Polaribacter is a genus in the family 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, and their optimal growth range is at a temperature between 10 and 32 °C and at a pH of 7.0 to 8.0. They are oxidase and catalase-positive and are able to grow using carbohydrates, amino acids, and organic acids.
There is evidence of two life strategies for members of the genus, Polaribacter. Some Polaribacter species are free-living and consume amino acids and carbohydrates, as well as have proteorhodopsin that enhances living in oligotrophic seawaters. Other species of Polaribacter attach to substrates in search of protein polymers.
In the context of climate change, algal blooms are becoming increasingly prevalent. Members of the genus Polaribacter decompose algal cells and thus may be important in biogeochemical cycling, as well as influence seawater chemistry and the composition of microbial communities as temperatures continue to rise. This may impact the efficiency of the biological pump in sequestering atmospheric carbon.
Polaribacter is a genus that is being continuously researched and to date there are 25 species that have been validly published under the International Code of Nomenclature of Prokaryotes (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.
The genus is sometimes incorrectly referred to as Polaribacer; Polarobacter or Polaribacteria.
Phylogeny This phylogeny is based on rRNA gene sequencing.
Distribution and abundance Members in the genus Polaribacter are abundant in polar oceans and are important in the export of dissolved organic matter (DOM). A small percentage of the bacterial community is responsible for the DOM uptake rate.
In northern latitude waters, the fraction of cells using glucose (fraction of active cells) is higher in summer than winter, and high abundances may occur after phytoplankton blooms, although a study in southern high-latitude waters found lower abundances of Polaribacter after an in situ diatom bloom.
Within the Arctic Ocean, there is no obvious pattern in the relative abundance between summer and winter. In the Chukchi Sea, the fraction of cells using leucine is higher in the winter than in summer. In the Beaufort Sea, the fraction of cells using leucine does not differ between seasons. In the coastal waters of Fildes Peninsula, Polaribacter dominated cells in the phylum Bacteriodetes.
Habitat
Microorganisms in the genus Polaribacter are widely distributed and various species are capable of living in a plethora of different environments. Some Polaribacter species have been isolated from brine pools in the Arctic Ocean. in addition to hypersaline environments, numerous Polaribacter species inhabit extreme environments ranging from -20 °C to 22 °C. In the past, it was thought that Polaribacter only flourished in cold waters as the members of the species that were first discovered (P. irgensii, P. filamentus, and P. franzmannii) in the Arctic and Southern Oceans could only survive in water with temperatures ranging from -20 °C to 10 °C. Subsequently, members of the genus Polaribacter have been shown to be very versatile microorganisms and can survive in oligotrophic and in copiotrophic environments. Polaribacter have also been found in sediments. For example, SM1202T, a phylogenetically close strain to Polaribacter was isolated from marine sediment in Kongsfjorden, Svalbard. Polaribacter have also been experimentally isolated from red macroalgae (Porphyra yezoensis) and green macroalgae (Ulva fenestrate).
Role in ecosystem Isolates of related Flavobacteria are able to degrade High-Molecular Weight (HMW) DOM. and Polaribacter may be among the first organisms to degrade particulate organic matter and break-down polymers into smaller particles that can be used by free-living bacterial heterotrophs. This suggests that they likely remineralize primary production matter within the food web.
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 in the genus Polaribacter. 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 members in the genus Polaribacter, are among the first bacterial taxa to respond to phytoplankton blooms, breaking down organic matter by direct attachment and the use of exoenzymes. Both particle-attached and free-living members of the family Rhodobacteraceae were also found in close association with phytoplankton blooms; however, bacteria in this family were found to use lower molecular weight substrates. This suggests that they're secondary in the microbial succession of substrates, using the byproducts of degradation by flavobacteria, which also includes members of the genus Polaribacter. The relative abundance of free-living bacteria belonging to the genus Polaribacter and in the family Rhodobacteraceae peaked at different points during phytoplankton blooms, suggesting a niche specialization contributing to successive degradation of phytoplankton-derived organic matter. Bacteria in the genus Polaribacter and family Rhodobacteraceae were found in clusters, with Polaribacter clusters forming earlier in the bloom, which further suggests a successive ecological interaction between various bacterial taxa.
For both the Arctic Ocean 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.
Metabolism Members of the genus Polaribacter are metabolically flexible depending on their physiology, 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 surface waters where nutrient concentrations are low and light exposure is high. Sequenced strains of the genus Polaribacter show a high prevalence of peptidase and glycoside hydrolase genes in comparison to other bacteria in the Flavobacteriaceae, indicating they contribute to 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 organic 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. Once they've degraded these molecules, the bacterium may then search for new particles to colonize, forcing them to freely-swim in environments where nutrients and organic carbon is not easily available.
CAZymes
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 role as a 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.
Proteorhodopsin
"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, Polaribacter can grow in oligotrophic environmental conditions.
Genome
General genome characteristics The genome of bacteria in the genus Polaribacter vary in size from 2.76 Mb (P. irgensii) to 4.10 Mb (P. reichenbachii) and the number of genes ranging from 2446 in P. irgensii to 3500 in P. reichenbachii, but have a fairly constant G+C content of approximately 30 mol%. Some notable features of the genome include genes for agar, alginate, and carrageenan degrading enzymes in Polaribacter species which colonize the surface of macroalgae. Agar degrading enzymes have also been found in strains of Polaribacter that colonize the gut of the comb pen shell. Proteases are also commonly found in the genomes of species that preferentially grow on solid substrates and degrade protein instead of using free amino acids and living a pelagic lifestyle. Some members of the genus encode proteorhodopsin, which has been implicated in supporting their central metabolism through photophosphorylation.
DNA sequencing of Polaribacter DNA sequencing has commonly been used to identify new strains of Polaribacter and help place species on a phylogenetic tree. DNA sequencing has also been used to help 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 the specific quinone, Menaquinone 6, also known as Vitamin K2; however, differentiating 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 genus Polaribacter. 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 seen in the phylogeny section, as well as identify common features in the genome.
Life strategies of Polaribacter based on genome analysis