually means oxygen. Aerobic may also refer to * Aerobic exercise, prolonged exercise of moderate intensity * Aerobics, a form of aerobic exercise * Aerobic respiration, the aerobic process of cel ...
, meaning they require oxygen to grow. Current data suggests that marine bacteria have generation times of several days, whereas new evidence exists that shows AAPB to have a much shorter generation time. Coastal/shelf waters often have greater amounts of AAPBs, some as high as 13.51% AAPB%. Phytoplankton also affect AAPB%, but little research has been performed in this area. They can also be abundant in various
oligotrophic An oligotroph is an organism that can live in an environment that offers very low levels of nutrients. They may be contrasted with copiotrophs, which prefer nutritionally rich environments. Oligotrophs are characterized by slow growth, low rates o ...
conditions, including the most oligotrophic regime of the world ocean. They are globally distributed in the
euphotic zone The photic zone, euphotic zone, epipelagic zone, or sunlight zone is the uppermost layer of a body of water that receives sunlight, allowing phytoplankton to perform photosynthesis. It undergoes a series of physical, chemical, and biological proc ...
and represent a hitherto unrecognized component of the marine microbial community that appears to be critical to the cycling of both organic and inorganic carbon in the ocean. *
Purple bacteria Purple bacteria or purple photosynthetic bacteria are Gram-negative proteobacteria that are phototrophic, capable of producing their own food via photosynthesis. They are pigmented with bacteriochlorophyll ''a'' or ''b'', together with variou ...
: *
Zetaproteobacteria The class Zetaproteobacteria is the sixth and most recently described class of the Pseudomonadota. Zetaproteobacteria can also refer to the group of organisms assigned to this class. The Zetaproteobacteria were originally represented by a single ...
: are iron-oxidizing
neutrophilic Neutrophils (also known as neutrocytes or heterophils) are the most abundant type of granulocytes and make up 40% to 70% of all white blood cells in humans. They form an essential part of the innate immune system, with their functions varying in ...
chemolithoautotrophs, distributed worldwide in estuaries and marine habitats. *
Hydrogen oxidizing bacteria Hydrogen-oxidizing bacteria are a group of facultative autotrophs that can use hydrogen as an electron donor. They can be divided into aerobes and anaerobes. The former use hydrogen as an electron donor and oxygen as an acceptor while the latter ...
are facultative autotrophs that can be divided into aerobes and anaerobes. The former use
hydrogen Hydrogen is the chemical element with the symbol H and atomic number 1. Hydrogen is the lightest element. At standard conditions hydrogen is a gas of diatomic molecules having the formula . It is colorless, odorless, tasteless, non-to ...
as an
electron donor In chemistry, an electron donor is a chemical entity that donates electrons to another compound. It is a reducing agent that, by virtue of its donating electrons, is itself oxidized in the process. Typical reducing agents undergo permanent chemi ...
and oxygen as an acceptor while the latter use sulphate or nitrogen dioxide as
electron acceptor An electron acceptor is a chemical entity that accepts electrons transferred to it from another compound. It is an oxidizing agent that, by virtue of its accepting electrons, is itself reduced in the process. Electron acceptors are sometimes mista ...
s.


Motility

Motility Motility is the ability of an organism to move independently, using metabolic energy. Definitions Motility, the ability of an organism to move independently, using metabolic energy, can be contrasted with sessility, the state of organisms th ...
is the ability of an
organism In biology, an organism () is any living system that functions as an individual entity. All organisms are composed of cells ( cell theory). Organisms are classified by taxonomy into groups such as multicellular animals, plants, and fu ...
to move independently, using metabolic energy.


Flagellar motility

Prokaryotes, both bacteria and archaea, primarily use
flagella A flagellum (; ) is a hairlike appendage that protrudes from certain plant and animal sperm cells, and from a wide range of microorganisms to provide motility. Many protists with flagella are termed as flagellates. A microorganism may have fro ...
for locomotion. * Bacterial flagella are helical filaments, each with a
rotary motor An electric motor is an electrical machine that converts electrical energy into mechanical energy. Most electric motors operate through the interaction between the motor's magnetic field and electric current in a wire winding to generate force ...
at its base which can turn clockwise or counterclockwise. They provide two of several kinds of bacterial motility. * Archaeal flagella are called ''archaella'', and function in much the same way as bacterial flagella. Structurally the archaellum is superficially similar to a bacterial flagellum, but it differs in many details and is considered non- homologous. The rotary motor model used by bacteria uses the protons of an
electrochemical gradient An electrochemical gradient is a gradient of electrochemical potential, usually for an ion that can move across a membrane. The gradient consists of two parts, the chemical gradient, or difference in solute concentration across a membrane, and ...
in order to move their flagella.
Torque In physics and mechanics, torque is the rotational equivalent of linear force. It is also referred to as the moment of force (also abbreviated to moment). It represents the capability of a force to produce change in the rotational motion of th ...
in the flagella of bacteria is created by particles that conduct protons around the base of the flagellum. The direction of rotation of the flagella in bacteria comes from the occupancy of the proton channels along the perimeter of the flagellar motor. Some eukaryotic cells also use flagella — and they can be found in some protists and plants as well as animal cells. Eukaryotic flagella are complex cellular projections that lash back and forth, rather than in a circular motion. Prokaryotic flagella use a rotary motor, and the eukaryotic flagella use a complex sliding filament system. Eukaryotic flagella are ATP-driven, while prokaryotic flagella can be ATP-driven (archaea) or proton-driven (bacteria).


Twitching motility

Twitching motility Twitching motility is a form of crawling bacterial motility used to move over surfaces. Twitching is mediated by the activity of hair-like filaments called type IV pili which extend from the cell's exterior, bind to surrounding solid substrates a ...
is a form of crawling bacterial motility used to move over surfaces. Twitching is mediated by the activity of hair-like filaments called type IV
pili Pili may refer to: Common names of plants * '' Canarium ovatum'', a Philippine tree that is a source of the pili nut * ''Heteropogon contortus'', a Hawaiian grass used to thatch structures Places * Pili, Camarines Sur, is a municipality in the ...
which extend from the cell's exterior, bind to surrounding solid substrates and retract, pulling the cell forwards in a manner similar to the action of a
grappling hook A grappling hook or grapnel is a device that typically has multiple hooks (known as ''claws'' or ''flukes'') attached to a rope; it is thrown, dropped, sunk, projected, or fastened directly by hand to where at least one hook may catch and ho ...
. The name ''twitching motility'' is derived from the characteristic jerky and irregular motions of individual cells when viewed under the microscope.


Gliding motility

Gliding motility Gliding motility is a type of translocation used by microorganisms that is independent of propulsive structures such as flagella, pili, and fimbriae. Gliding allows microorganisms to travel along the surface of low aqueous films. The mechanisms of ...
is a type of translocation that is independent of propulsive structures such as
flagella A flagellum (; ) is a hairlike appendage that protrudes from certain plant and animal sperm cells, and from a wide range of microorganisms to provide motility. Many protists with flagella are termed as flagellates. A microorganism may have fro ...
or
pili Pili may refer to: Common names of plants * '' Canarium ovatum'', a Philippine tree that is a source of the pili nut * ''Heteropogon contortus'', a Hawaiian grass used to thatch structures Places * Pili, Camarines Sur, is a municipality in the ...
. Gliding allows microorganisms to travel along the surface of low aqueous films. The mechanisms of this motility are only partially known. The speed of gliding varies between organisms, and the reversal of direction is seemingly regulated by some sort of internal clock. For example, the
apicomplexan The Apicomplexa (also called Apicomplexia) are a large phylum of parasitic alveolates. Most of them possess a unique form of organelle that comprises a type of non-photosynthetic plastid called an apicoplast, and an apical complex structure. The ...
s are able to travel at fast rates between 1–10 μm/s. In contrast ''
Myxococcus xanthus ''Myxococcus xanthus'' is a gram-negative, rod-shaped species of myxobacteria that exhibits various forms of self-organizing behavior in response to environmental cues. Under normal conditions with abundant food, it exists as a predatory, sapro ...
'' bacteria glide at a rate of 5 μm/min.


Swarming motility

Swarming motility Swarming motility is a rapid (2–10 μm/s) and coordinated translocation of a bacterial population across solid or semi-solid surfaces, and is an example of bacterial multicellularity and swarm behaviour. Swarming motility was first reported b ...
is a rapid (2–10 μm/s) and coordinated translocation of a bacterial population across solid or semi-solid surfaces, and is an example of bacterial multicellularity and
swarm behaviour Swarm behaviour, or swarming, is a collective animal behaviour, collective behaviour exhibited by entities, particularly animals, of similar size which aggregate together, perhaps milling about the same spot or perhaps moving ''en masse'' or a ...
. Swarming motility was first reported in 1972 by Jorgen Henrichsen.


Non-motile

Non-motile species lack the ability and structures that would allow them to propel themselves, under their own power, through their environment. When non-motile bacteria are cultured in a stab tube, they only grow along the stab line. If the bacteria are mobile, the line will appear diffuse and extend into the medium.


Taxis: Directed motion


Magnetotaxis

Magnetotactic bacteria Magnetotactic bacteria (or MTB) are a polyphyletic group of bacteria that orient themselves along the magnetic field lines of Earth's magnetic field. Discovered in 1963 by Salvatore Bellini and rediscovered in 1975 by Richard Blakemore, this ...
orient themselves along the
magnetic field lines A magnetic field is a vector field that describes the magnetic influence on moving electric charges, electric currents, and magnetic materials. A moving charge in a magnetic field experiences a force perpendicular to its own velocity and to ...
of
Earth's magnetic field Earth's magnetic field, also known as the geomagnetic field, is the magnetic field that extends from Earth's interior out into space, where it interacts with the solar wind, a stream of charged particles emanating from the Sun. The magneti ...
. This alignment is believed to aid these organisms in reaching regions of optimal oxygen concentration. To perform this task, these bacteria have biomineralised
organelle In cell biology, an organelle is a specialized subunit, usually within a cell, that has a specific function. The name ''organelle'' comes from the idea that these structures are parts of cells, as organs are to the body, hence ''organelle,'' th ...
s called magnetosomes that contain magnetic
crystal A crystal or crystalline solid is a solid material whose constituents (such as atoms, molecules, or ions) are arranged in a highly ordered microscopic structure, forming a crystal lattice that extends in all directions. In addition, macro ...
s. The biological phenomenon of microorganisms tending to move in response to the environment's magnetic characteristics is known as magnetotaxis. However, this term is misleading in that every other application of the term
taxis A taxis (; ) is the movement of an organism in response to a stimulus such as light or the presence of food. Taxes are innate behavioural responses. A taxis differs from a tropism (turning response, often growth towards or away from a stim ...
involves a stimulus-response mechanism. In contrast to the magnetoreception of animals, the bacteria contain fixed magnets that force the bacteria into alignment—even dead cells are dragged into alignment, just like a compass needle. Marine environments are generally characterized by low concentrations of nutrients kept in steady or intermittent motion by currents and turbulence. Marine bacteria have developed strategies, such as swimming and using directional sensing–response systems, to migrate towards favorable places in the nutrient gradients. Magnetotactic bacteria utilize Earth's magnetic field to facilitate downward swimming into the oxic–anoxic interface, which is the most favorable place for their persistence and proliferation, in chemically stratified sediments or water columns.Zhang, W.J. and Wu, L.F., 2020. Flagella and Swimming Behavior of Marine Magnetotactic Bacteria. Biomolecules, 10(3), p.460. . Modified text was copied from this source, which is available under
Creative Commons Attribution 4.0 International License
Depending on their latitude and whether the bacteria are north or south of the equator, the Earth's magnetic field has one of the two possible polarities, and a direction that points with varying angles into the ocean depths, and away from the generally more oxygen rich surface. Aerotaxis is the response by which bacteria migrate to an optimal oxygen concentration in an oxygen gradient. Various experiments have clearly shown that magnetotaxis and aerotaxis work in conjunction in magnetotactic bacteria. It has been shown that, in water droplets, one-way swimming magnetotactic bacteria can reverse their swimming direction and swim backwards under reducing conditions (less than optimal oxygen concentration), as opposed to oxic conditions (greater than optimal oxygen concentration). Regardless of their morphology, all magnetotactic bacteria studied so far are motile by means of flagella. Marine magnetotactic bacteria in particular tend to possess an elaborate flagellar apparatus which can involve up to tens of thousands of flagella. However, despite extensive research in recent years, it has yet to be established whether magnetotactic bacteria steer their flagellar motors in response to their alignment in magnetic fields.
Symbiosis Symbiosis (from Greek , , "living together", from , , "together", and , bíōsis, "living") is any type of a close and long-term biological interaction between two different biological organisms, be it mutualistic, commensalistic, or para ...
with magnetotactic bacteria has been proposed as the explanation for magnetoreception in some marine protists. Research is underway on whether a similar relationship may underlie magnetoreception in
vertebrate Vertebrates () comprise all animal taxa within the subphylum Vertebrata () ( chordates with backbones), including all mammals, birds, reptiles, amphibians, and fish. Vertebrates represent the overwhelming majority of the phylum Chordata, with ...
s as well. The oldest unambiguous magnetofossils come from the
Cretaceous The Cretaceous ( ) is a geological period that lasted from about 145 to 66 million years ago (Mya). It is the third and final period of the Mesozoic Era, as well as the longest. At around 79 million years, it is the longest geological period of ...
chalk beds of southern England, though less certain reports of magnetofossils extend to 1.9 billion years old Gunflint Chert.


Gas vacuoles

Some marine prokaryotes possess
gas vacuole Gas vesicles, also known as gas vacuoles, are nanocompartments in certain Prokaryote, prokaryotic organisms, which help in buoyancy. Gas vesicles are composed entirely of protein; no lipids or carbohydrates have been detected. Function Gas ve ...
s. Gas vacuole are nanocompartments freely permeable to gas which allow marine bacteria and archaea to control their
buoyancy Buoyancy (), or upthrust, is an upward force exerted by a fluid that opposes the weight of a partially or fully immersed object. In a column of fluid, pressure increases with depth as a result of the weight of the overlying fluid. Thus the ...
. They take the form of spindle-shaped membrane-bound
vesicles Vesicle may refer to: ; In cellular biology or chemistry * Vesicle (biology and chemistry), a supramolecular assembly of lipid molecules, like a cell membrane * Synaptic vesicle ; In human embryology * Vesicle (embryology), bulge-like features o ...
, and are found in some
plankton Plankton are the diverse collection of organisms found in water (or air) that are unable to propel themselves against a current (or wind). The individual organisms constituting plankton are called plankters. In the ocean, they provide a cruc ...
prokaryotes, including some ''
Cyanobacteria Cyanobacteria (), also known as Cyanophyta, are a phylum of gram-negative bacteria that obtain energy via photosynthesis. The name ''cyanobacteria'' refers to their color (), which similarly forms the basis of cyanobacteria's common name, bl ...
''. Positive buoyancy is needed to keep the cells in the upper reaches of the water column, so that they can continue to perform
photosynthesis Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that, through cellular respiration, can later be released to fuel the organism's activities. Some of this chemical energy is stored in ...
. Gas vacuoles are made up of a shell of protein that has a highly
hydrophobic In chemistry, hydrophobicity is the physical property of a molecule that is seemingly repelled from a mass of water (known as a hydrophobe). In contrast, hydrophiles are attracted to water. Hydrophobic molecules tend to be nonpolar and, ...
inner surface, making it impermeable to water (and stopping water vapour from condensing inside) but permeable to most gases. Because the gas vesicle is a hollow cylinder, it is liable to collapse when the surrounding
pressure Pressure (symbol: ''p'' or ''P'') is the force applied perpendicular to the surface of an object per unit area over which that force is distributed. Gauge pressure (also spelled ''gage'' pressure)The preferred spelling varies by country a ...
increases. Natural selection has fine tuned the structure of the gas vesicle to maximise its resistance to
buckling In structural engineering, buckling is the sudden change in shape ( deformation) of a structural component under load, such as the bowing of a column under compression or the wrinkling of a plate under shear. If a structure is subjected to a ...
, including an external strengthening protein, GvpC, rather like the green thread in a braided hosepipe. There is a simple relationship between the diameter of the gas vesicle and pressure at which it will collapse – the wider the gas vesicle the weaker it becomes. However, wider gas vesicles are more efficient, providing more buoyancy per unit of protein than narrow gas vesicles. Different species produce gas vesicle of different diameter, allowing them to colonise different depths of the water column (fast growing, highly competitive species with wide gas vesicles in the top most layers; slow growing, dark-adapted, species with strong narrow gas vesicles in the deeper layers). The cell achieves its height in the water column by synthesising gas vesicles. As the cell rises up, it is able to increase its
carbohydrate In organic chemistry, a carbohydrate () is a biomolecule consisting of carbon (C), hydrogen (H) and oxygen (O) atoms, usually with a hydrogen–oxygen atom ratio of 2:1 (as in water) and thus with the empirical formula (where ''m'' may o ...
load through increased photosynthesis. Too high and the cell will suffer photobleaching and possible death, however, the carbohydrate produced during photosynthesis increases the cell's density, causing it to sink. The daily cycle of carbohydrate build-up from photosynthesis and carbohydrate
catabolism Catabolism () is the set of metabolic pathways that breaks down molecules into smaller units that are either oxidized to release energy or used in other anabolic reactions. Catabolism breaks down large molecules (such as polysaccharides, li ...
during dark hours is enough to fine-tune the cell's position in the water column, bring it up toward the surface when its carbohydrate levels are low and it needs to photosynthesis, and allowing it to sink away from the harmful
UV radiation Ultraviolet (UV) is a form of electromagnetic radiation with wavelength from 10 nm (with a corresponding frequency around 30  PHz) to 400 nm (750  THz), shorter than that of visible light, but longer than X-rays. UV radiatio ...
when the cell's carbohydrate levels have been replenished. An extreme excess of carbohydrate causes a significant change in the internal pressure of the cell, which causes the gas vesicles to buckle and collapse and the cell to sink out. Large vacuoles are found in three
genera Genus ( plural genera ) is a taxonomic rank used in the biological classification of living and fossil organisms as well as viruses. In the hierarchy of biological classification, genus comes above species and below family. In binomial nomenclat ...
of filamentous sulfur bacteria, the '' Thioploca'', ''
Beggiatoa ''Beggiatoa'' is a genus of '' Gammaproteobacteria'' belonging the order ''Thiotrichales,'' in the '' Pseudomonadota'' phylum. This genus was one of the first bacteria discovered by Ukrainian botanist Sergei Winogradsky. During his research in ...
'' and ''
Thiomargarita ''Thiomargarita'' is a genus (family Thiotrichaceae) which includes the vacuolate sulfur bacteria species ''Thiomargarita namibiensis'', ''Candidatus Thiomargarita nelsonii'', and ''Ca. Thiomargarita joergensii''. In 2022, scientists working ...
''. The cytosol is extremely reduced in these genera and the vacuole can occupy between 40 and 98% of the cell. The vacuole contains high concentrations of
nitrate Nitrate is a polyatomic ion with the chemical formula . Salts containing this ion are called nitrates. Nitrates are common components of fertilizers and explosives. Almost all inorganic nitrates are soluble in water. An example of an insolu ...
ions and is therefore thought to be a storage
organelle In cell biology, an organelle is a specialized subunit, usually within a cell, that has a specific function. The name ''organelle'' comes from the idea that these structures are parts of cells, as organs are to the body, hence ''organelle,'' th ...
.


Bioluminescence

Bioluminescent bacteria are light-producing
bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were am ...
that are predominantly present in sea water, marine sediments, the surface of decomposing fish and in the gut of marine animals. While not as common, bacterial bioluminescence is also found in terrestrial and freshwater bacteria. These bacteria may be free living (such as '' Vibrio harveyi'') or in symbiosis with animals such as the
Hawaiian Bobtail squid __NOTOC__ ''Euprymna scolopes'', also known as the Hawaiian bobtail squid, is a species of bobtail squid in the family Sepiolidae native to the central Pacific Ocean, where it occurs in shallow coastal waters off the Hawaiian Islands and Midway Is ...
('' Aliivibrio fischeri'') or terrestrial
nematode The nematodes ( or grc-gre, Νηματώδη; la, Nematoda) or roundworms constitute the phylum Nematoda (also called Nemathelminthes), with plant- parasitic nematodes also known as eelworms. They are a diverse animal phylum inhabiting a bro ...
s (''
Photorhabdus luminescens ''Photorhabdus luminescens'' (previously called ''Xenorhabdus luminescens'') is a Gammaproteobacterium of the family Morganellaceae, and is a lethal pathogen of insects. It lives in the gut of an entomopathogenic nematode of the family Hetero ...
''). The host organisms provide these bacteria a safe home and sufficient nutrition. In exchange, the hosts use the light produced by the bacteria for camouflage, prey and/or mate attraction. Bioluminescent bacteria have evolved symbiotic relationships with other organisms in which both participants benefit close to equally. Another possible reason bacteria use luminescence reaction is for
quorum sensing In biology, quorum sensing or quorum signalling (QS) is the ability to detect and respond to cell population density by gene regulation. As one example, QS enables bacteria to restrict the expression of specific genes to the high cell densities at ...
, an ability to regulate gene expression in response to bacterial cell density. The
Hawaiian bobtail squid __NOTOC__ ''Euprymna scolopes'', also known as the Hawaiian bobtail squid, is a species of bobtail squid in the family Sepiolidae native to the central Pacific Ocean, where it occurs in shallow coastal waters off the Hawaiian Islands and Midway Is ...
lives in symbiosis with the bioluminescent bacteria '' Aliivibrio fischeri'' which inhabits a special light organ in the squid's mantle. The bacteria are fed sugar and
amino acid Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha ...
by the squid and in return hide the squid's silhouette when viewed from below, counter-illuminating it by matching the amount of light hitting the top of the mantle. The squid serves as a model organism for animal-bacterial symbiosis and its relationship with the bacteria has been widely studied. '' Vibrio harveyi'' is a rod-shaped, motile (via polar
flagella A flagellum (; ) is a hairlike appendage that protrudes from certain plant and animal sperm cells, and from a wide range of microorganisms to provide motility. Many protists with flagella are termed as flagellates. A microorganism may have fro ...
) bioluminescent bacterium which grows optimally between 30° and 35 °C. It can be found free-swimming in tropical marine waters, commensally in the gut microflora of
marine Marine is an adjective meaning of or pertaining to the sea or ocean. Marine or marines may refer to: Ocean * Maritime (disambiguation) * Marine art * Marine biology * Marine debris * Marine habitats * Marine life * Marine pollution Military ...
animals, and as both a primary and opportunistic pathogen of a number of marine animals. It is thought to be the cause of the milky seas effect, where a uniform blue glow is emitted from seawater during the night. Some glows can cover nearly .


Microbial rhodopsin

Phototrophic metabolism relies on one of three energy-converting pigments:
chlorophyll Chlorophyll (also chlorophyl) is any of several related green pigments found in cyanobacteria and in the chloroplasts of algae and plants. Its name is derived from the Greek words , ("pale green") and , ("leaf"). Chlorophyll allow plants to ...
, bacteriochlorophyll, and
retinal Retinal (also known as retinaldehyde) is a polyene chromophore. Retinal, bound to proteins called opsins, is the chemical basis of visual phototransduction, the light-detection stage of visual perception (vision). Some microorganisms use reti ...
. Retinal is the
chromophore A chromophore is the part of a molecule responsible for its color. The color that is seen by our eyes is the one not absorbed by the reflecting object within a certain wavelength spectrum of visible light. The chromophore is a region in the mo ...
found in
rhodopsin Rhodopsin, also known as visual purple, is a protein encoded by the RHO gene and a G-protein-coupled receptor (GPCR). It is the opsin of the rod cells in the retina and a light-sensitive receptor protein that triggers visual phototransductio ...
s. The significance of chlorophyll in converting light energy has been written about for decades, but phototrophy based on retinal pigments is just beginning to be studied. In 2000 a team of microbiologists led by
Edward DeLong Edward Francis DeLong (born 1958), is a marine microbiologist and professor in the Department of Oceanography at the University of Hawaii, Manoa, and is considered a pioneer in the field of metagenomics. He is best known for his discovery of the ...
made a crucial discovery in the understanding of the marine carbon and energy cycles. They discovered a gene in several species of bacteria responsible for production of the protein
rhodopsin Rhodopsin, also known as visual purple, is a protein encoded by the RHO gene and a G-protein-coupled receptor (GPCR). It is the opsin of the rod cells in the retina and a light-sensitive receptor protein that triggers visual phototransductio ...
, previously unheard of in bacteria. These proteins found in the cell membranes are capable of converting light energy to biochemical energy due to a change in configuration of the rhodopsin molecule as sunlight strikes it, causing the pumping of a
proton A proton is a stable subatomic particle, symbol , H+, or 1H+ with a positive electric charge of +1 ''e'' elementary charge. Its mass is slightly less than that of a neutron and 1,836 times the mass of an electron (the proton–electron mass ...
from inside out and a subsequent inflow that generates the energy.''Bacteria with Batteries'', Popular Science, January 2001, Page 55. The archaeal-like rhodopsins have subsequently been found among different taxa, protists as well as in bacteria and archaea, though they are rare in complex
multicellular organism A multicellular organism is an organism that consists of more than one cell, in contrast to unicellular organism. All species of animals, land plants and most fungi are multicellular, as are many algae, whereas a few organisms are partially uni ...
s. Research in 2019 shows these "sun-snatching bacteria" are more widespread than previously thought and could change how oceans are affected by global warming. "The findings break from the traditional interpretation of marine ecology found in textbooks, which states that nearly all sunlight in the ocean is captured by chlorophyll in algae. Instead, rhodopsin-equipped bacteria function like hybrid cars, powered by organic matter when available — as most bacteria are — and by sunlight when nutrients are scarce." There is an astrobiological conjecture called the
Purple Earth hypothesis The Purple Earth hypothesis is an astrobiological hypothesis that photosynthetic life forms of early Earth were based on the simpler molecule retinal rather than the more complex chlorophyll, making Earth appear purple rather than green. An examp ...
which surmises that original life forms on Earth were retinal-based rather than chlorophyll-based, which would have made the Earth appear purple instead of green.


Symbiosis

Some marine organisms have a
symbiosis Symbiosis (from Greek , , "living together", from , , "together", and , bíōsis, "living") is any type of a close and long-term biological interaction between two different biological organisms, be it mutualistic, commensalistic, or para ...
with bacteria or archaea. Pompeii worms live at great depths by hydrothermal vents at temperatures up to 80 °C. They have what appear to be hairy backs, but these "hairs" are actually colonies of bacteria such as '' Nautilia profundicola'', which are thought to afford the worm some degree of insulation. Glands on the worm's back secrete a mucus on which the bacteria feed, a form of
symbiosis Symbiosis (from Greek , , "living together", from , , "together", and , bíōsis, "living") is any type of a close and long-term biological interaction between two different biological organisms, be it mutualistic, commensalistic, or para ...
. File:Alvinella pompejana01.jpg, The "hairy" backs of
Pompeii worm ''Alvinella pompejana'', the Pompeii worm, is a species of deep-sea polychaete worm (commonly referred to as "bristle worms"). It is an extremophile found only at hydrothermal vents in the Pacific Ocean, discovered in the early 1980s off the Gal� ...
s are colonies of symbiotic bacteria File:Hesiocaeca methanicola noaa.jpg, '' Hesiocaeca methanicola'' lives at great depths on methane ice and appear to survive in symbiosis with bacteria which metabolize the
clathrate A clathrate is a chemical substance consisting of a lattice that traps or contains molecules. The word ''clathrate'' is derived from the Latin (), meaning ‘with bars, latticed’. Most clathrate compounds are polymeric and completely envelo ...
. File:Olavius algarvensis from Elba, Italy.jpg, '' Olavius algarvensis'' depends on five different species of symbiotic bacteria for its nutrition File:Cyanobacteria in symbiosis with a diatom.png, Epiphytic '' Calothrix ''cyanobacteria (arrows) in symbiosis with a ''
Chaetoceros ''Chaetoceros'' is probably the largest genus of marine planktonic diatoms with approximately 400 species described, although many of these descriptions are no longer valid. It is often very difficult to distinguish between different ''Chaeto ...
'' diatom. Scale bar 50 μm.
Endosymbiont An ''endosymbiont'' or ''endobiont'' is any organism that lives within the body or cells of another organism most often, though not always, in a mutualistic relationship. (The term endosymbiosis is from the Greek: ἔνδον ''endon'' "within ...
bacteria are bacteria that live within the body or cells of another organism. Some types of cyanobacteria are
endosymbiont An ''endosymbiont'' or ''endobiont'' is any organism that lives within the body or cells of another organism most often, though not always, in a mutualistic relationship. (The term endosymbiosis is from the Greek: ἔνδον ''endon'' "within ...
and cyanobacteria have been found to possess genes that enable them to undergo nitrogen fixation. Organisms typically establish a symbiotic relationship due to their limited availability of resources in their habitat or due to a limitation of their food source. Symbiotic, chemosynthetic bacteria that have been discovered associated with mussels (
Bathymodiolus ''Bathymodiolus'' is a genus of deep-sea mussels, marine bivalve molluscs in the family Mytilidae. Many of them contain intracelluar chemoautotrophic bacterial symbionts. Species Modern (non-fossil) species within the genus ''Bathymodiolus'' i ...
) located near hydrothermal vents have a gene that enables them to utilize hydrogen as a source of energy, in preference to sulphur or methane as their energy source for production of energy. '' Olavius algarvensis'' is a worm which lives in coastal sediments in the Mediterranean and depends on symbiotic bacteria for its nutrition. It lives with five different species of bacteria located under its cuticle: two sulfide-oxidizing , two sulfate-reducing and one
spirochaete A spirochaete () or spirochete is a member of the phylum Spirochaetota (), (synonym Spirochaetes) which contains distinctive diderm (double-membrane) gram-negative bacteria, most of which have long, helically coiled (corkscrew-shaped or s ...
. The symbiotic bacteria also allow the worm to use
hydrogen Hydrogen is the chemical element with the symbol H and atomic number 1. Hydrogen is the lightest element. At standard conditions hydrogen is a gas of diatomic molecules having the formula . It is colorless, odorless, tasteless, non-to ...
and
carbon monoxide Carbon monoxide ( chemical formula CO) is a colorless, poisonous, odorless, tasteless, flammable gas that is slightly less dense than air. Carbon monoxide consists of one carbon atom and one oxygen atom connected by a triple bond. It is the simpl ...
as energy sources, and to metabolise organic compounds like
malate Malic acid is an organic compound with the molecular formula . It is a dicarboxylic acid that is made by all living organisms, contributes to the sour taste of fruits, and is used as a food additive. Malic acid has two stereoisomeric forms (L ...
and
acetate An acetate is a salt formed by the combination of acetic acid with a base (e.g. alkaline, earthy, metallic, nonmetallic or radical base). "Acetate" also describes the conjugate base or ion (specifically, the negatively charged ion called ...
. '' Astrangia poculata'', the northern star coral, is a temperate
stony coral Scleractinia, also called stony corals or hard corals, are marine animals in the phylum Cnidaria that build themselves a hard skeleton. The individual animals are known as polyps and have a cylindrical body crowned by an oral disc in which a mo ...
, widely documented along the eastern coast of the United States. The coral can live with and without
zooxanthellae Zooxanthellae is a colloquial term for single-celled dinoflagellates that are able to live in symbiosis with diverse marine invertebrates including demosponges, corals, jellyfish, and nudibranchs. Most known zooxanthellae are in the genus ''S ...
(algal symbionts), making it an ideal
model organism A model organism (often shortened to model) is a non-human species that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the model organism will provide insight into the workin ...
to study microbial community interactions associated with symbiotic state. However, the ability to develop primers and probes to more specifically target key microbial groups has been hindered by the lack of full length 16S rRNA sequences, since sequences produced by the Illumina platform are of insufficient length (approximately 250 base pairs) for the design of primers and probes. In 2019, Goldsmith et al. demonstrated
Sanger sequencing Sanger sequencing is a method of DNA sequencing that involves electrophoresis and is based on the random incorporation of chain-terminating dideoxynucleotides by DNA polymerase during in vitro DNA replication. After first being developed by Fred ...
was capable of reproducing the biologically-relevant diversity detected by deeper
next-generation sequencing Massive parallel sequencing or massively parallel sequencing is any of several high-throughput approaches to DNA sequencing using the concept of massively parallel processing; it is also called next-generation sequencing (NGS) or second-generation ...
, while also producing longer sequences useful to the research community for probe and primer design (see diagram on right). Modified text was copied from this source, which is available under
Creative Commons Attribution 4.0 International License


Roles in marine food webs

Most of the volume of the world ocean is in darkness. The processes occurring within the thin illuminated surface layer (the photic layer from the surface down to between 50 and 170 metres) are of major significance to the global biosphere. For example, the visible region of the solar spectrum (the so-called photosynthetically available radiation or PAR) reaching this sunlit layer fuels about half of the
primary productivity In ecology, primary production is the synthesis of organic compounds from atmospheric or aqueous carbon dioxide. It principally occurs through the process of photosynthesis, which uses light as its source of energy, but it also occurs through c ...
of the planet, and is responsible for about half of the atmospheric oxygen necessary for most life on Earth. Heterotrophic
bacterioplankton Bacterioplankton refers to the bacterial component of the plankton that drifts in the water column. The name comes from the Ancient Greek word ' ('), meaning "wanderer" or "drifter", and ', a Latin term coined in the 19th century by Christian ...
are main consumers of
dissolved organic matter Dissolved organic carbon (DOC) is the fraction of organic carbon operationally defined as that which can pass through a filter with a pore size typically between 0.22 and 0.7 micrometers. The fraction remaining on the filter is called parti ...
(DOM) in pelagic marine food webs, including the sunlit upper layers of the ocean. Their sensitivity to ultraviolet radiation (UVR), together with some recently discovered mechanisms bacteria have evolved to benefit from photosynthetically available radiation (PAR), suggest that natural sunlight plays a relevant, yet difficult to predict role in modulating bacterial biogeochemical functions in the oceans. Ocean surface habitats sit at the interface between the atmosphere and the ocean. The biofilm-like habitat at the surface of the ocean harbours surface-dwelling microorganisms, commonly referred to as neuston. This vast air–water interface sits at the intersection of major air–water exchange processes spanning more than 70% of the global surface area . Bacteria in the surface microlayer of the ocean, called bacterioneuston, are of interest due to practical applications such as air-sea gas exchange of greenhouse gases, production of climate-active marine aerosols, and remote sensing of the ocean. Of specific interest is the production and degradation of
surfactant Surfactants are chemical compounds that decrease the surface tension between two liquids, between a gas and a liquid, or interfacial tension between a liquid and a solid. Surfactants may act as detergents, wetting agents, emulsion#Emulsifiers , ...
s (surface active materials) via microbial biochemical processes. Major sources of surfactants in the open ocean include phytoplankton, terrestrial runoff, and deposition from the atmosphere. Unlike coloured algal blooms, surfactant-associated bacteria may not be visible in ocean colour imagery. Having the ability to detect these "invisible" surfactant-associated bacteria using
synthetic aperture radar Synthetic-aperture radar (SAR) is a form of radar that is used to create two-dimensional images or three-dimensional reconstructions of objects, such as landscapes. SAR uses the motion of the radar antenna over a target region to provide fine ...
has immense benefits in all-weather conditions, regardless of cloud, fog, or daylight. This is particularly important in very high winds, because these are the conditions when the most intense air-sea gas exchanges and marine aerosol production take place. Therefore, in addition to colour satellite imagery, SAR satellite imagery may provide additional insights into a global picture of biophysical processes at the boundary between the ocean and atmosphere, air-sea greenhouse gas exchanges and production of climate-active marine aerosols. The diagram on the right shows links among the ocean's
biological pump The biological pump (or ocean carbon biological pump or marine biological carbon pump) is the ocean's biologically driven sequestration of carbon from the atmosphere and land runoff to the ocean interior and seafloor sediments.Sigman DM & GH ...
and the pelagic food web and the ability to sample these components remotely from ships, satellites, and autonomous vehicles. Light blue waters are the
euphotic zone The photic zone, euphotic zone, epipelagic zone, or sunlight zone is the uppermost layer of a body of water that receives sunlight, allowing phytoplankton to perform photosynthesis. It undergoes a series of physical, chemical, and biological proc ...
, while the darker blue waters represent the twilight zone. Modified text was copied from this source, which is available under
Creative Commons Attribution 4.0 International License


Roles in biogeochemical cycling

Archaea recycle elements such as
carbon Carbon () is a chemical element with the symbol C and atomic number 6. It is nonmetallic and tetravalent—its atom making four electrons available to form covalent chemical bonds. It belongs to group 14 of the periodic table. Carbon ma ...
,
nitrogen Nitrogen is the chemical element with the symbol N and atomic number 7. Nitrogen is a nonmetal and the lightest member of group 15 of the periodic table, often called the pnictogens. It is a common element in the universe, estimated at se ...
, and
sulfur Sulfur (or sulphur in British English) is a chemical element with the symbol S and atomic number 16. It is abundant, multivalent and nonmetallic. Under normal conditions, sulfur atoms form cyclic octatomic molecules with a chemical formul ...
through their various habitats. Archaea carry out many steps in the
nitrogen cycle The nitrogen cycle is the biogeochemical cycle by which nitrogen is converted into multiple chemical forms as it circulates among atmospheric, terrestrial, and marine ecosystems. The conversion of nitrogen can be carried out through both biolo ...
. This includes both reactions that remove nitrogen from ecosystems (such as
nitrate Nitrate is a polyatomic ion with the chemical formula . Salts containing this ion are called nitrates. Nitrates are common components of fertilizers and explosives. Almost all inorganic nitrates are soluble in water. An example of an insolu ...
-based respiration and
denitrification Denitrification is a microbially facilitated process where nitrate (NO3−) is reduced and ultimately produces molecular nitrogen (N2) through a series of intermediate gaseous nitrogen oxide products. Facultative anaerobic bacteria perform denit ...
) as well as processes that introduce nitrogen (such as nitrate assimilation and
nitrogen fixation Nitrogen fixation is a chemical process by which molecular nitrogen (), with a strong triple covalent bond, in the air is converted into ammonia () or related nitrogenous compounds, typically in soil or aquatic systems but also in industry. Atmo ...
). Researchers recently discovered archaeal involvement in
ammonia Ammonia is an inorganic compound of nitrogen and hydrogen with the formula . A stable binary hydride, and the simplest pnictogen hydride, ammonia is a colourless gas with a distinct pungent smell. Biologically, it is a common nitrogenous ...
oxidation reactions. These reactions are particularly important in the oceans. In the
sulfur cycle The sulfur cycle is a biogeochemical cycle in which the sulfur moves between rocks, waterways and living systems. It is important in geology as it affects many minerals and in life because sulfur is an essential element (CHNOPS), being a con ...
, archaea that grow by oxidizing
sulfur Sulfur (or sulphur in British English) is a chemical element with the symbol S and atomic number 16. It is abundant, multivalent and nonmetallic. Under normal conditions, sulfur atoms form cyclic octatomic molecules with a chemical formul ...
compounds release this element from rocks, making it available to other organisms, but the archaea that do this, such as ''Sulfolobus'', produce
sulfuric acid Sulfuric acid (American spelling and the preferred IUPAC name) or sulphuric acid ( Commonwealth spelling), known in antiquity as oil of vitriol, is a mineral acid composed of the elements sulfur, oxygen and hydrogen, with the molecular fo ...
as a waste product, and the growth of these organisms in abandoned mines can contribute to
acid mine drainage Acid mine drainage, acid and metalliferous drainage (AMD), or acid rock drainage (ARD) is the outflow of acidic water from metal mines or coal mines. Acid rock drainage occurs naturally within some environments as part of the rock weathering ...
and other environmental damage. In the
carbon cycle The carbon cycle is the biogeochemical cycle by which carbon is exchanged among the biosphere, pedosphere, geosphere, hydrosphere, and atmosphere of the Earth. Carbon is the main component of biological compounds as well as a major compon ...
, methanogen archaea remove hydrogen and play an important role in the decay of organic matter by the populations of microorganisms that act as decomposers in anaerobic ecosystems, such as sediments and marshes.


See also

*
Bacterioplankton counting methods Bacterioplankton counting is the estimation of the abundance of bacterioplankton in a specific body of water, which is useful information to marine microbiologists. Various counting methodologies have been developed over the years to determine th ...
* Bioluminescent bacteria *
Iron-oxidizing bacteria Iron-oxidizing bacteria are chemotrophic bacteria that derive energy by oxidizing dissolved ferrous iron. They are known to grow and proliferate in waters containing iron concentrations as low as 0.1 mg/L. However, at least 0.3 ppm of dissolved o ...
*
Pelagibacterales The Pelagibacterales are an order in the Alphaproteobacteria composed of free-living marine bacteria that make up roughly one in three cells at the ocean's surface. Overall, members of the ''Pelagibacterales'' are estimated to make up between a q ...
– model organisms in streamlining theory *
Streamlining theory Genomic streamlining is a theory in evolutionary biology and microbial ecology that suggests that there is a reproductive benefit to prokaryotes having a smaller genome size with less non-coding DNA and fewer non-essential genes. There is a lot of v ...


References


Bibliography

* * * {{microorganisms, state=expanded Microorganisms Marine organisms Planktology Biological oceanography Marine biology