Marine microorganism

A microorganism (or microbe) is a microscopic living organism, which may be single-celled^[1] or multicellular. Microorganisms are very diverse and include all bacteria, archaea and most protozoa. This group also contains some species of fungi, algae, and 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 nonliving.^[2][3] In July 2016, scientists reported identifying a set of 355 genes from the last universal common ancestor (LUCA) of all life, including microorganisms, living on Earth.^[4]

Microorganisms are crucial to nutrient recycling in ecosystems as they act as decomposers. A small proportion of microorganisms are pathogenic, causing disease and even death in plants and animals.^[5] 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.^[6]

Microscopic life in the oceans is very diverse and still poorly understood. For example, the role of viruses in marine ecosystems has barely being explored even in the beginning of the 21st century.^[7]

Overview

microbial mats

Microbial mats are the earliest form of life on Earth for which there is good fossil evidence. The image shows a cyanobacterial-algal mat.

Stromatolites are formed from microbial mats as microbes slowly move upwards to avoid being smothered by sediment.

Marine microbial loop

A teaspoon of seawater contains about one million viruses.^[8] Most of these are bacteriophages, which are harmless to plants and animals, and are in fact essential to the regulation of saltwater and freshwater ecosystems.^[9] 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.^[10] Viral activity may also contribute to the biological pump, the process whereby carbon is sequestered in the deep ocean.^[11]

Marine bacteriophages are viruses that live as obligate parasitic agents in marine bacteria such as cyanobacteria.^[12] Their existence was discovered through electron microscopy and epifluorescence microscopy of ecological water samples, and later through metagenomic sampling of uncultured viral samples.^[12][13] The tailed bacteriophages appear to dominate marine ecosystems in number and diversity of organisms.^[12] However, viruses belonging to families Corticoviridae,^[14] Inoviridae^[15] and Microviridae^[16] are also known to infect diverse marine bacteria. Metagenomic evidence suggests that microviruses (icosahedral ssDNA phages) are particularly prevalent in marine habitats.^[16]

Bacteriophages, viruses that are parasitic on bacteria, were first discovered in the early twentieth century. Scientists today consider that their importance in ecosystems, particularly marine ecosystems, has been underestimated, leading to these infectious agents being poorly investigated and their numbers and species biodiversity being greatly under reported.^[17]

Microorganisms constitute more than 90% of the biomass in the sea. It is estimated that viruses kill approximately 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,^[18] which often kill other marine life.^[19] The number of viruses in the oceans decreases further offshore and deeper into the water, where there are fewer host organisms.^[11]

Microscopic organisms live in every part of 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).^[20] Barophilic marine microbes have been found at more than a depth of 10,000 m (33,000 ft; 6.2 mi) in the Mariana Trench, the deepest spot in the Earth's oceans.^[21] In fact, single-celled life forms have been found in the deepest part of the Mariana Trench, by the Challenger Deep, at depths of 11,034 m (36,201 ft; 6.856 mi).^[22][23][24] Other researchers reported related studies that microorganisms thrive inside rocks up to 580 m (1,900 ft; 0.36 mi) below the sea floor under 2,590 m (8,500 ft; 1.61 mi) of ocean off the coast of the northwestern United States,^[23][25] as well as 2,400 m (7,900 ft; 1.5 mi) beneath the seabed off Japan.^[26] The greatest known temperature at which microbial life can exist is 122 °C (252 °F) (Methanopyrus kandleri).^[27] On 20 August 2014, scientists confirmed the existence of microorganisms living 800 m (2,600 ft; 0.50 mi) below the ice of Antarctica.^[28][29] According to one researcher, "You can find microbes everywhere — they're extremely adaptable to conditions, and survive wherever they are."^[23]

Marine viruses

Transmission electron micrograph of multiple bacteriophages attached to a bacterial cell wall

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.^[30]

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 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.^[31] 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"^[32] and as replicators.^[33]

Viruses are found wherever there is life and have probably existed since living cells first evolved.^[34] 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.^[35]

Viruses are now recognised as ancient and as having origins that pre-date the divergence of life into the three domains.^[36]

Opinions differ on whether viruses are a form of life, or organic structures that interact with living organisms.^[33] They have been described as "organisms at the edge of life",^[32] since they resemble organisms in that they possess genes, evolve by natural selection,^[37] and reproduce by creating multiple copies of themselves through self-assembly. Although they have genes, they do not have a cellular structure, which is often seen as the basic unit of life. Viruses do not have their own metabolism, and require a host cell to make new products. They therefore cannot naturally reproduce outside a host cell.^[38]

Bacterial viruses, called bacteriophages, are a common and diverse group of viruses and are the most abundant form of biological entity in aquatic environments – there are up to ten times more of these viruses in the oceans than there are bacteria,^[39] reaching levels of 250,000,000 bacteriophages per millilitre of seawater.^[40]

There are also archaean viruses, which replicate within archaea: these are double-stranded DNA viruses with unusual and sometimes unique shapes.^[41][42] These viruses have been studied in most detail in the thermophilic archaea, particularly the orders Sulfolobales and Thermoproteales.^[43]

A teaspoon of seawater contains about one million viruses.^[8] Most of these are bacteriophages, which are harmless to plants and animals, and are in fact essential to the regulation of saltwater and freshwater ecosystems.^[9] 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.^[10] Viral activity may also contribute to the biological pump, the process whereby carbon is sequestered in the deep ocean.^[11]

Microorganisms constitute more than 90% of the biomass in the sea. It is estimated that viruses kill approximately 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,^[18] which often kill other marine life.^[19] The number of viruses in the oceans decreases further offshore and deeper into the water, where there are fewer host organisms.^[11]

Viruses are an important natural means of transferring genes between different species, which increases genetic diversity and drives evolution.^[31] 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.^[44] Viruses are still one of the largest reservoirs of unexplored genetic diversity on Earth.^[11]

Prokaryotes

Marine bacteria

Vibrio vulnificus, a virulent bacterium found in estuaries and along coastal areas

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,^[45] 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.^[46]

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.^[47][48] 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.^[49] 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.^[50][51] 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.^[52][53] This is known as secondary endosymbiosis.

• 
  The marine Thiomargarita namibiensis, largest known bacterium
• 
  Cyanobacteria blooms can contain lethal cyanotoxins
• 
  Chloroplasts, such as the chloroplasts of this glaucophyte, may have originated from cyanobacteria.^[54]
• 
  Bacteria can be beneficial. This Pompeii worm, an extremophile found only at hydrothermal vents, has a protective cover of bacteria.

The largest known bacterium, the marine Thiomargarita namibiensis, can be visible to the naked eye and sometimes attains 0.75 mm (750 µm).^[55][56]

Marine archaea

Archaea were initially viewed as extremophiles living in harsh environments, such as the yellow archaea pictured here in a hot spring, but they have since been found in a much broader range of habitats.^[57]

The archaea (Greek for ancient ^[58]) 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.^[59] 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.^[60] 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. Unlike viruses and bacteria, no known archaea is a pathogen.

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.

• 
  Halobacteria, found in water saturated or nearly saturated with salt, are now recognized as being archaea.
• 
  The flat and square-shaped cells of the archaea Haloquadratum walsbyi
• 
  Crystal structure of prefoldin from the heat-loving marine archaea Pyrococcus horikoshii^[61]
• 
  Methanosarcina barkeri, a marine archaea that produces methane

Eukaryotes

Marine fungi

Marine Ascomycete fungus

Lichen on a rock in a marine splash zone. Lichens are mutualistic associations between a fungus and an alga or cyanobacterium.

Over 1500 species of fungi are known from marine environments.^[62] These are parasitic on marine algae or animals, or are saprobes on algae, corals, protozoan cysts, sea grasses, wood and other substrata, and can also be found in sea foam.^[63] Spores of many species have special appendages that facilitate attachment to the substratum.^[64] A very diverse range of unusual secondary metabolites is produced by marine fungi.^[65]

Mycoplankton are saprotropic members of the plankton communities of marine and freshwater ecosystems.^[66][67] They are composed of filamentous free-living fungi and yeasts that are associated with planktonic particles or phytoplankton.^[68] Similar to bacterioplankton, these aquatic fungi play a significant role in heterotrophic mineralization and nutrient cycling.^[69] Mycoplankton can be up to 20 mm in diameter and over 50 mm in length.^[70]

In a typical milliliter of seawater, there are approximately 10³ to 10⁴ fungal cells.^[71] This number is greater in coastal ecosystems and estuaries due to nutritional runoff from terrestrial communities. The greatest diversity and number of species of mycoplankton is found in surface waters (< 1000 m), and the vertical profile depends on the abundance of phytoplankton.^[72][73] Furthermore, this difference in distribution may vary between seasons due to nutrient availability.^[74] Marine fungi survive in a constant oxygen deficient environment, and therefore depend on oxygen diffusion by turbulence and oxygen generated by photosynthetic organisms.^[75]

Marine fungi can be classified as:^[75]

• 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.^[72]

Lichens are mutualistic associations between a fungus, usually an ascomycete, and an alga or a cyanobacterium. Several lichens are found in marine environments.^[76] Many more occur in the splash zone, where they occupy different vertical zones depending on how tolerant they are to submersion.^[77] Fossil marine lichens 600 million years old have been discovered in the late Neoproterozoic marine phosphate rocks in the sedimentary, fossil-rich Doushantuo Formation in China.^[78]

According to fossil records, fungi date back to the late Proterozoic era 900-570 million years ago. It has been hypothesized that mycoplankton evolved from terrestrial fungi, likely in the Paleozoic era (390 million years ago).^[79]

Marine protists

Of eukaryotic groups, the protists are most commonly unicellular and microscopic. This is a highly diverse group of organisms that are not easy to classify.^[80][81] Several algae species are multicellular protists, and there are marine slime molds have unique life cycles that involve switching between unicellular, colonial, and multicellular forms.^[82] The number of species of protists is unknown, and we may have identified only a small portion. Studies from 2001-2004 have shown that a high degree of protist diversity exists in oceans, deep sea-vents, river sediment and an acidic river, which suggests that a large number of eukaryotic microbial communities have yet to be discovered.^[83][84]

Marine algae

Algae can grow as single cells, or in long chains of cells. Green algae are a large group of photosynthetic eukaryotes that include many microscopic organisms. Green algae includes unicellular and colonial flagellates as well as various colonial, coccoid, and filamentous forms. There are about 6000 species.^[85]

• Marine algae
• 
  Phytoplankton are the foundation of the oceanic food chain and account for half of all photosynthetic activity on Earth.^[86][87]
• 
  Assorted diatoms found living between crystals of annual sea ice in Antarctica
• 
  Pleurosigma angulatum, a diatom frequently used for test purposes in microscopy

Marine animals

At least one microscopic animal group, the parasitic cnidarian Myxozoa, is unicellular in its adult form, and includes marine species. Other marine micro-animals are multicellular. Microscopic arthropods are more commonly found inland in freshwater, but there are marine species as well. Microscopic marine crustaceans include some copepods, cladocera and water bears. Some marine nematodes and rotifers are also too small to be seen with the naked eye, as are many loricifera, including the recently discovered anaerobic species that spend their lives in an anoxic environment.^[88][89] Copepods contribute more to the secondary productivity and carbon sink of the world oceans than any other group of organisms.

• Marine micro-animals
• 
  Over 10,000 marine species are copepods, small, often microscopic crustaceans
• 
  Darkfield photo of a gastrotrich, which form a phylum of worm-like animals living mostly between particles of sediment
• 
  Armoured Pliciloricus enigmaticus of the phylum Loricifera live in the spaces between marine gravel

See also

• Marine life
• Marine microbial symbiosis
• Microbial ecology
• Microbial food web
• Microbial loop
• Microbially induced sedimentary structure
• International Census of Marine Microbes

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