Marine prokaryotes

Marine prokaryotes are defined by their habitat as prokaryotes that live in marine environments, that is, in the saltwater of seas or oceans or the brackish water of coastal estuaries. Life forms can be divided into prokaryotes and eukaryotes. Eukaryotes are organisms whose cells have a nucleus enclosed within membranes, whereas prokaryotes have neither a nucleus nor a membrane. The three-domain system of classifying life adds a third division: the prokaryotes are divided into two domains of life, archaea and bacteria, while the eukaryotes become the third domain.

Background

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

Sea spray containing marine microorganisms, including prokaryotes, can be swept high into the atmosphere and may travel the globe before falling back to earth.

The word prokaryote comes from the Greek pro meaning "before" and karyon meaning "nut" or "kernel". The division between prokaryotes and eukaryotes was firmly established by the microbiologists Roger Stanier and C. B. van Niel in their 1962 paper The concept of a bacterium One reason for this classification was so what was then often called blue-green algae (now called cyanobacteria) would cease to be classified as plants but grouped with bacteria.

In the three-domain system introduced by Carl Woese et al. in 1990 prokaryotes were further split into into archaea, bacteria domains, while the eukaryote become a domain in their own right. The key difference from earlier classifications is the splitting of archaea from bacteria.

Prokaryotes are asexual, reproducing without fusion of gametes. The first organisms may have been marine prokaryotes.

Prokaryotes can play important roles in nutrient recycling in ecosystems as they act as decomposers. Some prokaryotes are pathogenic, causing disease and even death in plants and animals. Prokaryotes are responsible for significant levels of the photosynthesis that occurs in the ocean, as well as significant cycling of carbon and other nutrients.

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. 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. Viral activity may also contribute to the biological pump, the process whereby carbon is sequestered in the deep ocean.

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.

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).

The earliest evidence for life on earth comes from biogenic carbon signatures and stromatolite fossils discovered in 3.7 billion-year-old metasedimentary rocks from western Greenland. In 2015, possible "remains of biotic life" were found in 4.1 billion-year-old rocks in Western Australia. In March 2017, putative evidence of possibly the oldest forms of life on Earth was reported in the form of fossilized microorganisms discovered in hydrothermal vent precipitates in the Nuvvuagittuq Belt of Quebec, Canada, that may have lived as early as 4.28 billion years ago, not long after the oceans formed 4.4 billion years ago, and not long after the formation of the Earth 4.54 billion years ago.

Microbial mats of coexisting bacteria and archaea were the dominant form of life in the early Archean Epoch and many of the major steps in early evolution are thought to have taken place in this environment. The evolution of photosynthesis, around 3.5 Ga, eventually led to a buildup of its waste product, oxygen, in the atmosphere, leading to the great oxygenation event, beginning around 2.4 Ga. The earliest evidence of eukaryotes (complex cells with organelles) dates from 1.85 Ga, and while they may have been present earlier, their diversification accelerated when they started using oxygen in their metabolism. Later, around 1.7 Ga, multicellular organisms began to appear, with differentiated cells performing specialised functions.

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.

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. Crenarchaeota (eocytes) are a phylum of archaea thought to be very abundant in marine environments and one of the main contributors to the fixation of carbon.

• 
  Eocytes may be the most abundant of marine archaea
• 
  Halobacteria, found in water near saturated with salt, are now recognised as archaea.
• 
  Flat, square-shaped cells of the archaea Haloquadratum walsbyi
• 
  Methanosarcina barkeri, a marine archaea that produces methane
• 
  Thermophiles, such as Pyrolobus fumarii, survive well over 100 °C

Maine archaea may be classified as follows:

• Marine Group I (MG-I or MGI): marine Thaumarchaeota with subgroups Ia (aka I.a) up to Id
• Marine Group II (MG-II): marine Euryarchaeota, order Poseidoniales with subgroups IIa up to IId (IIa resembling Poseidoniaceae, IIb resembling Thalassarchaceae)
  Viruses parasiting MGII are classified as magroviruses
• Marine Group III (MG-III): also marine Euryarchaeota, Marine Benthic Group D
• Marine Group IV (MG-IV): also marine Euryarchaeota

Marine bacteria

Pelagibacter ubique, the most abundant bacteria in the ocean, plays a major role in the global carbon cycle.

Scanning electron micrograph of a strain of Roseobacter, a widespread and important genus of marine bacteria. For scale, the membrane pore size is 0.2 μm in diameter.

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.

See also: Bacterioplankton

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.

Bacteria grow to a fixed size and then reproduce through binary fission, a form of asexual reproduction. Under optimal conditions, bacteria can grow and divide extremely rapidly, and bacterial populations can double as quickly as every 9.8 minutes.

Pelagibacter ubique and its relatives may be the most abundant microorganisms in the ocean, and it has been claimed that they are possibly the most abundant bacteria in the world. They make up about 25% of all microbial plankton 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 is probably the most common organism on the planet.

Roseobacter is also one of the most abundant and versatile microorganisms in the ocean. They are diversified across different types of marine habitats, from coastal to open oceans and from sea ice to sea floor, and make up about 25% of coastal marine bacteria. Members of the Roseobacter genus play important roles in marine biogeochemical cycles and climate change, processing a significant portion of the total carbon in the marine environment. They form symbiotic relationships which allow them to degrade aromatic compounds and uptake trace metals. They are widely used in aquaculture and quorum sensing. During algal blooms, 20-30% of the prokaryotic community are Roseobacter.

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

• 
  The marine Thiomargarita namibiensis, largest known bacterium
• 
  The bacterium Marinomonas arctica grows inside Arctic sea ice at subzero temperatures

A microbial mat encrusted with iron oxide on the flank of a seamount can harbour microbial communities dominated by the iron-oxidizing Zetaproteobacteria

• Aerobic anoxygenic phototrophic bacteria (AAPBs) are widely distributed marine plankton that may constitute over 10% of the open ocean microbial community. Marine AAPBs are classified in two marine (Erythrobacter and Roseobacter) genera. They can be particularly abundant in oligotrophic conditions where they were found to be 24% of the community. These are heterotrophic organisms that use light to produce energy, but are unable to utilise carbon dioxide as their primary carbon source. Most are obligately aerobic, meaning they require oxygen to grow. Current data suggests that marine bacteria have generation times of several days, whereas new evidence exists that shows AAPB to have a much shorter generation time. Coastal/shelf waters often have greater amounts of AAPBs, some as high as 13.51% AAPB%. Phytoplankton also affect AAPB%, but little research has been performed in this area. They can also be abundant in various oligotrophic conditions, including the most oligotrophic regime of the world ocean. They are globally distributed in the euphotic zone and represent a hitherto unrecognized component of the marine microbial community that appears to be critical to the cycling of both organic and inorganic carbon in the ocean.

• Purple bacteria:

• Zetaproteobacteria: are iron-oxidizing neutrophilic chemolithoautotrophs, distributed worldwide in estuaries and marine habitats.

• Hydrogen oxidizing bacteria are facultative autotrophs that can be divided into aerobes and anaerobes. The former use hydrogen as an electron donor and oxygen as an acceptor while the latter use sulphate or nitrogen dioxide as electron acceptors.

Phototrophy

• Phototrophy is a noticeable and significant marker that should always play a primary role in bacterial classification.

Cyanobacteria

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

NASA image of a large bloom of Nodularia cyanobacteria swirling in the Baltic Sea

External videos
How cyanobacteria took over the world

Cyanobacteria were the first organisms to evolve an ability to turn sunlight into chemical energy. They form a phylum (division) of bacteria which range from unicellular to filamentous and include colonial species. They are found almost everywhere on earth: in damp soil, in both freshwater and marine environments, and even on Antarctic rocks. In particular, some species occur as drifting cells floating in the ocean, and as such were amongst the first of the phytoplankton.

The first primary producers that used photosynthesis were oceanic cyanobacteria about 2.3 billion years ago. 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.

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 and an estimated 20% of the oxygen in the Earth's atmosphere. It is possibly the most plentiful genus on Earth: a single millilitre of surface seawater may contain 100,000 cells or more.

Originally, biologists classified cyanobacteria as an 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.

• 
  Cyanobacteria blooms can contain lethal cyanotoxins
• 
  The chloroplasts of glaucophytes have a peptidoglycan layer, evidence suggesting their endosymbiotic origin from cyanobacteria.

Symbiosis

See also: Marine microbial symbiosis

Some marine organisms have a symbiosis with bacteria or archaea. Pompeii worms live at great depths by hydrothermal vents at temperatures up to 80°C. They have "hairy" backs; these "hairs" are actually colonies of bacteria such as Nautilia profundicola, which are thought to afford the worm some degree of insulation. Glands on the worm's back secrete a mucus on which the bacteria feed, a form of symbiosis.

• 
  The "hairy" backs of Pompeii worms are actually colonies of symbiotic bacteria
• 
  Hesiocaeca methanicola lives at great depths on methane ice and appear to survive in symbiosis with bacteria which metabolize the clathrate.

Microbial rhodopsin

Model of the energy generating mechanism in marine bacteria

      (1) When sunlight strikes a rhodopsin molecule
      (2) it changes its configuration so a proton is expelled from the cell
      (3) the chemical potential causes the proton to flow back to the cell
      (4) thus generating energy
      (5) in the form of adenosine triphosphate.

Main article: Microbial rhodopsin

Phototrophic metabolism relies on one of three energy-converting pigments: chlorophyll, bacteriochlorophyll, and retinal. Retinal is the chromophore found in rhodopsins. The significance of chlorophyll in converting light energy has been written about for decades, but phototrophy based on retinal pigments is just beginning to be studied.

Halobacteria in salt evaporation ponds coloured purple by bacteriorhodopsin

In 2000 a team of microbiologists led by Edward DeLong made a crucial discovery in the understanding of the marine carbon and energy cycles. They discovered a gene in several species of bacteria responsible for production of the protein rhodopsin, previously unheard of in bacteria. These proteins found in the cell membranes are capable of converting light energy to biochemical energy due to a change in configuration of the rhodopsin molecule as sunlight strikes it, causing the pumping of a proton from inside out and a subsequent inflow that generates the energy. The archaeal-like rhodopsins have subsequently been found among different taxa, protists as well as in bacteria and archaea, though they are rare in complex multicellular organisms.

Research in 2019 shows these "sun-snatching bacteria" are more widespread than previously thought and could change how oceans are affected by global warming. "The findings break from the traditional interpretation of marine ecology found in textbooks, which states that nearly all sunlight in the ocean is captured by chlorophyll in algae. Instead, rhodopsin-equipped bacteria function like hybrid cars, powered by organic matter when available — as most bacteria are — and by sunlight when nutrients are scarce."

There is an astrobiological conjecture called the Purple Earth hypothesis which surmises that original life forms on Earth were retinal-based rather than chlorophyll-based, which would have made the Earth appear purple instead of green.

Role in chemical cycling

Further information: Biogeochemical cycle, microbial oxidation of sulfur, and hydrothermal vent microbial communities

Archaea recycle elements such as carbon, nitrogen, and sulfur through their various habitats. Archaea carry out many steps in the nitrogen cycle. This includes both reactions that remove nitrogen from ecosystems (such as nitrate-based respiration and denitrification) as well as processes that introduce nitrogen (such as nitrate assimilation and nitrogen fixation).

Researchers recently discovered archaeal involvement in ammonia oxidation reactions. These reactions are particularly important in the oceans. In the sulfur cycle, archaea that grow by oxidizing sulfur compounds release this element from rocks, making it available to other organisms, but the archaea that do this, such as Sulfolobus, produce sulfuric acid as a waste product, and the growth of these organisms in abandoned mines can contribute to acid mine drainage and other environmental damage. In the carbon cycle, methanogen archaea remove hydrogen and play an important role in the decay of organic matter by the populations of microorganisms that act as decomposers in anaerobic ecosystems, such as sediments and marshes.