Marine microorganisms

[9] However marine microorganisms recycle the major chemical elements, both producing and consuming about half of all organic matter generated on the planet every year.

In July 2016, scientists reported identifying a set of 355 genes from the last universal common ancestor (LUCA) of all life on the planet, including the marine microorganisms.

[8] Viruses Bacteria Archaea Protists Microfungi Microanimals 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.

[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.

[38] However, as a result of more recent research, non-tailed viruses appear to be dominant in multiple depths and oceanic regions, followed by the Caudovirales families of myoviruses, podoviruses, and siphoviruses.

[32] 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.

[81] 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.

[89][90] 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.

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.

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.

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.

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.

[157] Phytoplankton include cyanobacteria (above), diatoms, various other types of algae (red, green, brown, and yellow-green), dinoflagellates, euglenoids, coccolithophorids, cryptomonads, chlorophytes, prasinophytes, and silicoflagellates.

"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.

Many protozoans (single-celled protists that prey on other microscopic life) are zooplankton, including zooflagellates, foraminiferans, radiolarians, some dinoflagellates and marine microanimals.

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.

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.

In 2020 it was reported that researchers have examined the chemical composition of thousands of samples of these benthic forams and used their findings to build the most detailed climate record of Earth ever.

[227][228][229] The concept of the holobiont was initially defined by Dr. Lynn Margulis in her 1991 book Symbiosis as a Source of Evolutionary Innovation as an assemblage of a host and the many other species living in or around it, which together form a discrete ecological unit.

[244] Viral shunting helps maintain diversity within the microbial ecosystem by preventing a single species of marine microbe from dominating the micro-environment.

[256] As their infections are often fatal, they constitute a significant source of mortality and thus have widespread influence on biological oceanographic processes, evolution and biogeochemical cycling within the ocean.

[259] Like in other marine environments, deep-sea hydrothermal viruses affect abundance and diversity of prokaryotes and therefore impact microbial biogeochemical cycling by lysing their hosts to replicate.

[260] However, in contrast to their role as a source of mortality and population control, viruses have also been postulated to enhance survival of prokaryotes in extreme environments, acting as reservoirs of genetic information.

Lower down, these are not available, so they make use of "edibles" (electron donors) such as hydrogen released from rocks by various chemical processes, methane, reduced sulfur compounds and ammonium.

The microorganisms were found in organically poor sediments 68.9 metres (226 feet) below the seafloor in the South Pacific Gyre (SPG), "the deadest spot in the ocean".

This resulted in erroneous, distorted and confused classification, an example of which, noted Carl Woese, is Pseudomonas whose etymology ironically matched its taxonomy, namely "false unit".

[283] These new possibilities have revolutionized microbial ecology, because the analysis of genomes and metagenomes in a high-throughput manner provides efficient methods for addressing the functional potential of individual microorganisms as well as of whole communities in their natural habitats.

[6] Microorganisms have key roles in carbon and nutrient cycling, animal (including human) and plant health, agriculture and the global food web.

Unless we appreciate the importance of microbial processes, we fundamentally limit our understanding of Earth's biosphere and response to climate change and thus jeopardize efforts to create an environmentally sustainable future.

Over eons, the photosynthesis of marine microorganisms generated by oxygen has helped shape the chemical environment in the evolution of plants, animals and many other life forms.

Role of the microbial community in the marine carbon cycle
Relative sizes of microscopic entities
The range of sizes shown by prokaryotes (bacteria and archaea) and viruses relative to those of other organisms and biomolecules
Under a magnifier, a splash of seawater teems with microscopic life
Sea spray containing marine microorganisms can be swept high into the atmosphere where they become aeroplankton , and can travel the globe before falling back to earth.
Virus-host interactions in the marine ecosystem,
including viral infection of bacteria, phytoplankton and fish [ 30 ]
Virions of different families of tailed phages
These are cyanophages , viruses that infect cyanobacteria (scale bars indicate 100 nm)
The giant mimivirus
Largest known virus, Tupanvirus , named after Tupã , the Guarani supreme god of creation
Pelagibacter ubique , the most abundant bacteria in the ocean, plays a major role in the global carbon cycle .
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.
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 . [ 78 ]
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
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.
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 effectively 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.
Phytoplankton – such as this colony of Chaetoceros socialis – naturally gives off red fluorescent light which dissipates excess solar energy they cannot consume through photosynthesis. This glow can be detected by satellites as an indicator of how efficiently ocean phytoplankton is photosynthesising. [ 154 ] [ 155 ]
Structure of a centric diatom frustule [ 162 ]
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 . [ 165 ]
Halobacteria in salt evaporation ponds coloured purple by bacteriorhodopsin [ 167 ]
Amoeba engulfing a diatom
Stone dagger of Ötzi the Iceman who lived during the Copper Age . The blade is made of chert containing radiolarians, calcispheres, calpionellids and a few sponge spicules. The presence of calpionellids , which are extinct, was used to date this dagger. [ 216 ]
Archaea rock – this deep ocean rock harboured worms that consumed methane-eating archaea
Main types of microbial symbioses
(A) Microbial interactions range from mutually beneficial to harmful for one or more partners. Blue double headed arrows highlight that relationships can move between classifications often influenced by environmental conditions. (B) Host-microbe symbioses should be considered within the context of microbial communities where the host participates in multiple and often different symbiotic relationships. (C) Microbial communities are influenced by a variety of microbe-microbe symbioses ranging from cooperation (e.g., syntrophy or co-metabolism) to competition. Arrows depict generally beneficial (blue) and detrimental (red) outcomes for one (single arrowhead) or both (double arrowhead) members. Note as with host-microbe symbioses these relationships can be viewed as fluid and influenced by environmental conditions. [ 230 ]
Marine export production
Marine microbial loop
Roles of fungi in the marine carbon cycle [ 247 ]
The viral shunt pathway facilitates the flow of dissolved organic matter (DOM) and particulate organic matter (POM) through the marine food web
Size and classification of marine particles [ 249 ]
Adapted from Simon et al., 2002. [ 250 ]
Fluorescence microscopy of various picoplankton in the ocean, much of which cannot be effectively studied because they resist attempts at laboratory culture
Subsurface life environments
These aerobic microorganisms, found deep in organically poor sediments, have been in quasi-suspended animation for maybe 100 million years
Unidentified spherical algal microorganism, part of the microbial dark matter
Strategies for sampling plankton by size classes and abundance
The blue background indicates the filtered volume required to obtain sufficient organism numbers for analysis.
Actual volumes from which organisms are sampled are always recorded. [ 277 ]
DNA barcode alignment and comparison between the two species of marine bacteria pictured above [ 280 ]
Methods used to study phytoplankton
Three different possibilities to process the sample are using raw samples, fixation or preservation, and filtration. For microscopy and flow cytometry raw samples either are measured immediately or have to be fixed for later measurements. Since molecular methods, pigment analysis and detection of molecular tracers usually require concentrated cells, filter residues serve for phytoplankton measurements. Molecular characterization and quantification of trace molecules is performed using chromatography , mass spectrometry , and nuclear magnetic resonance spectroscopy. [ 281 ]
DNA sequencing technologies used in marine metagenomics
The discovery process involves marine sampling, DNA sequencing and contig generation . Previously unknown genes, pathways and even whole genomes are being discovered. These genome-editing technologies are used to retrieve and modify valuable microorganisms for production, particularly in marine metagenomics. Organisms may be cultivable or uncultivable. Metagenomics is providing especially valuable information for uncultivable samples. [ 287 ]
Meta-omics data based biogeochemical modeling [ 293 ]
A schematic conceptual framework for marine biogeochemical modeling from environmental, imaging, and meta-omics data. [ 294 ] A semi-automatic computational pipeline is schematized for combining biomarkers with biogeochemical data [ 295 ] that can be incorporated into classic biogeochemical models [ 296 ] for creating a next generation of biogeochemical trait-based meta-omics models by considering their respective traits. Such novel meta-omics-enabled approaches aim to improve the monitoring and prediction of ocean processes while respecting the complexity of the planktonic system. [ 297 ] [ 298 ]
Using omics data with marine phytoplankton [ 299 ]
As an example of how omics data can be used with marine phytoplankton to inform Earth system science , metatranscriptome sequences from natural phytoplankton communities were used to help identify physiological traits (cellular concentration of ribosomes and their rRNAs ) underpinning adaptation to environmental conditions (temperature). A mechanistic phytoplankton cell model was used to test the significance of the identified physiological trait for cellular stoichiometry . Environmental selection in a trait‐based global marine ecosystem model was then linking emergent growth and cellular allocation strategies to large‐scale patterns in light, nutrients and temperature in the surface marine environment. Global predictions of cellular resource allocation and stoichiometry (N:P ratio) were consistent with patterns in metatranscriptome data [ 300 ] and latitudinal patterns in the elemental ratios of marine plankton and organic matter. [ 301 ] The three‐dimensional view of ribosome shows rRNA in dark blue and dark red. Lighter colours represent ribosomal proteins . Bands above show temperature‐dependent abundance of the eukaryotic ribosomal protein S14. [ 300 ]
Microorganisms and climate change in marine and terrestrial biomes [ 6 ]