User:Cassba/Polaribacter

Polaribacter is a genus from the family of Flavobacteriaceae. They are gram-negative, aerobic bacteria that can be heterotrophic, psychrophilic or mesophilic. Most species are non-motile and species range from ovoid to rod-shaped. Polaribacter forms yellow- to orange-pigmented colonies. They have been mostly adapted to cool marine ecosystems. Their optimal growth range is at a temperature between 10-32°C and at a pH of 7.0-8.0. They are oxidase and catalase-positive and are able to grow from carbohydrates, amino acids, and organic acids. There is evidence of two life strategies for Polaribacter. Some species have evolved to a free-living lifestyle where amino acids and carbohydrates are consumed. Polaribacter with this lifestyle have proteorhodopsin that enhances living in oligotrophic seawaters. Other species of Polaribacter attach to substrate in search of protein polymers.

Polaribacter is a genus that is being continuously researched and to date there are 25 species that have been validly published under the ICNP: P. aquimarinus, P. atrinae, P. butkevichii, P. dokdonensis, P. filamentus, P. franzmannii, P. gangjinensis, P. glomeratus, P. haliotis, P. huanghezhanensis, P. insulae, P. irgensii, P. lacunae, P. litorisediminis, P. marinaquae, P. marinivivus, P. pacificus, P. porphyrae, P. reichenbachii, P. sejongensis, P. septentrionalilitoris, P. staleyi, P. tangerinus, P. undariae, P. vadi.

When referring to more than one species, the plural is Polaribacteria.

Phylogeny
This phylogeny is based on rRNA gene sequencing.

Habitat
Polaribacter are a very widely distributed microorganism as various species are capable of living in a plethora of different environments. Therefore, it has been acknowledged that Polaribacter have variable species which have the ability to inhabit environments that can be cold as -20°C and warm as               22°C. However, before this was common knowledge it was thought that Polaribacter only flourished in cold/ice waters because the first Polaribacter discovered was found in the Arctic and Antarctic Sea; and this particular species could only inhabit environments with temperatures ranging from -20°C to 10°C. Polaribacter are also a very versatile microorganism as they can survive in oligotrophic (low nutrients) and in copiotrophic (excess supply of carbon/high nutrient) environments. In addition to inhabiting seawater, it has been found that Polaribacter can be found in sediment. For example, in a study done by (Li et al) they were able to isolate a very phylogenetically close strain to Polaribacter called SM1202T from marine sediment in Kongsfjorden, Svalbard (Arctic Ocean). Furthermore, Polaribacter have been identified through experimental isolation to be present in red macroalgae called Porphyra yezoensis and Pacific green macroalgae called Ulva fenestrate.

Metabolism
Polaribacter are generally metabolically flexible depending on their physiologies, lifestyle and seasonality of the region they inhabit. Many research studies have found that Polaribacter can alternate between two lifestyles as a mechanism for adaptation in response to surface water environmental conditions, where nutrient concentrations are low and light exposure is high. Sequenced strains of Polaribacter showed for high degrees of peptidase and glycoside hydrolase genes in comparison to other Flavobacteriaceae, indicating they undergo the degradation and uptake of external proteins and oligopeptides.

In the pelagic water column, some species are well equipped to attach to particles and substrates to search for and degrade polymers. They are amongst the first organisms to degrade particulate matter and break-down polymers into smaller particles. Studies have shown that they will colonize and attach to particles, glide to search for substrates, and degrade them for carbon and nutrients (Cite). Once they’ve degraded these molecules,  the bacterium may then search for new particles to colonize, hence forcing them to freely-swim in environments where nutrients and organic carbon is not as easily available.

Genetic sequencing found that strains contain numerous genes which encode for CAZymes that are involved in polysaccharide degradation. For example, strain DSW-5 (a strain genetically very similar to strain MED-152), contains 85 genes encoding to CAZymes and 203 peptidases, which suggests its characteristics as free-living heterotrophs. However, the ratio of peptidases to glycoside hydrolase genes varies depending on the environmental conditions the strain is subjected to. For example, Polaribacter sp. MED134 lives in environmental conditions with extended starvation conditions and expresses twice as many peptidases as CAZymes. On the other hand, macroalgae-colonizing species that live in stable, eutrophic environments may express greater proportions of CAZymes than peptidases.

"Free-living" species have the proteorhodopsin gene, which allows them to complete inorganic carbon fixation using light as an energy source. By utilizing their proteorhodopsin to use light energy, this allows Polaribacter to grow in low-nutrient, oligotrophic environmental conditions.

Role in Ecosystem
Isolated samples show that Flavobacteria are well-developed to degrade High-Molecular Weight (HMW) DOM and Polaribacter may be among the first organisms to degrade particulate matter and break-down polymers into smaller particles that can be used by free-living bacterial heterotrophs, suggesting that their role within the food web might be remineralizers of primary production matter.

In the Southern Ocean:

The Antarctic Peninsula exhibits strong seasonal changes, which influences how bacteria respond to and live in these environmental conditions. The Antarctic spring is especially important as it brings about significant changes, including sea ice melting, thermal stratification due to warming surface waters, and increased dissolved organic matter (DOM) production. All these physical changes also result in phytoplankton blooms which are important in supporting higher trophic levels.

In the Southern Ocean, Flavobacteria dominate bacterial activity, particularly Flavobacteria of the Polaribacter genus. Typically, these bacteria are prevalent in sea ice, however, during seasonal melting in the summer, they dominate coastal waters as sea ice retreats. In the Southern Ocean, when phytoplankton blooms occur, Flavobacteria, and particularly Polaribacter, are among the first bacterial taxa to respond to phytoplankton blooms and break down the organic matter by direct attachment and the use of exoenzymes. Both particle-attached and free-living members of Rhodobacteraceae were also found in close association of the phytoplankton blooms, however, bacterium from this family were found to utilize lower molecular weight substrates, which suggests that they’re secondary in the microbial succession of substrates, utilizing the byproducts of degradation by Flavobacteria. The relative abundance of free-living Polaribacter and Rhodobacteraceae was also found to peak at different points during the phytoplankton blooms, suggesting a niche specialization contributing to successive degradation of phytoplankton-derived organic matter. Polaribacter and Rhodobacteraceae were found in clusters, with Polaribacter clusters forming earlier on in the bloom which further suggests a successive ecological interaction between various bacterial taxa.

For both the Arctic Oceans and the North Sea, Polaribacter exhibited similar trends pertaining to phytoplankton blooms in the summertime as well as assuming particular niches for organic matter degradation.

Genome
The Polaribacter genome varies in genome size (2.76 Mb (P. irgensii) - 4.10 Mb (P. reichenbachii)) and number of genes (2446 ''(P. irgensii) - 3500 (P. reichenbachii''))and a G+C content of approximately 30 mol%. Some notable features include the presence of agar, alginate, and carrageenan degrading enzymes in Polaribacter species colonizing the surface of macroalgae. Agar degrading enzymes have also been found in Polaribacter strains colonizing the gut of the comb pen shell. Proteases are also commonly found in the genomes of this genus, which preferentially grow on solid substrates and degrade protein over using free amino acids and living a pelagic lifestyle. Some members of the genus encode proteorhodopsin as well, which has been implicated in supporting their central metabolism through photophosphorylation.

Due to their relatively modern discovery, DNA sequencing has commonly been used to identify new strains of Polaribacter, help place species on the phylogenetic tree as well as helping to understand, or predict a species role in an environment due to the presence of certain genes. Members of the family Flavobacteriaceae can be identified through a specific quinone called Menaquinone 6 also known as Vitamin K2, however differentiating the species can be much more difficult. Species such as Polaribacter vadi and Polaribacter atrinae were identified as new species based on their similar but unique genome when compared to other members of the Polaribacter genus. New species can be identified through DNA hybridization or through the sequencing and comparison of a common gene such as 16S rRNA. This has allowed scientists to create phylogenetic trees of the genus based on genomic similarity as well as identify common features in the genome.

Genomic analysis on its own has allowed scientist to examine the relationships between different species of Polaribacter, however by combining genomic analysis and other analytical techniques such as chemotaxonomic and biochemical, scientists can theorize how a species might fit into an environment or how they believe a species is adapted to survive. An example of this is the Polaribacter strain MED152, a genomic analysis of this species found a considerable amount of genes that allow for surface or particle attachment, gliding motility and polymer degradation. These genes fit with the current understanding of how marine bacteroidetes survive through attaching to a surface and moving over it to look for nutrients. However the researchers also noticed that the organism had a proteorhodopsin gene as well as other genes which could be used to sense light, furthermore under light the species increased carbon dioxide fixation. This led the researchers to theorize that Polaribacter strain MED152 has two different life strategies, one where it acts like other marine bacteroidetes, attaching to surfaces and searching for nutrients and, the other life strategy is hypothesized to be if the organism was in a well lit, low nutrient area of the ocean, it would use carbon fixation to synthesize intermediates of metabolic pathways. Another example of this comes from the Polaribacter strains Hel1_33_49 and Hel1_85. The strain Hel1_33_49 has a genome which contains proteorhodopsin, fewer polysaccharide utilization loci and no mannitol dehydrogenase, which the researchers associate with a pelagic lifestyle. Hel1_85 on the other hand has a genome which contains twice as many fewer polysaccharide utilization loci, a mannitol dehydrogenase with no proteorhodopsin, pointing to a lifestyle with lower oxygen such as a biofilm.

Viral Pathogens
Two species of lytic phage are known to infect members of this genus and both have double stranded DNA with virions comprised of isometric heads and non-contractile tails. Viral lysis has been implicated as a major driver of changes in genus-level composition of microbial communities.

Applications/Uses
Cold water enzymes contained in psychrophilic bacteria like Polaribacter are valuable for biotechnology applications since they do not require high temperatures that may other enzyme systems do.

Psychrophilic Enzymes

Polaribacter is a psychrophilic bacterium that lends itself to a variety of applications in both academic and industrial settings. These cold dwelling bacteria are an abundant source of psychrophilic enzymes which have an interesting ability to retain higher catalytic activity at temperatures below 25°C. This is due to the highly malleable nature of these enzymes as this allows for better substrate - active site binding at colder temperatures. This is important as enzymes that operate at lower temperatures not only make the industrial processes more efficient, but they also minimize the chance of side reactions occurring. More of the substrate can directly be converted into the desired product all the while requiring less energy to do so. Psychrophilic enzymes can also aid with heat labile or volatile compounds, allowing reactions to occur without significant product loss. Another unique application for these enzymes is the ability to be inhibited without the need of external reagents. Usually to stop enzyme activity, chemical inhibitors are required which then require subsequent purification steps. With psychrophilic enzymes you can add slight heat to prevent any further reaction from occurring. Psychrophilic proteases derived from Polaribacter can be added to detergents allowing the washing of fabric at room temperature.

An example of this is the enzyme carrageenase, which has been shown to have anti-tumor, antiviral, antioxidant and immunomodulatory activities. However, carrageenase isolated from bacteria has historically had low enzyme activity and poor stability. Recently researchers have isolated and cloned the carrageenase gene from the Polaribacter sp. NJDZ03, which shows better thermostability, and the ability to be active at lower temperatures, making it a better choice for industrial uses.

Exopolysaccharide

EPS is a secreted exopolysaccharide which protects the cells, stabilizes membranes, and serve and carbon stores. Most EPS is similar but it is found that in extremophiles, the composition may be distinct. Specifically in Polaribacter sp. SM1127, where the EPS has antioxidant activity and has shown to protect human fibroblast cells at lower temperatures. Studies by Sun et al. were done to determine whether this can be utilized to protect and repair damage caused by frostbite. It was found that Polaribacter derived EPS helps facilitate the dermal fibroblast cell movement to the site of injury. This not only promotes healing during frostbite injury but other cutaneous wounds as well.