Marine Microbes

Marine microorganisms are defined by their habitat as microorganisms living in a marine environment, that is, in the saltwater of a sea or ocean or the brackish water of a coastal estuary. A microorganism (or microbe) is any microscopic living organism or virus, that is too small to see with the unaided human eye without magnification. Microorganisms are very diverse. They can be single-celled or multicellular and include bacteria, archaea, viruses and most protozoa, as well as some fungi, algae, and animals, such as rotifers and copepods. Many macroscopic animals and plants have microscopic juvenile stages. Some microbiologists also classify biologically active entities such as viruses and viroids as microorganisms, but others consider these as non-living.

Marine microorganisms have been variously estimated to make up about 70%, or about 90%, Modified text was copied from this source, which is available under
Creative Commons Attribution 4.0 International License
of the biomass in the ocean. Taken together they form the marine microbiome. Over billions of years this microbiome has evolved many life styles and adaptations and come to participate in the global cycling of almost all chemical elements. Microorganisms are crucial to nutrient recycling in ecosystems as they act as decomposers. They are also responsible for nearly all photosynthesis that occurs in the ocean, as well as the cycling of carbon, nitrogen, phosphorus and other nutrients and trace elements. Marine microorganisms sequester large amounts of carbon and produce much of the world's oxygen.

A small proportion of marine microorganisms are pathogenic, causing disease and even death in marine plants and animals.2002 WHO mortality data
Accessed 20 January 2007 However marine microorganisms recycle the major chemical elements, both producing and consuming about half of all organic matter generated on the planet every year. As inhabitants of the largest environment on Earth, microbial marine systems drive changes in every global system.

In July 2016, scientists reported identifying a set of 355 genes from the last universal common ancestor (LUCA) of all life on the planet, including the marine microorganisms. Despite its diversity, microscopic life in the oceans is still poorly understood. For example, the role of viruses in marine ecosystems has barely been explored even in the beginning of the 21st century.

Overview

Microorganisms make up about 70% of the marine biomass. A microorganism, or microbe, is a microscopic organism too small to be recognised adequately with the naked eye. In practice, that includes organisms smaller than about 0.1 mm.Glöckner, F.O., Gasol, J.M., McDonough, N., Calewaert, J.B. et al. (2012
Marine microbial diversity and its role in ecosystem functioning and environmental change
European Science Foundation, Position Paper 17.

Such organisms can be single-celled or multicellular. Microorganisms are diverse and include all bacteria and archaea, most protists including algae, protozoa and fungal-like protists, as well as certain microscopic animals such as rotifers. Many macroscopic animals and plants have microscopic juvenile stages. Some microbiologists also classify viruses (and viroids) as microorganisms, but others consider these as non-living.

Microorganisms are crucial to nutrient recycling in ecosystems as they act as decomposers. Some microorganisms are pathogenic, causing disease and even death in plants and animals. As inhabitants of the largest environment on Earth, microbial marine systems drive changes in every global system. Microbes are responsible for virtually all the photosynthesis that occurs in the ocean, as well as the cycling of carbon, nitrogen, phosphorus and other nutrients and trace elements.

Microscopic life undersea is diverse and still poorly understood, such as for the role of viruses in marine ecosystems. Most marine viruses are bacteriophages, which are harmless to plants and animals, but are essential to the regulation of saltwater and freshwater ecosystems.Shors p. 5 They infect and destroy bacteria 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.Shors p. 593 Viral activity may also contribute to the biological pump, the process whereby carbon is sequestered in the deep ocean.

A stream of airborne microorganisms 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. 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 organisms live throughout the biosphere. The mass of prokaryote microorganisms — which includes bacteria and archaea, but not the nucleated eukaryote microorganisms — may be as much as 0.8 trillion tons of carbon (of the total biosphere mass, estimated at between 1 and 4 trillion tons). Single-celled barophilic marine microbes have been found at a depth of in the Mariana Trench, the deepest spot in the Earth's oceans. Microorganisms live inside rocks below the sea floor under of ocean off the coast of the northwestern United States, as well as beneath the seabed off Japan. The greatest known temperature at which microbial life can exist is (''Methanopyrus kandleri''). In 2014, scientists confirmed the existence of microorganisms living below the ice of Antarctica. According to one researcher, "You can find microbes everywhere — they're extremely adaptable to conditions, and survive wherever they are." Marine microorganisms serve as "the foundation of all marine food webs, recycling major elements and producing and consuming about half the organic matter generated on Earth each year".

Marine viruses

A virus is a small infectious agent that replicates only inside the living cells of other organisms. Viruses can infect all types of life forms, from animals and plants to microorganisms, including bacteria and archaea.

When not inside an infected cell or in the process of infecting a cell, viruses exist in the form of independent particles. These viral particles, also known as '' virions'', consist of two or three parts: (i) the genetic material (genome) made from either DNA or RNA, long molecules that carry genetic information; (ii) a protein coat called the capsid, which surrounds and protects the genetic material; and in some cases (iii) an envelope of lipids that surrounds the protein coat when they are outside a cell. The shapes of these virus particles range from simple helical and icosahedral forms for some virus species to more complex structures for others. Most virus species have virions that are too small to be seen with an optical microscope. The average virion is about one one-hundredth the size of the average bacterium.

The origins of viruses in the evolutionary history of life are unclear: some may have evolved from plasmids—pieces of DNA that can move between cells—while others may have evolved from bacteria. In evolution, viruses are an important means of horizontal gene transfer, which increases genetic diversity. Viruses are considered by some to be a life form, because they carry genetic material, reproduce, and evolve through natural selection. However, they lack key characteristics (such as cell structure) that are generally considered necessary to count as life. Because they possess some but not all such qualities, viruses have been described as "organisms at the edge of life" and as replicators.

Viruses are found wherever there is life and have probably existed since living cells first evolved. The origin of viruses is unclear because they do not form fossils, so molecular techniques have been used to compare the DNA or RNA of viruses and are a useful means of investigating how they arose.

Viruses are now recognised as ancient and as having origins that pre-date the divergence of life into the three domains.

Opinions differ on whether viruses are a form of life or organic structures that interact with living organisms. They are considered by some to be a life form, because they carry genetic material, reproduce by creating multiple copies of themselves through self-assembly, and evolve through natural selection. However they lack key characteristics such as a cellular structure generally considered necessary to count as life. Because they possess some but not all such qualities, viruses have been described as replicators and as "organisms at the edge of life".

Phages

Bacteriophages, often just called ''phages'', are viruses that parasite bacteria and archaea. Marine phages parasite marine bacteria and archaea, such as cyanobacteria. They are a common and diverse group of viruses and are the most abundant biological entity in marine environments, because their hosts, bacteria, are typically the numerically dominant cellular life in the sea. Generally there are about 1 million to 10 million viruses in each mL of seawater, or about ten times more double-stranded DNA viruses than there are cellular organisms, although estimates of viral abundance in seawater can vary over a wide range.
For a long time, tailed phages of the order ''Caudovirales'' seemed to dominate marine ecosystems in number and diversity of organisms.
However, as a result of more recent research, non-tailed viruses appear to be dominant in multiple depths and oceanic regions, followed by the ''Caudovirales'' families of myoviruses, podoviruses, and siphoviruses.
Phages belonging to the families
''Corticoviridae'',
''Inoviridae'',
'' Microviridae'',
and '' Autolykiviridae''
are also known to infect diverse marine bacteria.

There are also archaean viruses which replicate within archaea: these are double-stranded DNA viruses with unusual and sometimes unique shapes. These viruses have been studied in most detail in the thermophilic archaea, particularly the orders Sulfolobales and Thermoproteales.

Role of viruses

Microorganisms make up about 70% of the marine biomass. It is estimated viruses kill 20% of this biomass each day and that there are 15 times as many viruses in the oceans as there are bacteria and archaea. Viruses are the main agents responsible for the rapid destruction of harmful algal blooms, which often kill other marine life.
The number of viruses in the oceans decreases further offshore and deeper into the water, where there are fewer host organisms.

Viruses are an important natural means of transferring genes between different species, which increases genetic diversity and drives evolution. It is thought that viruses played a central role in the early evolution, before the diversification of bacteria, archaea and eukaryotes, at the time of the last universal common ancestor of life on Earth. Viruses are still one of the largest reservoirs of unexplored genetic diversity on Earth.

Giant viruses

Viruses normally range in length from about 20 to 300 nanometers. This can be contrasted with the length of bacteria, which starts at about 400 nanometers. There are also giant viruses, often called ''giruses'', typically about 1000 nanometers (one micron) in length.
All giant viruses belongto phylum ''Nucleocytoviricota'' (NCLDV), together with poxviruses.
The largest known of these is '' Tupanvirus''. This genus of giant virus was discovered in 2018 in the deep ocean as well as a soda lake, and can reach up to 2.3 microns in total length.

The discovery and subsequent characterization of giant viruses has triggered some debate concerning their evolutionary origins. The two main hypotheses for their origin are that either they evolved from small viruses, picking up DNA from host organisms, or that they evolved from very complicated organisms into the current form which is not self-sufficient for reproduction. What sort of complicated organism giant viruses might have diverged from is also a topic of debate. One proposal is that the origin point actually represents a fourth domain of life, but this has been largely discounted.

Prokaryotes

Marine bacteria

Bacteria constitute a large domain of prokaryotic microorganisms. Typically a few micrometres 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, and are present in most of its habitats. Bacteria inhabit soil, water, acidic hot springs, radioactive waste, and the deep portions of Earth's crust. Bacteria also live in symbiotic and parasitic relationships with plants and animals.

Once regarded as plants constituting the class ''Schizomycetes'', bacteria are now classified as prokaryotes. Unlike cells of animals and other eukaryotes, bacterial cells do not contain a nucleus and rarely harbour membrane-bound organelles. Although the term ''bacteria'' traditionally included all prokaryotes, the scientific classification changed after the discovery in the 1990s that prokaryotes consist of two very different groups of organisms that evolved from an ancient common ancestor. These evolutionary domains are called ''Bacteria'' and ''Archaea''.

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 fossils exist, such as stromatolites, 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, 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 associations with the ancestors of eukaryotic cells, which were themselves possibly related to the Archaea. This involved the engulfment by proto-eukaryotic cells of alphaproteobacterial symbionts to form either mitochondria or hydrogenosomes, 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 chloroplasts 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.

File:Sulphide bacteria crop2.jpg, The marine '' Thiomargarita namibiensis'', largest known bacterium
File:Potomac river eutro.jpg, Cyanobacteria blooms can contain lethal cyanotoxins
File:Glaucocystis sp.jpg, The chloroplasts of glaucophytes have a peptidoglycan layer, evidence suggesting their endosymbiotic origin from cyanobacteria.
File:Marinomonas arctica.jpg, The bacterium ''Marinomonas arctica'' grows inside Arctic sea ice at subzero temperatures

'' Pelagibacter ubique'' and its relatives may be the most abundant organisms 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 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'' in February 2013 that the bacteriophage HTVC010P, which attacks ''P. ubique'', has been discovered and "it probably really is the commonest organism on the planet".

The largest known bacterium, the marine '' Thiomargarita namibiensis'', can be visible to the naked eye and sometimes attains .

Marine archaea

The archaea (Greek for ''ancient'') constitute a domain and kingdom of single-celled microorganisms. These microbes are prokaryotes, meaning they have no cell nucleus or any other membrane-bound organelles in their cells.

Archaea were initially classified as bacteria, but this classification is outdated. Archaeal cells have unique properties separating them from the other two domains of life, Bacteria and Eukaryota. The Archaea are further divided into multiple recognized phyla. Classification is difficult because the majority have not been isolated in the laboratory and have only been detected by analysis of their nucleic acids in samples from their environment.

Archaea and bacteria 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''. Despite this morphological similarity to bacteria, archaea possess genes and several metabolic pathways that are more closely related to those of eukaryotes, notably the enzymes involved in transcription and translation. Other aspects of archaeal biochemistry are unique, such as their reliance on ether lipids in their cell membranes, such as archaeols. Archaea use more energy sources than eukaryotes: these range from organic compounds, such as sugars, to ammonia, metal ions or even hydrogen gas. Salt-tolerant archaea (the Haloarchaea) use sunlight as an energy source, and other species of archaea fix carbon; however, unlike plants and cyanobacteria, no known species of archaea does both. Archaea reproduce asexually by binary fission, fragmentation, or budding; unlike bacteria and eukaryotes, no known species forms spores.

Archaea are particularly numerous in the oceans, and the archaea in plankton 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 and the nitrogen cycle. Thermoproteota (also known as eocytes or Crenarchaeota) 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, 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''
File:Methanosarcina barkeri fusaro.gif, '' Methanosarcina barkeri'', a marine archaea that produces methane
File:Thermophile bacteria2.jpg, Thermophiles, such as '' Pyrolobus fumarii'', survive well over 100 °C

Eukaryotes

All living organisms can be grouped as either prokaryotes or eukaryotes. Life originated as single-celled prokaryotes and later evolved into the more complex eukaryotes. In contrast to prokaryotic cells, eukaryotic cells are highly organised. Prokaryotes are the bacteria and archaea, while eukaryotes are the other life forms — protists, plants, fungi and animals. Protists are usually single-celled, while plants, fungi and animals are usually multi-celled.

It seems very plausible that the root of the eukaryotes lie within archaea; the closest relatives nowadays known may be the Heimdallarchaeota phylum of the proposed Asgard superphylum. This theory is a modern version of a scenario originally proposed in 1984 as Eocyte hypothesis, when Thermoproteota were the closest known archaeal relatives of eukaryotes then.
A possible transitional form of microorganism between a prokaryote and a eukaryote was discovered in 2012 by Japanese scientists. ''Parakaryon myojinensis'' is a unique microorganism larger than a typical prokaryote, but with nuclear material enclosed in a membrane as in a eukaryote, and the presence of endosymbionts. This is seen to be the first plausible evolutionary form of microorganism, showing a stage of development from the prokaryote to the eukaryote.

Marine protists

Protists are eukaryotes that cannot be classified as plants, fungi or animals. They are usually single-celled and microscopic. Life originated as single-celled prokaryotes (bacteria and archaea) and later evolved into more complex eukaryotes. Eukaryotes are the more developed life forms known as plants, animals, fungi and protists. The term protist came into use historically as a term of convenience for eukaryotes that cannot be strictly classified as plants, animals or fungi. They are not a part of modern cladistics, because they are paraphyletic (lacking a common ancestor).

By trophic mode

Protists can be broadly divided into four groups depending on whether their nutrition is plant-like, animal-like, fungal-like, or a mixture of these.

Protists are highly diverse organisms currently organised into 18 phyla, but are not easy to classify. Studies have shown high protist diversity exists in oceans, deep sea-vents and river sediments, suggesting a large number of eukaryotic microbial communities have yet to be discovered. There has been little research on mixotrophic protists, but recent studies in marine environments found mixotrophic protests contribute a significant part of the protist biomass. Since protists are eukaryotes they possess within their cell at least one nucleus, as well as organelles such as mitochondria and Golgi bodies. Protists are asexual but can reproduce rapidly through mitosis or by fragmentation.

File:Diatoms through the microscope.jpg, Diatoms are a major algae group generating about 20% of world oxygen production.The Air You're Breathing? A Diatom Made That
/ref>
File:Diatom algae Amphora sp.jpg, Diatoms have glass like cell walls made of silica and called frustules.
File:Triceratium morlandii var. morlandii.jpg, Fossil diatom frustule from 32 to 40 mya
File:Podocyrtis papalis Ehrenberg - Radiolarian (30448963206).jpg, Radiolarian
File:Gephyrocapsa oceanica color (lightened).jpg, Single-celled alga, ''Gephyrocapsa oceanica''
File:CSIRO ScienceImage 7609 SEM dinoflagellate.jpg, Two dinoflagellates
File:Zooxanthellae.jpg, Zooxanthellae is a photosynthetic algae that lives inside hosts like coral
File:Paramecium bursaria.jpg, A single-celled ciliate with green zoochlorellae living inside endosymbiotically
File:Euglenoid movement.jpg, Euglenoid
File:The ciliate Frontonia sp.jpg, This ciliate is digesting cyanobacteria. The cytostome or mouth is at the bottom right.

File:Frontonia ingesting a diatom.ogg, Ciliate ingesting a diatom
File:Amoeba engulfing diatom.ogv, Amoeba engulfing a diatom

In contrast to the cells of prokaryotes, the cells of eukaryotes are highly organised. Plants, animals and fungi are usually multi-celled and are typically macroscopic. Most protists are single-celled and microscopic. But there are exceptions. Some single-celled marine protists are macroscopic. Some marine slime molds have unique life cycles that involve switching between unicellular, colonial, and multicellular forms. Other marine protist are neither single-celled nor microscopic, such as seaweed.

unicellular macroalgae →)" mode="packed" heights="130px" style="float:left;">
File:Chaos carolinensis Wilson 1900.jpg, The single-celled '' giant amoeba'' has up to 1000 nuclei and reaches lengths of 5 mm
File:Gromia in situ closeup.png, ''Gromia sphaerica'' is a large spherical testate amoeba which makes mud trails. Its diameter is up to 3.8 cm.
File:Spiculosiphon oceana AB.png, ''Spiculosiphon oceana'', a unicellular foraminiferan with an appearance and lifestyle that mimics a sponge, grows to 5 cm long.
File:Xenophyophore.jpg, The xenophyophore, another single-celled foraminiferan, lives in abyssal zones. It has a giant shell up to 20 cm across.
File:Giant Kelp.jpg, Giant kelp, a brown algae, is not a true plant, yet it is multicellular and can grow to 50m

Protists have been described as a taxonomic grab bag of misfits where anything that doesn't fit into one of the main biological kingdoms can be placed. Some modern authors prefer to exclude multicellular organisms from the traditional definition of a protist, restricting protists to unicellular organisms. This more constrained definition excludes many brown, multicellular red and green algae, and slime molds.

By locomotion

Another way of categorising protists is according to their mode of locomotion. Many unicellular protists, particularly protozoans, are motile and can generate movement using flagella, cilia or pseudopods. Cells which use flagella for movement are usually referred to as flagellates, cells which use cilia are usually referred to as ciliates, and cells which use pseudopods are usually referred to as amoeba or amoeboids. Other protists are not motile, and consequently have no movement mechanism.

Flagellates include bacteria as well as protists. The rotary motor model used by bacteria uses the protons of an electrochemical gradient in order to move their flagella. Torque 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.

Ciliates generally have hundreds to thousands of cilia that are densely packed together in arrays. During movement, an individual cilium deforms using a high-friction power stroke followed by a low-friction recovery stroke. Since there are multiple cilia packed together on an individual organism, they display collective behavior in a metachronal rhythm. This means the deformation of one cilium is in phase with the deformation of its neighbor, causing deformation waves that propagate along the surface of the organism. These propagating waves of cilia are what allow the organism to use the cilia in a coordinated manner to move. A typical example of a ciliated microorganism is the '' Paramecium'', a one-celled, ciliated protozoan covered by thousands of cilia. The cilia beating together allow the ''Paramecium'' to propel through the water at speeds of 500 micrometers per second.

File:Flagellum base diagram-en.svg, Bacterial flagellum rotated by a molecular motor at its base
File:PSM V61 D203 Salmon spermatozoa for artificial propagation.png, Salmon spermatozoa
File:Инфузория туфелька поедает бактерии!.gif, Paramecium feeding on bacteria
File:Oxytricha trifallax.jpg, The ciliate ''Oxytricha trifallax'' with cilia clearly visible
File:Collection Penard MHNG Specimen 05bis-1-1 Amoeba proteus.tif, Amoeba with ingested diatoms

Marine fungi

Over 1500 species of fungi are known from marine environments. These are parasitic on marine algae or animals, or are saprobes feeding on dead organic matter from algae, corals, protozoan cysts, sea grasses, and other substrata. Spores of many species have special appendages which facilitate attachment to the substratum. Marine fungi can also be found in sea foam and around hydrothermal areas of the ocean. A diverse range of unusual secondary metabolites is produced by marine fungi.

Mycoplankton are saprotropic members of the plankton communities of marine and freshwater ecosystems. They are composed of filamentous free-living fungi and yeasts associated with planktonic particles or phytoplankton. Similar to bacterioplankton, these aquatic fungi play a significant role in heterotrophic mineralization and nutrient cycling. While mostly microscopic, some mycoplankton can be up to 20 mm in diameter and over 50 mm in length.

A typical milliliter of seawater contains about 10³ to 10⁴ fungal cells. This number is greater in coastal ecosystems and estuaries due to nutritional runoff from terrestrial communities. A higher diversity of mycoplankton is found around coasts and in surface waters down to 1000 metres, with a vertical profile that depends on how abundant phytoplankton is. This profile changes between seasons due to changes in nutrient availability.Gutierrez, Marcelo H; Pantoja, Silvio; Quinones, Renato a and Gonzalez, Rodrigo R. First record of flamentous fungi in the coastal upwelling ecosystem off central Chile. ''Gayana (Concepc.)'' nline 2010, vol.74, n.1, pp. 66-73. .
Marine fungi survive in a constant oxygen deficient environment, and therefore depend on oxygen diffusion by turbulence and oxygen generated by photosynthetic organisms.

Marine fungi can be classified as:
* Lower fungi – adapted to marine habitats (zoosporic fungi, including mastigomycetes: oomycetes and chytridiomycetes)
* Higher fungi – filamentous, modified to planktonic lifestyle ( hyphomycetes, ascomycetes, basidiomycetes). Most mycoplankton species are higher fungi.

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