Polaribacter

{{Short description|Genus of bacteria}} {{Italic title}}{{Automatic_taxobox | taxon = Polaribacter | authority = Gosink ''et al''. 1998<ref name="NamesforLife">{{cite journal | vauthors = Parte AC | editor1-first= Charles Thomas | editor1-last= Parker | editor2-first= George M | editor2-last= Garrity | title= Polaribacter | url = https://www.namesforlife.com/10.1601/nm.8177 | journal = NamesforLife | year= 2013 |doi=10.1601/nm.8177| url-access= subscription }}</ref> | type_species = ''Polaribacter filamentus''<ref name="NamesforLife"/> | subdivision_ranks = Species | subdivision = ''P. aestuariivivens''<ref name="NamesforLife"/> ''P. aquimarinus''<ref name="NamesforLife"/> ''P. atrinae''<ref name="NamesforLife"/> ''P. butkevichii''<ref name="NamesforLife"/> ''P. dokdonensis''<ref name="NamesforLife"/> ''P. filamentus''<ref name="NamesforLife"/> ''P. franzmannii''<ref name="NamesforLife"/> ''P. gangjinensis''<ref name="NamesforLife"/> ''P. glomeratus''<ref name="NamesforLife"/> ''P. haliotis''<ref name="NamesforLife"/> ''P. huanghezhanensis''<ref name="NamesforLife"/> ''P. insulae''<ref name="NamesforLife"/> ''P. irgensii''<ref name="NamesforLife"/> ''P. lacunae''<ref name="NamesforLife"/> ''P. litorisediminis''<ref name="NamesforLife"/> ''P. marinaquae''<ref name="NamesforLife"/> ''P. marinivivus''<ref name="NamesforLife"/> ''P. pacificus''<ref name="NamesforLife"/> ''P. porphyrae''<ref name="NamesforLife"/> ''P. reichenbachii''<ref name="NamesforLife"/> ''P. sejongensis''<ref name="NamesforLife"/> ''P. septentrionalilitoris''<ref name="NamesforLife"/> ''P. staleyi''<ref name="NamesforLife"/> ''P. tangerinus''<ref name="NamesforLife"/> ''P. undariae''<ref name="NamesforLife"/> ''P. vadi''<ref name="NamesforLife"/> }}

'''''Polaribacter''''' is a genus in the family ''Flavobacteriaceae''. They are gram-negative, aerobic bacteria that can be heterotrophic, psychrophilic or mesophilic.<ref name="Bowman_2018">{{Cite journal | vauthors = Bowman JP |date=2018-11-19 |title=''Polaribacter'' |journal=Bergey's Manual of Systematics of Archaea and Bacteria |pages=1–21 |doi=10.1002/9781118960608.gbm00333.pub2|isbn=978-1-118-96060-8 |s2cid=239787623 }}</ref> Most species are non-motile and species range from ovoid to rod-shaped.<ref name="Bowman_2018" /> ''Polaribacter'' forms yellow- to orange-pigmented colonies.<ref name="Bowman_2018" /> 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.<ref name="Bowman_2018" /><ref>{{cite journal | vauthors = Park S, Park JM, Jung YT, Lee KC, Lee JS, Yoon JH | title = Polaribacter marinivivus sp. nov., a member of the family Flavobacteriaceae isolated from seawater | journal = Antonie van Leeuwenhoek | volume = 106 | issue = 6 | pages = 1139–1146 | date = December 2014 | pmid = 25224356 | doi = 10.1007/s10482-014-0283-4 | s2cid = 18062687 }}</ref> They are oxidase and catalase-positive and are able to grow using carbohydrates, amino acids, and organic acids.<ref name="Bowman_2018" />

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.<ref name="González_2008" /> Other species of ''Polaribacter'' attach to substrates in search of protein polymers.<ref name="González_2008" />

In the context of climate change, algal blooms are becoming increasingly prevalent.<ref>{{Cite web |last=US EPA |first=OW |date=2013-09-05 |title=Climate Change and Harmful Algal Blooms |url=https://www.epa.gov/habs/climate-change-and-freshwater-harmful-algal-blooms |access-date=2022-04-06 |website=United States Environmental Protection Agency |language=en}}</ref> 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.<ref name="Avcı_2020">{{cite journal |vauthors=Avcı B, Krüger K, Fuchs BM, Teeling H, Amann RI |date=June 2020 |title=Polysaccharide niche partitioning of distinct Polaribacter clades during North Sea spring algal blooms |journal=The ISME Journal |volume=14 |issue=6 |pages=1369–1383 |doi=10.1038/s41396-020-0601-y |pmc=7242417 |pmid=32071394 |bibcode=2020ISMEJ..14.1369A }}</ref>

''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''.<ref>{{Cite web |title=Genus: Polaribacter |url=https://www.bacterio.net/genus/polaribacter |access-date=2022-02-16 |website=www.bacterio.net |language=en}}</ref>

== Phylogeny == This phylogeny is based on rRNA gene sequencing.<ref name="Xu_2020"/> {{Clade|{{clade |1=''P. huanghezhanensis'' |2={{clade |1=''P. porphyrae'' |2=''P. marinivivus'' |3={{clade |1=''P. aquimarinus'' |2=''P. gangjinensis'' |3={{clade |1=''P. reichenbachii'' |2=''P. marinaquae'' |3={{clade |1={{clade |1=''P. dokdonensis'' |2=''P.sp.MED152'' |3={{clade |1={{clade |1=''P. insulae'' |2=''P. vadi'' |3={{clade |1={{clade |1=''P. litorisediminis'' |2=''P. haliotis'' |3={{clade |1={{clade |1=''P. tangerinus'' |2={{clade |1=''P. atrinae'' |2={{clade |1=''P. butkevichii'' |2={{clade |1=''P. undariae'' |2={{clade |1=''P. sejongensis''}} }} }} }} }} |4={{clade |1=''P. irgensii'' |2={{clade |1=''P. franzmannii'' |2={{clade |1=''P. filamentus'' |2={{clade |1=''P. glomeratus'' }} }} }} }} }} }} }} }} }} }} }} }} }} }} }}|''Tenacibaculum''|label1='''''Polaribacter'''''|label2=outgroup|style=font-size:75%;line-height:75%}}

== Distribution and abundance == thumb|Collection sites (red circles) that have identified ''Polaribacter'' in water samples.|leftMembers in the genus ''Polaribacter'' are abundant in polar oceans and are important in the export of dissolved organic matter (DOM).<ref name="Malmstrom_2007">{{Cite journal | vauthors = Malmstrom RR, Straza TR, Cottrell MT, Kirchman DL |date=2007-04-03 |title=Diversity, abundance, and biomass production of bacterial groups in the western Arctic Ocean |journal= Aquatic Microbial Ecology |language=en |volume=47 |pages=45–55 |doi=10.3354/ame047045 |issn=0948-3055|doi-access=free }}</ref><ref>{{Cite journal | vauthors = Straza TR, Ducklow HW, Murray AE, Kirchman D |date = November 2010 |title=Abundance and single-cell activity of bacterial groups in Antarctic coastal waters |journal=Limnology and Oceanography |language=en |volume=55 |issue=6 |pages=2526–2536 |doi=10.4319/lo.2010.55.6.2526|bibcode = 2010LimOc..55.2526S |s2cid = 86616866 |doi-access=free }}</ref> A small percentage of the bacterial community is responsible for the DOM uptake rate.<ref name="Nikrad_2012">{{cite journal | vauthors = Nikrad MP, Cottrell MT, Kirchman DL | title = Abundance and single-cell activity of heterotrophic bacterial groups in the western Arctic Ocean in summer and winter | journal = Applied and Environmental Microbiology | volume = 78 | issue = 7 | pages = 2402–2409 | date = April 2012 | pmid = 22286998 | pmc = 3302604 | doi = 10.1128/AEM.07130-11 | bibcode = 2012ApEnM..78.2402N }}</ref>

In northern latitude waters, the fraction of cells using glucose (fraction of active cells) is higher in summer than winter,<ref name="Nikrad_2012" /> and high abundances may occur after phytoplankton blooms,<ref>{{cite journal | vauthors = Hahnke RL, Bennke CM, Fuchs BM, Mann AJ, Rhiel E, Teeling H, Amann R, Harder J | display-authors = 6 | title = Dilution cultivation of marine heterotrophic bacteria abundant after a spring phytoplankton bloom in the North Sea | journal = Environmental Microbiology | volume = 17 | issue = 10 | pages = 3515–3526 | date = October 2015 | pmid = 24725270 | doi = 10.1111/1462-2920.12479 | bibcode = 2015EnvMi..17.3515H }}</ref><ref>{{cite journal | vauthors = Cordone A, D'Errico G, Magliulo M, Bolinesi F, Selci M, Basili M, de Marco R, Saggiomo M, Rivaro P, Giovannelli D, Mangoni O | display-authors = 6 | title = Bacterioplankton Diversity and Distribution in Relation to Phytoplankton Community Structure in the Ross Sea Surface Waters | journal = Frontiers in Microbiology | volume = 13 | article-number = 722900 | date = 2022-01-27 | pmid = 35154048 | pmc = 8828583 | doi = 10.3389/fmicb.2022.722900 | doi-access = free }}</ref> although a study in southern high-latitude waters found lower abundances of ''Polaribacter'' after an ''in situ'' diatom bloom.<ref>{{cite journal | vauthors = Landa M, Blain S, Harmand J, Monchy S, Rapaport A, Obernosterer I | title = Major changes in the composition of a Southern Ocean bacterial community in response to diatom-derived dissolved organic matter | journal = FEMS Microbiology Ecology | volume = 94 | issue = 4 | date = April 2018 | pmid = 29547927 | doi = 10.1093/femsec/fiy034 | doi-access = free | hdl = 20.500.12210/72379 | hdl-access = free }}</ref>

Within the Arctic Ocean, there is no obvious pattern in the relative abundance between summer and winter.<ref name="Nikrad_2012" /> In the Chukchi Sea, the fraction of cells using leucine is higher in the winter than in summer.<ref name="Nikrad_2012" /> In the Beaufort Sea, the fraction of cells using leucine does not differ between seasons.<ref name="Nikrad_2012" /> In the coastal waters of Fildes Peninsula, ''Polaribacter'' dominated cells in the phylum Bacteriodetes.<ref name="Diversity of bacterioplankton in co">{{cite journal | vauthors = Zeng YX, Yu Y, Qiao ZY, Jin HY, Li HR | title = Diversity of bacterioplankton in coastal seawaters of Fildes Peninsula, King George Island, Antarctica | journal = Archives of Microbiology | volume = 196 | issue = 2 | pages = 137–147 | date = February 2014 | pmid = 24408126 | doi = 10.1007/s00203-013-0950-2 | bibcode = 2014ArMic.196..137Z | s2cid = 15257869 }}</ref>

=== Habitat === [[File:Neopyropia yezoensis.jpg|thumb|''Porphyra yezoensis'': Red macroalgae that inhabit ''Polaribacter''.]] 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.<ref name="Comeau_2011">{{cite journal | vauthors = Comeau AM, Li WK, Tremblay JÉ, Carmack EC, Lovejoy C | title = Arctic Ocean microbial community structure before and after the 2007 record sea ice minimum | journal = PLOS ONE | volume = 6 | issue = 11 | article-number = e27492 | date = 2011-11-09 | pmid = 22096583 | pmc = 3212577 | doi = 10.1371/journal.pone.0027492 | bibcode = 2011PLoSO...627492C | doi-access = free }}</ref> in addition to hypersaline environments, numerous ''Polaribacter'' species inhabit extreme environments ranging from -20 °C to 22 °C.<ref name="Xing_2015">{{cite journal | vauthors = Xing P, Hahnke RL, Unfried F, Markert S, Huang S, Barbeyron T, Harder J, Becher D, Schweder T, Glöckner FO, Amann RI, Teeling H | display-authors = 6 | title = Niches of two polysaccharide-degrading Polaribacter isolates from the North Sea during a spring diatom bloom | journal = The ISME Journal | volume = 9 | issue = 6 | pages = 1410–1422 | date = June 2015 | pmid = 25478683 | pmc = 4438327 | doi = 10.1038/ismej.2014.225 | bibcode = 2015ISMEJ...9.1410X }}</ref> 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.<ref name="Xing_2015" /><ref name="Gosink_1998">{{cite journal |vauthors=Gosink JJ, Woese CR, Staley JT |date=January 1998 |title=Polaribacter gen. nov., with three new species, P. irgensii sp. nov., P. franzmannii sp. nov. and P. filamentus sp. nov., gas vacuolate polar marine bacteria of the Cytophaga-Flavobacterium-Bacteroides group and reclassification of 'Flectobacillus glomeratus' as Polaribacter glomeratus comb. nov |journal=International Journal of Systematic Bacteriology |volume=48 |issue=1 |pages=223–235 |doi=10.1099/00207713-48-1-223 |pmid=9542092|doi-access=free }}</ref> Subsequently, members of the genus ''Polaribacter'' have been shown to be very versatile microorganisms and can survive in oligotrophic and in copiotrophic environments.<ref name="Xing_2015" /> ''Polaribacter'' have also been found in sediments.<ref name="Li_2014">{{cite journal | vauthors = Li H, Zhang XY, Liu C, Lin CY, Xu Z, Chen XL, Zhou BC, Shi M, Zhang YZ | display-authors = 6 | title = Polaribacter huanghezhanensis sp. nov., isolated from Arctic fjord sediment, and emended description of the genus Polaribacter | journal = International Journal of Systematic and Evolutionary Microbiology | volume = 64 | issue = Pt 3 | pages = 973–978 | date = March 2014 | pmid = 24425815 | doi = 10.1099/ijs.0.056788-0 }}</ref> For example, SM1202T, a phylogenetically close strain to ''Polaribacter'' was isolated from marine sediment in Kongsfjorden, Svalbard.<ref name="Li_2014" /> ''Polaribacter'' have also been experimentally isolated from red macroalgae (''Porphyra yezoensis) a''nd green macroalgae (''Ulva fenestrate)''.<ref>{{cite journal | vauthors = Fukui Y, Abe M, Kobayashi M, Saito H, Oikawa H, Yano Y, Satomi M | title = Polaribacter porphyrae sp. nov., isolated from the red alga Porphyra yezoensis, and emended descriptions of the genus Polaribacter and two Polaribacter species | journal = International Journal of Systematic and Evolutionary Microbiology | volume = 63 | issue = Pt 5 | pages = 1665–1672 | date = May 2013 | pmid = 22904227 | doi = 10.1099/ijs.0.041434-0 | bibcode = 2013IJSEM..63.1665F }}</ref><ref>{{cite journal | vauthors = Nedashkovskaya OI, Kukhlevskiy AD, Zhukova NV | title = Polaribacter reichenbachii sp. nov.: a new marine bacterium associated with the green alga Ulva fenestrata | journal = Current Microbiology | volume = 66 | issue = 1 | pages = 16–21 | date = January 2013 | pmid = 23053482 | doi = 10.1007/s00284-012-0200-x | s2cid = 18765393 }}</ref>

== Role in ecosystem == Isolates of related Flavobacteria are able to degrade High-Molecular Weight (HMW) DOM.<ref name="Malmstrom_2007" />{{irrelevant citation|date=May 2022|reason=citation does not refer to degradation of 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.<ref name="Wilkins_2013">{{cite journal |display-authors=6 |vauthors=Wilkins D, Yau S, Williams TJ, Allen MA, Brown MV, DeMaere MZ, Lauro FM, Cavicchioli R |date=May 2013 |title=Key microbial drivers in Antarctic aquatic environments |journal=FEMS Microbiology Reviews |volume=37 |issue=3 |pages=303–335 |doi=10.1111/1574-6976.12007 |pmid=23062173|s2cid=206922820 |hdl=1959.4/unsworks_49940 |hdl-access=free }}</ref> This suggests that they likely remineralize primary production matter within the food web.<ref name="Wilkins_2013" />

=== 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.<ref name="Luria_2016">{{cite journal |vauthors=Luria CM, Amaral-Zettler LA, Ducklow HW, Rich JJ |date=2016 |title=Seasonal Succession of Free-Living Bacterial Communities in Coastal Waters of the Western Antarctic Peninsula |journal=Frontiers in Microbiology |volume=7 |page=1731 |doi=10.3389/fmicb.2016.01731 |pmc=5093341 |pmid=27857708 |doi-access=free |bibcode=2016FrMic...701731L }}</ref>

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.<ref name="Wilkins_2013" /> 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.<ref name="Luria_2016" /><ref>{{cite journal | vauthors = Grzymski JJ, Riesenfeld CS, Williams TJ, Dussaq AM, Ducklow H, Erickson M, Cavicchioli R, Murray AE | display-authors = 6 | title = A metagenomic assessment of winter and summer bacterioplankton from Antarctica Peninsula coastal surface waters | journal = The ISME Journal | volume = 6 | issue = 10 | pages = 1901–1915 | date = October 2012 | pmid = 22534611 | pmc = 3446801 | doi = 10.1038/ismej.2012.31 | bibcode = 2012ISMEJ...6.1901G }}</ref> 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.<ref name="Luria_2016" /> 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''.<ref name="Luria_2016" /> 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.<ref name="Luria_2016" /> 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.<ref name="Luria_2016" />

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.<ref name="Comeau_2011" />

== Metabolism == Members of the genus ''Polaribacter'' are metabolically flexible depending on their physiology, lifestyle and seasonality of the region they inhabit.<ref name="Xing_2015" /> 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.<ref name="González_2008"/> 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.<ref name="Xing_2015" />

thumb|Schematic diagram representing transporters in the membrane of ''Polaribacter'' strain MED152.

In the pelagic water column, some species are well equipped to attach to particles and substrates to search for and degrade polymers.<ref>{{cite journal | vauthors = Gómez-Pereira PR, Schüler M, Fuchs BM, Bennke C, Teeling H, Waldmann J, Richter M, Barbe V, Bataille E, Glöckner FO, Amann R | display-authors = 6 | title = Genomic content of uncultured Bacteroidetes from contrasting oceanic provinces in the North Atlantic Ocean | journal = Environmental Microbiology | volume = 14 | issue = 1 | pages = 52–66 | date = January 2012 | pmid = 21895912 | doi = 10.1111/j.1462-2920.2011.02555.x | bibcode = 2012EnvMi..14...52G }}</ref> They are amongst the first organisms to degrade particulate organic matter and break-down polymers into smaller particles.<ref name="Xing_2015" /> Studies have shown that they will colonize and attach to particles, glide to search for substrates, and degrade them for carbon and nutrients.<ref name="Xing_2015" /> 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.<ref name="Xing_2015" />

=== CAZymes ===

Genetic sequencing found that strains contain numerous genes which encode for CAZymes that are involved in polysaccharide degradation.<ref name="Yoon_2017">{{cite journal | vauthors = Yoon K, Song JY, Kwak MJ, Kwon SK, Kim JF | title = Genome characteristics of the proteorhodopsin-containing marine flavobacterium Polaribacter dokdonensis DSW-5 | journal = Journal of Microbiology | volume = 55 | issue = 7 | pages = 561–567 | date = July 2017 | pmid = 28432541 | doi = 10.1007/s12275-017-6427-2 | s2cid = 8668865 }}</ref> 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.<ref name="Yoon_2017" /> However, the ratio of peptidases to glycoside hydrolase genes varies depending on the environmental conditions the strain is subjected to.<ref name="Xing_2015" /> For example, ''Polaribacter'' sp. MED134 lives in environmental conditions with extended starvation conditions and expresses twice as many peptidases as CAZymes.<ref name="Xing_2015" /> On the other hand, macroalgae-colonizing species that live in stable, eutrophic environments may express greater proportions of CAZymes than peptidases.<ref name="Xing_2015" />

=== Proteorhodopsin ===

"Free-living" species have the proteorhodopsin gene, which allows them to complete inorganic-carbon fixation using light as an energy source.<ref name="González_2008">{{cite journal | vauthors = González JM, Fernández-Gómez B, Fernàndez-Guerra A, Gómez-Consarnau L, Sánchez O, Coll-Lladó M, Del Campo J, Escudero L, Rodríguez-Martínez R, Alonso-Sáez L, Latasa M, Paulsen I, Nedashkovskaya O, Lekunberri I, Pinhassi J, Pedrós-Alió C | display-authors = 6 | title = Genome analysis of the proteorhodopsin-containing marine bacterium Polaribacter sp. MED152 (Flavobacteria) | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 105 | issue = 25 | pages = 8724–8729 | date = June 2008 | pmid = 18552178 | pmc = 2438413 | doi = 10.1073/pnas.0712027105 | doi-access = free }}</ref> By utilizing their proteorhodopsin to use light energy, ''Polaribacter'' can grow in oligotrophic environmental conditions.<ref name="González_2008" /><ref name="Xing_2015" />

== 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%.<ref name="Zhang_2022">{{cite journal | vauthors = Zhang Q, Fu L, Gui Y, Miao J, Li J | title = Complete genome sequence of Polaribacter sejongensis NJDZ03 exhibiting diverse macroalgal polysaccharide-degrading activity | journal = Marine Genomics | volume = 61 | article-number = 100913 | date = February 2022 | pmid = 35058032 | doi = 10.1016/j.margen.2021.100913 | s2cid = 240140283 | doi-access = free | bibcode = 2022MarGn..6100913Z }}</ref><ref name="Kim_2017">{{cite journal | vauthors = Kim E, Shin SK, Choi S, Yi H | title = Polaribacter vadi sp. nov., isolated from a marine gastropod | journal = International Journal of Systematic and Evolutionary Microbiology | volume = 67 | issue = 1 | pages = 144–147 | date = January 2017 | pmid = 27902220 | doi = 10.1099/ijsem.0.001591 | doi-access = free }}</ref> Some notable features of the genome include genes for agar, alginate, and carrageenan degrading enzymes in ''Polaribacter'' species which colonize the surface of macroalgae.<ref name="Zhang_2022" /> Agar degrading enzymes have also been found in strains of ''Polaribacter'' that colonize the gut of the comb pen shell.<ref name="Zhang_2022" /><ref name="Hyun_2014">{{cite journal | vauthors = Hyun DW, Shin NR, Kim MS, Kim PS, Jung MJ, Kim JY, Whon TW, Bae JW | display-authors = 6 | title = Polaribacter atrinae sp. nov., isolated from the intestine of a comb pen shell, Atrina pectinata | journal = International Journal of Systematic and Evolutionary Microbiology | volume = 64 | issue = Pt 5 | pages = 1654–1661 | date = May 2014 | pmid = 24510977 | doi = 10.1099/ijs.0.060889-0 | doi-access = free }}</ref> 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.<ref name="González_2008" /> Some members of the genus encode proteorhodopsin, which has been implicated in supporting their central metabolism through photophosphorylation.<ref name="González_2008" />

=== 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.<ref name="Kim_2017" /> 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''.<ref name="Hyun_2014" /><ref name="Kim_2017" /> New species can be identified through DNA hybridization or through the sequencing and comparison of a common gene such as 16S rRNA.<ref name="Kim_2017" /> 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.<ref name="Kim_2017" />

=== Life strategies of ''Polaribacter'' based on genome analysis === Genomic analysis has allowed scientists to examine the relationships between different species of ''Polaribacter''. However, by combining genomic analysis with 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.<ref name="Hyun_2014" /><ref name="González_2008" /> A genomic analysis of the ''Polaribacter'' strain MED152, found a considerable amount of genes that allow for surface or particle attachment, gliding motility and polymer degradation.<ref name="González_2008" /> 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.<ref name="González_2008" /> However the researchers also noticed that the organism had a proteorhodopsin gene as well as other genes which could be used to sense light and found that under light the species increased carbon dioxide fixation.<ref name="González_2008" /> 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, another life strategy where, if the strain was in a well lit, low nutrient area of the ocean, it would use carbon fixation to synthesize intermediates of metabolic pathways.<ref name="González_2008" />

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.<ref name="Xing_2015" /> Hel1_85 on the other hand, has a genome which contains twice as many polysaccharide utilization loci, a mannitol dehydrogenase and no proteorhodopsin, pointing to a lifestyle with lower oxygen availability such as a biofilm.<ref name="Xing_2015" />

==== Species ==== {| class="wikitable" !Name !Type strain<ref name=":0">{{Cite journal |title=Polaribacter |year=2013 |language=en |doi=10.1601/nm.8177|last1=Parker |first1=Charles Thomas |last2=Garrity |first2=George M. |editor1-first=Charles Thomas |editor1-last=Parker |editor2-first=George M |editor2-last=Garrity }}</ref><ref name="NamesforLife" /> !DNA G+C content (mol%)<ref name=":0" /> !Description<ref name=":0" /> |- |''P. aestuariivivens'' |JDTF-33, KCTC 52838, NBRC 112782<ref name="Park_2017">{{cite journal | vauthors = Park S, Choi SJ, Choi J, Yoon JH | title = Paraglaciecola aestuariivivens sp. nov., isolated from a tidal flat | journal = International Journal of Systematic and Evolutionary Microbiology | volume = 67 | issue = 11 | pages = 4754–4759 | date = November 2017 | pmid = 28984552 | doi = 10.1099/ijsem.0.002370 | doi-access = free }}</ref> |41.7<ref name="Park_2017" /> |Ovoid, coccoid or rod-shaped. Form smooth, glistening, circular, and yellowish-white colonies.<ref name="Park_2017" /> |- |''P. aquimarinus'' |ZY113, KCTC 62374, MCCC 1H00296<ref name="Xu_2020">{{cite journal | vauthors = Xu W, Chen XY, Wei XT, Lu DC, Du ZJ | title = Polaribacter aquimarinus sp. nov., isolated from the surface of a marine red alga | journal = Antonie van Leeuwenhoek | volume = 113 | issue = 3 | pages = 407–415 | date = March 2020 | pmid = 31628626 | doi = 10.1007/s10482-019-01350-z | s2cid = 204757649 }}</ref> |30.1<ref name="Xu_2020" /> |Rod-shaped. Form smooth, circular, and orange colonies<ref name="Xu_2020" /> |- |''P. atrinae'' |WP2, KACC 17473, JCM 19202 |30.4 |Rod-shaped, aerobic and non-motile. Form circular, convex, yellow-orange colonies.<ref name="Hyun_2014" /> |- |''P. butkevichii'' |KMM 3938, KCTC 12100, CCUG 48005 |32.4 |Rod-shaped, mesophillic cells. |- |''P. dokdonensis'' |DSW-5, DSM 17204, KCTC 12392 |30.0 |Straight or curved rod-shaped. Form smooth, convex, orange colonies. |- |''P. filamentus'' |215, ATCC 700397, CIP 106479 |32.0 |Filamentous or rod-shaped. Form gas vesicles. Form orange, flat-convex colonies. |- |''P. franzmannii'' |301, ATCC 700399, CIP 106480. |32.5 |Filamentous or rod-shaped. Psychrophilic or psychrotolerant. Form gas vesicles. |- |''P. gangjinensis'' |K17-16, JCM 16152, KCTC 22729 |34.6 |Gliding motility. Mesophillic. Form smooth, convex, and circular colonies. |- |''P. glomeratus'' |ATCC 43844, CIP 103112, LMG 13858 |33.0 |Curved or coiled. Psychrophilic or psychrotolerant. |- |''P. haliotis'' |RA4-7, KCTC 52418, NBRC 112383 |29.9 |Ovoid or rod-shaped. Form smooth, glistening, convex, and light yellow colonies. |- |''P. huanghezhanensis'' |SM1202, CCTCC AB 2013148, KCTC 32516 |36.4 |Rod-shaped. Form glistening, circular, and orange colonies. |- |''P. insulae'' |OITF-22, KCTC 52658, NBRC 112706 |32.3 |Ovoid or rod-shaped. Form smooth, glistening, circular, and light orange-yellow colonies. |- |''P. irgensii'' |23-P, ATCC 700398, CIP 106478 |34.5 |Filamentous or rod-shaped. Form gas vesicles. Psychrophilic or psychrotolerant. Form translucent, circular, and orange colonies. |- |''P. lacunae'' |HMF2268, KCTC 42191, CECT 8862 |34.3 |Rod-shaped. Form smooth, circular, and yellow colonies. |- |''P. litorisediminis'' |OITF-11, KCTC 52500, NBRC 112457 |32.2 |Filamentous, ovoid, or rod-shaped. Form smooth, glistening, circular, and light orange-yellow colonies. |- |''P. marinaquae'' |RZW3-2, JCM 30825, KCTC 42664, MCCC1K00696 |30.5 |Rod-shaped. Form circular, convex, and yellow colonies. |- |''P. marinivivus'' |GYSW-15, CECT 8655, KCTC 42156 |31.2 |Rod-shaped. Form smooth, glistening, circular, and yellow colonies. |- |''P. pacificus'' |HRA130-1, KCTC 52370, MCCC 1K03199, JCM31460, CGMCC 1.15763 |35.9 |Rod-shaped. Form circular, nontransparent, and yellow colonies. |- |''P. porphyrae'' |LNM-20, LMG 26671, NBRC 108759 |28.6 |Rod-shaped with pointy ends. Lack gas vesicles and polar flagella. Form circular, convex, and pale yellow colonies. |- |''P. reichenbachii'' |6Alg 8, KCTC 23969, LMG 26443 |29.1–29.5 |Rod-shaped. Form shiny, circular, and yellow colonies. |- |''P. sejongensis'' |KOPRI 21160, KCTC 23670, JCM 18092 |29.8 |Rod-shaped. Form circular, convex, and light yellow colonies. |- |''P. septentrionalilitoris''<ref name="Choo_2020">{{cite journal | vauthors = Choo S, Borchert E, Wiese J, Saha M, Künzel S, Weinberger F, Hentschel U | title = ''Polaribacter septentrionalilitoris'' sp. nov., isolated from the biofilm of a stone from the North Sea | journal = International Journal of Systematic and Evolutionary Microbiology | volume = 70 | issue = 7 | pages = 4305–4314 | date = July 2020 | pmid = 32579104 | doi = 10.1099/ijsem.0.004290 | s2cid = 220049277 | doi-access = free }}</ref> |ANORD1, DSM 110039, NCIMB 15081, MTCC 12685<ref name="Choo_2020" /> |30.6<ref name="Choo_2020" /> |Cocci or rod-shaped. Form translucent, circular, and bright yellow colonies.<ref name="Choo_2020" /> |- |''P. staleyi'' |10Alg 139, KCTC 5277, KMM 6729 |31.8 |Rod-shaped. Form shiny, circular, and yellow colonies. |- |''P. tangerinus'' |S2-14, KCTC 52275, MCCC 1H00163 |31.2 |Ovoid or rod-shaped. Form smooth, circular, and orange colonies. |- |''P. undariae'' |W-BA7, KCTC 42175, CECT 8670 |31.9 |Ovoid or rod-shapted. Form smooth, glistening, circular, and pale yellow colonies. |- |''P. vadi'' |LPB0003, KACC 18704, JCM 31217 |29.6 |Curved and rod-shaped. Form circular, convex, and yellow colonies.<ref name="Kim_2017" /> |}

== Viral pathogens == thumb|Phylogenetic tree of different viruses infecting Flavobacteriia. [[File:Viruses_found_infecting_Polaribacter_spp.webp|thumb|Siphoviruses of class ''Caudoviricetes'' infecting ''Polaribacter'' strains: species ''Incheonvirus P12002L'' (Polaribacter phage P12002L, '''a''') and species ''Incheonvirus P12002S'' (Polaribacter phage P12002S, '''b'''). Capsids are round and dark, tails can be seen extending out from the capsids.]] Only two species of lytic phage are known to infect members of this genus, and both have double stranded DNA with virions that include isometric heads and non-contractile tails (class ''Caudoviricetes'', morphotype: siphoviruses).<ref>{{cite journal | vauthors = Kang I, Jang H, Cho JC | title = Complete genome sequences of bacteriophages P12002L and P12002S, two lytic phages that infect a marine Polaribacter strain | journal = Standards in Genomic Sciences | volume = 10 | issue = 1 | article-number = 82 | date = December 2015 | pmid = 26500718 | pmc = 4615864 | doi = 10.1186/s40793-015-0076-z | doi-access = free | bibcode = 2015SGenS..10...82K }}</ref> Viral lysis has been implicated as a major driver of changes in genus-level composition of microbial communities.<ref>{{Cite journal | vauthors = Bartlau N, Wichels A, Krohne G, Adriaenssens EM, Heins A, Fuchs BM, Amann R, Moraru C |title=Highly diverse flavobacterial phages isolated from North Sea spring blooms |journal=The ISME Journal |date=2022 |volume=16 |issue=2 |pages=555–568 |doi=10.1038/s41396-021-01097-4 |language=en |biorxiv=10.1101/2021.05.20.444936|pmc=8776804 }}</ref>

== 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.<ref>{{cite journal | vauthors = Urbanek AK, Rymowicz W, Mirończuk AM | title = Degradation of plastics and plastic-degrading bacteria in cold marine habitats | journal = Applied Microbiology and Biotechnology | volume = 102 | issue = 18 | pages = 7669–7678 | date = September 2018 | pmid = 29992436 | pmc = 6132502 | doi = 10.1007/s00253-018-9195-y }}</ref>

=== 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.<ref name="Annapure_2022">{{cite book | vauthors = Annapure US, Pratisha N | chapter = Chapter 14 - Psychrozymes: A novel and promising resource for industrial applications |date= January 2022 | chapter-url = https://www.sciencedirect.com/science/article/pii/B978012822945300018X | title = Microbial Extremozymes |pages=185–195 | veditors = Kuddus M |publisher=Academic Press | doi = 10.1016/B978-0-12-822945-3.00018-X |language=en |isbn=978-0-12-822945-3 |access-date=2022-04-08}}</ref><ref name="Feller_2003">{{cite journal | vauthors = Feller G, Gerday C | title = Psychrophilic enzymes: hot topics in cold adaptation | journal = Nature Reviews. Microbiology | volume = 1 | issue = 3 | pages = 200–208 | date = December 2003 | pmid = 15035024 | doi = 10.1038/nrmicro773 | s2cid = 6441046 }}</ref> This is due to the highly malleable nature of these enzymes as this allows for better substrate - active site binding at colder temperatures.<ref name="Annapure_2022" /> 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.<ref name="Annapure_2022" /><ref name="Feller_2003" /> 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.<ref name="Annapure_2022" /> Another unique application for these enzymes is the ability to be inhibited without the need of external reagents.<ref name="Annapure_2022" /> 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.<ref name="Annapure_2022" />

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.<ref name="Gui_2021">{{cite journal | vauthors = Gui Y, Gu X, Fu L, Zhang Q, Zhang P, Li J | title = Expression and Characterization of a Thermostable Carrageenase From an Antarctic ''Polaribacter'' sp. NJDZ03 Strain | journal = Frontiers in Microbiology | volume = 12 | article-number = 631039 | date = 2021 | pmid = 33776960 | pmc = 7994522 | doi = 10.3389/fmicb.2021.631039 | doi-access = free }}</ref> 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.<ref name="Gui_2021" />

=== Exopolysaccharide ===

EPS is a secreted exopolysaccharide which protects the cells, stabilizes membranes, and serve and carbon stores.<ref name="Sun_2020">{{cite journal | vauthors = Sun ML, Zhao F, Chen XL, Zhang XY, Zhang YZ, Song XY, Sun CY, Yang J | display-authors = 6 | title = Promotion of Wound Healing and Prevention of Frostbite Injury in Rat Skin by Exopolysaccharide from the Arctic Marine Bacterium ''Polaribacter'' sp. SM1127 | journal = Marine Drugs | volume = 18 | issue = 1 | page = 48 | date = January 2020 | pmid = 31940773 | doi = 10.3390/md18010048 | pmc = 7024241 | doi-access = free }}</ref> Most EPS is similar but it is found that in extremophiles, the composition may be distinct.<ref name="Sun_2020" /> Specifically in Polaribacter sp. SM1127, where the EPS has antioxidant activity and has shown to protect human fibroblast cells at lower temperatures.<ref name="Sun_2020" /> Studies by Sun et al. were done to determine whether this can be utilized to protect and repair damage caused by frostbite.<ref name="Sun_2020" /> 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/<ref name="Sun_2020" />

== References == {{Reflist}}

== Further reading == {{refbegin|30em}} * {{cite journal | vauthors = Hyun DW, Shin NR, Kim MS, Kim PS, Jung MJ, Kim JY, Whon TW, Bae JW | display-authors = 6 | title = Polaribacter atrinae sp. nov., isolated from the intestine of a comb pen shell, Atrina pectinata | journal = International Journal of Systematic and Evolutionary Microbiology | volume = 64 | issue = Pt 5 | pages = 1654–1661 | date = May 2014 | pmid = 24510977 | doi = 10.1099/ijs.0.060889-0 | doi-access = free }} * {{cite journal | vauthors = Nedashkovskaya OI, Kim SB, Lysenko AM, Kalinovskaya NI, Mikhailov VV, Kim IS, Bae KS | title = Polaribacter butkevichii sp. nov., a novel marine mesophilic bacterium of the family Flavobacteriaceae | journal = Current Microbiology | volume = 51 | issue = 6 | pages = 408–412 | date = December 2005 | pmid = 16235024 | doi = 10.1007/s00284-005-0105-z | s2cid = 27074806 }} * {{cite journal | vauthors = Gosink JJ, Woese CR, Staley JT | title = Polaribacter gen. nov., with three new species, P. irgensii sp. nov., P. franzmannii sp. nov. and P. filamentus sp. nov., gas vacuolate polar marine bacteria of the Cytophaga-Flavobacterium-Bacteroides group and reclassification of 'Flectobacillus glomeratus' as Polaribacter glomeratus comb. nov | journal = International Journal of Systematic Bacteriology | volume = 48 | issue = 1 | pages = 223–235 | date = January 1998 | pmid = 9542092 | doi = 10.1099/00207713-48-1-223 | doi-access = free }} * {{cite journal | vauthors = Kim E, Shin SK, Choi S, Yi H | title = Polaribacter vadi sp. nov., isolated from a marine gastropod | journal = International Journal of Systematic and Evolutionary Microbiology | volume = 67 | issue = 1 | pages = 144–147 | date = January 2017 | pmid = 27902220 | doi = 10.1099/ijsem.0.001591 | doi-access = free }} * {{cite journal | vauthors = Xu W, Chen XY, Wei XT, Lu DC, Du ZJ | title = Polaribacter aquimarinus sp. nov., isolated from the surface of a marine red alga | journal = Antonie van Leeuwenhoek | volume = 113 | issue = 3 | pages = 407–415 | date = March 2020 | pmid = 31628626 | doi = 10.1007/s10482-019-01350-z | s2cid = 204757649 }} * {{cite journal | vauthors = Kim YO, Park IS, Park S, Nam BH, Park JM, Kim DG, Yoon JH | title = Polaribacter haliotis sp. nov., isolated from the gut of abalone Haliotis discus hannai | journal = International Journal of Systematic and Evolutionary Microbiology | volume = 66 | issue = 12 | pages = 5562–5567 | date = December 2016 | pmid = 27902190 | doi = 10.1099/ijsem.0.001557 | doi-access = free }} {{refend}}

Category:Flavobacteria Category:Bacteria genera Category:Psychrophiles Category:Marine microorganisms