Marine microorganism

Role of microorganisms in the marine carbon cycle

Marine microorganisms are defined by their habitat as the 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 or microbial) is any microscopic living organism, that is, any life form too small for the naked human eye to really see, needing a microscope. Microorganisms are very diverse. They can be single-celled[1] or multicellular and include all bacteria and archaea and most protozoa, as well as some species of fungi, algae, and certain microscopic animals, such as rotifers and copepods. 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]

Marine microorganisms constitute about 70% of the biomass in the sea.[5] They 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.[6] 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.[7]

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.[8]

Overview[edit]

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.
The range of sizes shown by prokaryotes (bacteria and archaea) and viruses relative to those of other organisms and biomolecules

Microorganisms make up about 70% of the marine biomass.[5] A microorganism, or microbe, is a microscopic organism too small to be recognised adequately with the naked eye. In practice, that includes organism smaller than about 0.1 mm.[9]:13

Such organisms can be single-celled[1] 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 nonliving.[10][3]

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.[11] 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.[12]

Marine microorganisms   

Viruses Bacteriophage2.png

  Prokaryotes  

Bacteria Prokaryote cell.svg

Archaea     Haloquadratum walsbyi00 (cropped).png

Eukaryotes

Protists Diatomee - Diatom (fossile) - Stephanopyxis sp. - 630x (14117161428).jpg

Microfungi   S cerevisiae under DIC microscopy.jpg

Microanimals   SEM image of Milnesium tardigradum in active state - journal.pone.0045682.g001-2.png

While recent technological developments and scientific discoveries have been substantial, we still lack a major understanding at all levels of the basic ecological questions in relation to the microorganisms in our seas and oceans. These fundamental questions are:

1. What is out there? Which microorganisms are present in our seas and oceans and in what numbers do they occur?
2. What are they doing? What functions do each of these microorganisms perform in the marine environment and how do they contribute to the global cycles of energy and matter?

3. What are the factors that determine the presence or absence of a microorganism and how do they influence biodiversity and function and vice versa?

European Science Foundation, 2012[9]:14

Under a magnifier, a splash of seawater teems with microscopic life
Sea spray containing marine microorganisms can be swept high into the atmosphere and may travel the globe before falling back to earth.

Microscopic life undersea is diverse and still poorly understood, such as for the role of viruses in marine ecosystems.[13] Most marine viruses are bacteriophages, which are harmless to plants and animals, but are essential to the regulation of saltwater and freshwater ecosystems.[14] 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.[15] Viral activity may also contribute to the biological pump, the process whereby carbon is sequestered in the deep ocean.[16]

A stream of airborne microorganisms circles the planet above weather systems but below commercial air lanes.[17] 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.[18][19]

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).[20] Single-celled barophilic marine microbes have been found at a depth of 10,900 m (35,800 ft) in the Mariana Trench, the deepest spot in the Earth's oceans.[21][22] Microorganisms live inside rocks 580 m (1,900 ft) below the sea floor under 2,590 m (8,500 ft) of ocean off the coast of the northwestern United States,[21][23] as well as 2,400 m (7,900 ft; 1.5 mi) beneath the seabed off Japan.[24] The greatest known temperature at which microbial life can exist is 122 °C (252 °F) (Methanopyrus kandleri).[25] In 2014, scientists confirmed the existence of microorganisms living 800 m (2,600 ft) below the ice of Antarctica.[26][27] According to one researcher, "You can find microbes everywhere — they're extremely adaptable to conditions, and survive wherever they are."[21]

Marine viruses[edit]

Virus-host interactions in the marine ecosystem,
including viral infection of bacteria, phytoplankton and fish [28]

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.[29]

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.[30] 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"[31] and as replicators.[32]

Bacteriophages (phages)
Multiple phages attached to a bacterial cell wall at 200,000x magnification
Phage injecting its genome into bacteria.svg
Diagram of a typical tailed phage
                  Phage injecting its genome into bacteria

Viruses are found wherever there is life and have probably existed since living cells first evolved.[33] 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.[34]

Viruses are now recognised as ancient and as having origins that pre-date the divergence of life into the three domains.[35]

Opinions differ on whether viruses are a form of life or organic structures that interact with living organisms.[36] 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[37] and as "organisms at the edge of life".[31]

Phages[edit]

In terms of individual counts, tailed phage are the most abundant biological entities in the sea.
These are cyanophages, viruses that infect cyanobacteria (scale bars indicate 100 nm)

Bacteriophages, often just called phages, are viruses that parasite bacteria and archaea. Marine phages parasite marine bacteria and archaea, such as cyanobacteria.[38] 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,[39][40] although estimates of viral abundance in seawater can vary over a wide range.[41][42] Tailed bacteriophages appear to dominate marine ecosystems in number and diversity of organisms.[38] Bacteriophages belonging to the families Corticoviridae,[43] Inoviridae[44] and Microviridae[45] are also known to infect diverse marine bacteria.

Role of viruses[edit]

Microorganisms make up about 70% of the marine biomass.[5] 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,[46] which often kill other marine life.[47] The number of viruses in the oceans decreases further offshore and deeper into the water, where there are fewer host organisms.[16]

There are also archaean viruses which replicate within archaea: these are double-stranded DNA viruses with unusual and sometimes unique shapes.[48][49] These viruses have been studied in most detail in the thermophilic archaea, particularly the orders Sulfolobales and Thermoproteales.[50]

Viruses are an important natural means of transferring genes between different species, which increases genetic diversity and drives evolution.[30] 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.[51] Viruses are still one of the largest reservoirs of unexplored genetic diversity on Earth.[16]

Giant viruses[edit]

The giant mimivirus
Largest known virus, Tupanvirus, named after Tupã, the Guarani supreme god of creation

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, typically about 1000 nanometers (one micron) in length. 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.[52]

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.[53] 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,[54][55] but this has been largely discounted.[56][57]

Prokaryotes[edit]

Marine bacteria[edit]

Vibrio vulnificus, a virulent bacterium found in estuaries and along coastal areas
Electron micrograph showing a species of the widespread cyanobacteria Synechococcus. Carboxysomes appear as polyhedral dark structures.

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,[58] 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.[59]

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.[60][61] 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.[62] 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.[63][64] 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.[65][66] This is known as secondary endosymbiosis.

The largest known bacterium, the marine Thiomargarita namibiensis, can be visible to the naked eye and sometimes attains 0.75 mm (750 μm).[68][69]

Marine archaea[edit]

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.[70]

The archaea (Greek for ancient[71]) 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.[72] 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.[73] 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.

Eukaryotes[edit]

Parakaryon myojinensis, a possible transitional form between a prokaryote and a eukaryote

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. Plants, fungi and animals are usually multi-celled.

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.[74][75]

Marine protists[edit]

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[edit]

Protists can be broadly divided into four groups depending on whether their nutrition is plant-like, animal-like, fungal-like,[76] or a mixture of these.[77]

Protists according to how they get food
Type of protist Description Example Some other examples
Plant-like Autotrophic protists that make their own food without needing to consume other organisms, usually by using photosynthesis Pyramimonas sp.jpg Green algae, Pyramimonas Red and brown algae, diatoms and some dinoflagellates. Plant-like protists are important components of phytoplankton discussed below.
Animal-like Heterotrophic protists that get their food consuming other organisms (bacteria, archaea and small algae) Haeckel Spumellaria detail.png Radiolarian protist as drawn by Haeckel Foraminiferans, and some marine amoebae, ciliates and flagellates.
Fungal-like Saprotrophic protists that get their food from the remains of organisms that have broken down and decayed Aplanonet3.jpg Marine slime nets form labyrinthine networks of tubes in which amoeba without pseudopods can travel Marine lichen
Mixotropes
Various
Mixotrophic and osmotrophic protists that get their food from a combination of the above Euglena mutabilis - 400x - 1 (10388739803) (cropped).jpg Euglena mutabilis, a photosynthetic flagellate Many marine mixotropes are found among protists, including among ciliates, Rhizaria and dinoflagellates [78]
micrograph
cell schematic
Choanoflagellates, unicellular "collared" flagellate protists, are thought to be the closest living relatives of the animals.[79]

Protists are highly diverse organisms currently organised into 18 phyla, but are not easy to classify.[80][81] 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.[82][83] 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.[78]

Video of a ciliate ingesting 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.[86] Other marine protist are neither single-celled nor microscopic, such as seaweed.

Protists have been described as a taxonomic grab bag where anything that doesn't fit into one of the main biological kingdoms can be placed.[89] Some modern authors prefer to exclude multicellular organisms from the traditional definition of a protist, restricting protists to unicellular organisms.[90][91] This more constrained definition excludes many brown, multicellular red and green algae, and slime molds.[92]

By locomotion[edit]

Another way of categorising protists is according to their mode of locomotion. Most unicellular protists are motile and can generate movement using flagella, cilia or pseudopods. Cells which use flagella are usually referred to as flagellates, cells which use cilia for movement are usually referred to as ciliates, and cells which use pseudopods are usually referred to as amoeba or amoeboids.

Protists according to how they move
Type of protist Movement mechanism Description Example Some other examples
Flagellates A flagellum (from Latin for whip) is a lash-like appendage that protrudes from the cell body of some protists (as well as some bacteria). Flagellates use from one to several flagella for locomotion and sometimes as feeding and sensory organelle. CSIRO ScienceImage 6743 SEM Cryptophyte.jpg Cryptophytes Dinoflagellates, choanoflagellates, silicoflagellates, most green algae, and as gametes, some radiolarians and foraminiferans. Excavates may be the most basal flagellate lineage.[93]
Ciliates A cilium (from Latin for eyelash) is a tiny flagellum. Ciliates use multiple cilia, which can number in many hundreds, to power themselves through the water. Stichotricha secunda - 400x (14974779356).jpg Paramecium bursaria
click to see cillia
Foraminiferans, and some marine amoebae, ciliates and flagellates.
Amoebas
(amoeboids)
Amoeba have the ability to alter shape by extending and retracting pseudopods (from Greek for false feet).[94] Amoeba proteus.jpg Amoeba proteus Found in every major protist lineage. Amoeboid cells occur among the protozoa, but also in the algae and the fungi.[95][96]

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.[97]

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.[98]

Marine fungi[edit]

Lichen on a rock in a marine splash zone. Lichens are mutualistic associations between a fungus and an alga or cyanobacterium.
A sea snail, Littoraria irrorata, covered in lichen. This snail farms intertidal ascomycetous fungi

Over 1500 species of fungi are known from marine environments.[99] 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.[100] Spores of many species have special appendages which facilitate attachment to the substratum.[101] Marine fungi can also be found in sea foam and around hydrothermal areas of the ocean.[102] A diverse range of unusual secondary metabolites is produced by marine fungi.[103]

Mycoplankton are saprotropic members of the plankton communities of marine and freshwater ecosystems.[104][105] They are composed of filamentous free-living fungi and yeasts associated with planktonic particles or phytoplankton.[106] Similar to bacterioplankton, these aquatic fungi play a significant role in heterotrophic mineralization and nutrient cycling.[107] While mostly microscopic, some mycoplankton can be up to 20 mm in diameter and over 50 mm in length.[108]

A typical milliliter of seawater contains about 103 to 104 fungal cells.[109] 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.[110][111] This profile changes between seasons due to changes in nutrient availability.[112] Marine fungi survive in a constant oxygen deficient environment, and therefore depend on oxygen diffusion by turbulence and oxygen generated by photosynthetic organisms.[113]

Marine fungi can be classified as:[113]

Lichens are mutualistic associations between a fungus, usually an ascomycete, and an alga or a cyanobacterium. Several lichens are found in marine environments.[114] Many more occur in the splash zone, where they occupy different vertical zones depending on how tolerant they are to submersion.[115] Some lichens live a long time; one species has been dated at 8,600 years.[116] However their lifespan is difficult to measure because what defines the same lichen is not precise.[117] Lichens grow by vegetatively breaking off a piece, which may or may not be defined as the same lichen, and two lichens of different ages can merge, raising the issue of whether it is the same lichen.[117]

The sea snail Littoraria irrorata damages plants of Spartina in the sea marshes where it lives, which enables spores of intertidal ascomycetous fungi to colonise the plant. The snail then eats the fungal growth in preference to the grass itself.[118]

According to fossil records, fungi date back to the late Proterozoic era 900-570 million years ago. Fossil marine lichens 600 million years old have been discovered in China.[119] It has been hypothesized that mycoplankton evolved from terrestrial fungi, likely in the Paleozoic era (390 million years ago).[120]

Marine microanimals[edit]

As juveniles, animals develop from microscopic stages, which can include spores, eggs and larvae. At least one microscopic animal group, the parasitic cnidarian Myxozoa, is unicellular in its adult form, and includes marine species. Other adult marine microanimals are multicellular. Microscopic adult arthropods are more commonly found inland in freshwater, but there are marine species as well. Microscopic adult marine crustaceans include some copepods, cladocera and tardigrades (water bears). Some marine nematodes and rotifers are also too small to be recognised with the naked eye, as are many loricifera, including the recently discovered anaerobic species that spend their lives in an anoxic environment.[121][122] Copepods contribute more to the secondary productivity and carbon sink of the world oceans than any other group of organisms.

Primary producers[edit]

Composite image showing the global distribution of photosynthesis, including both oceanic phytoplankton and terrestrial vegetation. Dark red and blue-green indicate regions of high photosynthetic activity in the ocean and on land, respectively.

Primary producers are the autotroph organisms that make their own food instead of eating other organisms. This means primary producers become the starting point in the food chain for heterotroph organisms that do eat other organisms. Some marine primary producers are specialised bacteria and archaea which are chemotrophs, making their own food by gathering around hydrothermal vents and cold seeps and using chemosynthesis. However most marine primary production comes from organisms which use photosynthesis on the carbon dioxide dissolved in the water. This process uses energy from sunlight to convert water and carbon dioxide[123]:186–187 into sugars that can be used both as a source of chemical energy and of organic molecules that are used in the structural components of cells.[123]:1242 Marine primary producers are important because they underpin almost all marine animal life by generating most of the oxygen and food that provide other organisms with the chemical energy they need to exist.

The principal marine primary producers are cyanobacteria, algae and marine plants. The oxygen released as a by-product of photosynthesis is needed by nearly all living things to carry out cellular respiration. In addition, primary producers are influential in the global carbon and water cycles. They stabilize coastal areas and can provide habitats for marine animals. The term division has been traditionally used instead of phylum when discussing primary producers, but the International Code of Nomenclature for algae, fungi, and plants now accepts both terms as equivalents.[124]

Cyanobacteria[edit]

Cyanobacteria
Cyanobacteria from a microbial mat. Cyanobacteria were the first organisms to release oxygen via photosynthesis
The tiny cyanobacterium Prochlorococcus is a major contributor to atmospheric oxygen

Cyanobacteria are a phylum (division) of bacteria which range from unicellular to filamentous 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.[125] In particular, some species occur as drifting cells floating in the ocean, and as such were amongst the first of the phytoplankton.

The first primary producers that used photosynthesis were oceanic cyanobacteria about 2.3 billion years ago.[126][127] The release of molecular oxygen by cyanobacteria 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.[128]

The tiny (0.6 µm) marine cyanobacterium Prochlorococcus, discovered in 1986, forms today an important part of the base of the ocean food chain and accounts for much of the photosynthesis of the open ocean[129] and an estimated 20% of the oxygen in the Earth's atmosphere.[130] It is possibly the most plentiful genus on Earth: a single millilitre of surface seawater may contain 100,000 cells or more.[131]

Originally, biologists thought cyanobacteria was algae, and referred to it as "blue-green algae". The more recent view is that cyanobacteria is a bacteria, and hence is not even in the same Kingdom as algae. Most authorities exclude all prokaryotes, and hence cyanobacteria from the definition of algae.[132][133]

Algae[edit]

Algae is an informal term for a widespread and diverse group of photosynthetic protists which are not necessarily closely related and are thus polyphyletic. Marine algae can be divided into six groups: green, red and brown algae, euglenophytes, dinoflagellates and diatoms.

Not all algae are microscopic. for example, green, red and brown algae all have multicellular macroscopic forms that make up the familiar seaweeds. Green algae, an informal group containing about 8,000 recognised species.[134] Many species live most of their lives as single cells or are filamentous, while others form colonies made up from long chains of cells, or are highly differentiated macroscopic seaweeds. Red algae, a (disputed) phylum containing about 7,000 recognised species,[135] mostly multicellular and including many notable seaweeds.[135][136] Brown algae form a class containing about 2,000 recognised species,[137] mostly multicellular and including many seaweeds such as kelp Unlike higher plants, algae lack roots, stems, or leaves. They can be classified by size as microalgae or macroalgae.

Dinoflagellates and diatoms are important components of marine algae and have their own sections below.

Euglenophytes are a phylum of unicellular flagellates with only a few marine members.

Microalgae are the microscopic types of algae, not visible to the naked eye. They are mostly unicellular species which exist as individuals or in chains or groups, though some are multicellular. Microalgae are important components of the marine protists discussed above, as well as the phytoplankton discussed below. They are very diverse. It has been estimated there are 200,000-800,000 species of which about 50,000 species have been described.[138] Depending on the species, their sizes range from a few micrometers (µm) to a few hundred micrometers. They are specially adapted to an environment dominated by viscous forces.

Macroalgae are the larger, multicellular and more visible types of algae, commonly called seaweeds. Seaweeds usually grow in shallow coastal waters where they are anchored to the seafloor by a holdfast. Like microalgae, macroalgae (seaweeds) can be regarded as marine protists since they are not true plants. But they are not microorganisms, so they are not within the scope of this article.

Unicellular organisms are usually microscopic, less than one tenth of a millimeter long. There are exceptions. Mermaid's wineglass, a genus of subtropical green algae, is single-celled but remarkably large and complex in form with a single large nucleus, making it a model organism for studying cell biology.[140] Another single-celled algae, Caulerpa taxifolia, has the appearance of a vascular plant including "leaves" arranged neatly up stalks like a fern. Selective breeding in aquariums to produce hardier strains resulted in an accidental release into the Mediterranean where it has become an invasive species known colloquially as killer algae.[141]

Marine microplankton[edit]

Six relatively large variously-shaped organisms with dozens of small light-colored dots all against a dark background. Some of the organisms have antennae that are longer than their bodies.
Plankton are drifting or floating organisms that cannot swim against a current, and include organisms from most areas of life: bacteria, archaea, algae, protozoa and animals.
Red, orange, yellow and green represent areas where algal blooms abound. Blue areas represent nutrient-poor zones where phytoplankton exist in lower concentrations.

Plankton (from Greek for wanderers) are a diverse group of organisms that live in the water column of large bodies of water but cannot swim against a current. As a result, they wander or drift with the currents.[142] Plankton are defined by their ecological niche, not by any phylogenetic or taxonomic classification. They are a crucial source of food for many marine animals, from forage fish to whales. Plankton can be divided into a plant-like component and an animal component.

Phytoplankton[edit]

Phytoplankton are the plant-like components of the plankton community ("phyto" comes from the Greek for plant). They are autotrophic (self-feeding), meaning they generate their own food and do not need to consume other organisms.

Phytoplankton perform three crucial functions: they generate nearly half of the world atmospheric oxygen, they regulate ocean and atmospheric carbon dioxide levels, and they form the base of the marine food web. When conditions are right, blooms of phytoplankton algae can occur in surface waters. Phytoplankton are r-strategists which grow rapidly and can double their population every day. The blooms can become toxic and deplete the water of oxygen. However, phytoplankton numbers are usually kept in check by the phytoplankton exhausting available nutrients and by grazing zooplankton.[143]

Phytoplankton consist mainly of microscopic photosynthetic eukaryotes which inhabit the upper sunlit layer in all oceans. They need sunlight so they can photosynthesize. Most phytoplankton are single-celled algae, but other phytoplankton are bacteria and some are protists.[144] Phytoplankton include cyanobacteria (above), diatoms, various other types of algae (red, green, brown, and yellow-green), dinoflagellates, euglenoids, coccolithophorids, cryptomonads, chlorophytes, prasinophytes, and silicoflagellates. They form the base of the primary production that drives the ocean food web, and account for half of the current global primary production, more than the terrestrial forests.[145]

Diatoms[edit]

Diatom shapes
          Drawings by Haeckel 1904 (click for details)

Diatoms form a (disputed) phylum containing about 100,000 recognised species of mainly unicellular algae. Diatoms generate about 20 percent of the oxygen produced on the planet each year,[146] take in over 6.7 billion metric tons of silicon each year from the waters in which they live,[147] and contribute nearly half of the organic material found in the oceans.

Diatoms
Diatoms have a silica shell (frustule) with radial (centric) or bilateral (pennate) symmetry

Diatoms are enclosed in protective silica (glass) shells called frustules. Each frustule is made from two interlocking parts covered with tiny holes through which the diatom exchanges nutrients and wastes.[143] The frustules of dead diatoms drift to the ocean floor where, over millions of years, they can build up as much as half a mile deep.[148]

Coccolithophores[edit]

Coccolithophores are minute unicellular photosynthetic protists with two flagella for locomotion. Most of them are protected by a shell covered with ornate circular plates or scales called coccoliths. The coccoliths are made from calcium carbonate. The term coccolithophore derives from the Greek for a seed carrying stone, referring to their small size and the coccolith stones they carry. Under the right conditions they bloom, like other phytoplankton, and can turn the ocean milky white.[150]

Coccolithophores
...have plates called coccoliths
...extinct fossil
Coccolithophores build calcite skeletons important to the marine carbon cycle [151]

Zooplankton[edit]

Zooplankton are the animal component of the planktonic community ("zoo" comes from the Greek for animal). They are heterotrophic (other-feeding), meaning they cannot produce their own own food and must consume instead other plants or animals as food. In particular, this means they eat phytoplankton.

Zooplankton are generally larger than phytoplankton, mostly still microscopic but some can be seen with the naked eye. Many protozoans (single-celled protists that prey on other microscopic life) are zooplankton, including zooflagellates, foraminiferans, radiolarians, some dinoflagellates and marine microanimals. Macroscopic zooplankton (not covered further here) include pelagic cnidarians, ctenophores, molluscs, arthropods and tunicates, as well as planktonic arrow worms and bristle worms.

Microzooplankton: major grazers of the plankton...

Radiolarians[edit]

Radiolarian shapes
          Drawings by Haeckel 1904 (click for details)

Radiolarians are unicellular predatory protists encased in elaborate globular shells made of silica and pierced with holes. They catch prey by extending parts of their body through the holes. As with the silica frustules of diatoms, radiolarian shells can sink to the ocean floor when radiolarians die and become preserved as part of the ocean sediment. These remains, as microfossils, can provide valuable information about past oceanic conditions.[152]

As with diatoms, radiolarians also come in many shapes
Turing and radiolarian morphology
Shell of a spherical radiolarian
Shell micrographs
Computer simulations of Turing patterns on a sphere
closely replicate some radiolarian shell patterns [153]

Foraminiferans[edit]

Foraminiferan shapes
          Drawings by Haeckel 1904 (click for details)

Like radiolarians, foraminiferans are single-celled predatory protists, also protected with shells. Their shells, often called tests, are chambered (foraminifera add more chambers as they grow). The shells are usually made of calcite, but are sometimes made of agglutinated sediment particles or chiton, and (rarely) of silica. Most foraminifera are benthic, but about 40 species are planktic.[154] They are widely researched with well established fossil records which allow scientists to infer a lot about past environments and climates.[152]

Foraminiferans
...can have more than one nucleus
...and defensive spines
Foraminiferans are important unicellular zooplankton protists, with calcium tests

A number of forams are mixotrophic (see below). These have unicellular algae as endosymbionts, from diverse lineages such as the green algae, red algae, golden algae, diatoms, and dinoflagellates.[154] Mixotrophic foraminifers are particularly common in nutrient-poor oceanic waters.[155] Some forams are kleptoplastic, retaining chloroplasts from ingested algae to conduct photosynthesis.[156]

Mixotrophs[edit]

A mixotroph is an organism that can use a mix of different sources of energy and carbon, instead of having a single trophic mode on the continuum from complete autotrophy at one end to heterotrophy at the other. It is estimated that mixotrophs comprise more than half of all microscopic plankton.[157] There are two types of eukaryotic mixotrophs: those with their own chloroplasts, and those with endosymbionts—and others that acquire them through kleptoplasty or by enslaving the entire phototrophic cell.[158]

The distinction between plants and animals often breaks down in very small organisms. Possible combinations are photo- and chemotrophy, litho- and organotrophy, auto- and heterotrophy or other combinations of these. Mixotrophs can be either eukaryotic or prokaryotic.[159] They can take advantage of different environmental conditions.[160]

Mixotrophic radiolarians
White Phaeocystis algal foam washing up on a beach
Acantharian radiolarian hosts Phaeocystis symbionts

Phaeocystis is an important algal genus found as part of the marine phytoplankton around the world. It has a polymorphic life cycle, ranging from free-living cells to large colonies.[161] It has the ability to form floating colonies, where hundreds of cells are embedded in a gel matrix, which can increase massively in size during blooms.[162] As a result, Phaeocystis is an important contributor to the marine carbon[163] and sulfur cycles.[164] Phaeocystis species are endosymbionts to acantharian radiolarians.[165][166]

Dinoflagellates[edit]

Dinoflagellate shapes
Unarmored dinoflagellates Kofoid (1921)
Haeckel Peridinea (1904)

Dinoflagellates are part of the algae group, and form a phylum of unicellular flagellates with about 2,000 marine species.[167] The name comes from the Greek "dinos" meaning whirling and the Latin "flagellum" meaning a whip or lash. This refers to the two whip-like attachments (flagella) used for forward movement. Most dinoflagellates are protected with red-brown, cellulose armour. Like other phytoplankton, dinoflagellates are r-strategists which under right conditions can bloom and create red tides.

By trophic orientation dinoflagellates are all over the place. Some dinoflagellates are known to be photosynthetic, but a large fraction of these are in fact mixotrophic, combining photosynthesis with ingestion of prey (phagotrophy).[168] Some species are endosymbionts of marine animals and other protists, and play an important part in the biology of coral reefs. Others predate other protozoa, and a few forms are parasitic. Many dinoflagellates are mixotrophic and could also be classified as phytoplankton.

A surf wave at night sparkles with blue light due to the presence of a bioluminescent dinoflagellate, such as Lingulodinium polyedrum
Suggested explanation for glowing seas[169]
Dinoflagellates
        Armoured
        Unarmoured
Traditionally dinoflagellates have been presented as armoured or unarmoured

Dinoflagellates often live in symbiosis with other organisms. Many nassellarian radiolarians house dinoflagellate symbionts within their tests.[170] The nassellarian provides ammonium and carbon dioxide for the dinoflagellate, while the dinoflagellate provides the nassellarian with a mucous membrane useful for hunting and protection against harmful invaders.[171] There is evidence from DNA analysis that dinoflagellate symbiosis with radiolarians evolved independently from other dinoflagellate symbioses, such as with foraminifera.[172]

Some dinoflagellates are bioluminescent. At night, ocean water can light up internally and sparkle with blue light because of these dinoflagellates.[173][174] Bioluminescent dinoflagellates possess scintillons, individual cytoplasmic bodies which contain dinoflagellate luciferase, the main enzyme involved in the luminescence. The luminescence, sometimes called the phosphorescence of the sea, occurs as brief (0.1 sec) blue flashes or sparks when individual scintillons are stimulated, usually by mechanical disturbances from, for example, a boat or a swimmer or surf.[175]

Marine microbenthos[edit]

Marine microfossils[edit]

Thickness of marine sediments

Sediments at the bottom of the ocean have two main origins, terrigenous and biogenous. Terrigenous sediments account for about 45% of the total marine sediment, and originate in the erosion of rocks on land, transported by rivers and land runoff, windborne dust, volcanoes, or grinding by glaciers.

Biogenous sediments account for the other 55% of the total sediment, and originate in the skeletal remains of marine protists (single-celled plankton and benthos microorganisms). Much smaller amounts of precipitated minerals and meteoric dust can also be present. Ooze, in the context of a marine sediment, does not refer to the consistency of the sediment but to its biological origin. The term ooze was originally used by John Murray, the "father of modern oceanography", who proposed the term radiolarian ooze for the silica deposits of radiolarian shells brought to the surface during the Challenger Expedition.[179] A biogenic ooze is a pelagic sediment containing at least 30 percent from the skeletal remains of marine organisms.

Main types of biogenic ooze
type mineral
forms
protist
involved
name of skeleton typical size
(mm)
description
Siliceous ooze SiO2
silica
quartz
glass
opal
chert
diatom Lyrella hennedy 1600x contrast invertion.jpg frustule 0.002 to 0.2[180]
radiolarian Calocycloma sp. - Radiolarian (32163186535).jpg test or shell 0.1 to 0.2
Calcareous ooze CaCO3
calcite
aragonite
limestone
marble
chalk
foraminiferan Foram-globigerina hg.jpg test or shell under 1 There are about 10,000 living species of foraminiferans [181]
coccolithophore Coccolithus pelagicus 2.jpg coccoliths under 0.1 [182] Coccolithophores are spherical cells enclosed by calcareous plates called coccoliths.[182] They are important microfossils, the largest global source of biogenic calcium carbonate, and make significant contributions to the global carbon cycle.[183] They are the main constituent of chalk deposits such as the white cliffs of Dover.

Marine food web[edit]

The viral shunt pathway facilitates the flow of dissolved organic matter (DOM) and particulate organic matter (POM) through the marine food web

Marine microorganisms play central roles in the marine food web.

The viral shunt pathway is a mechanism that prevents marine microbial particulate organic matter (POM) from migrating up trophic levels by recycling them into dissolved organic matter (DOM), which can be readily taken up by microorganisms.[184] Viral shunting helps maintain diversity within the microbial ecosystem by preventing a single species of marine microbe from dominating the micro-environment.[185] The DOM recycled by the viral shunt pathway is comparable to the amount generated by the other main sources of marine DOM.[186]

Deep biosphere and dark matter[edit]

Fluorescence microscopy of various picoplankton in the ocean, much of which cannot be effectively studied because they resist attempts at laboratory culture

The deep biosphere is that part of the biosphere that resides below the first few meters of the surface. It extends at least 5 kilometers below the continental surface and 10.5 kilometers below the sea surface, with temperatures that may exceed 100°C.

Above the surface living organisms consume organic matter and oxygen. Lower down, these are not available, so they make use of "edibles" (electron acceptors) such as hydrogen released from rocks by various chemical processes, methane, reduced sulfur compounds and ammonium. They "breathe" electron donors such as nitrates and nitrites, manganese and iron oxides, oxidized sulfur compounds and carbon dioxide.

There is very little energy at greater depths, and metabolism can be up to a million times slower than at the surface. Cells may live for thousands of years before dividing and there is no known limit to their age. The subsurface accounts for about 90% of the biomass in bacteria and archaea, and 15% of the total biomass for the biosphere. Eukaryotes are also found, mostly microscopic, but including some multicellular life. Viruses are also present and infect the microbes.

Unidentified spherical algal microorganism, part of the microbial dark matter

In 2018, researchers from the Deep Carbon Observatory announced that life forms, including 70% of the bacteria and archaea on Earth, totaling a biomass of 23 billion tonnes carbon, live up to 4.8 km (3.0 mi) deep underground, including 2.5 km (1.6 mi) below the seabed.[187][188][189] In 2019 microbial organisms were discovered living 7,900 feet (2,400 m) below the surface, breathing sulfur and eating rocks such as pyrite as their regular food source.[190][191][192] This discovery occurred in the oldest known water on Earth.[193]

To date biologists have been unable to culture in the laboratory the vast majority of microorganisms. This applies particularly to bacteria and archaea, and is due to a lack of knowledge or ability to supply the required growth conditions.[194][195] The term microbial dark matter has come to be used to describe microorganisms scientists know are there but have been unable to culture, and whose properties therefore remain elusive.[194] Microbial dark matter is unrelated to the dark matter of physics and cosmology, but is so-called for the difficulty in effectively studying it. It is hard to estimate its relative magnitude, but the accepted gross estimate is that less than one percent of microbial species in a given ecological niche is culturable. In recent years effort is being put to decipher more of the microbial dark matter by means of learning their genome DNA sequence from environmental samples[196] and then by gaining insights to their metabolism from their sequenced genome, promoting the knowledge required for their cultivation.

Anthropogenic impacts[edit]

Microorganisms and climate change in marine and terrestrial biomes [197]

See also[edit]

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