Roseobacter

Roseobacter is 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. They make up around 25% of marine communities. During algal blooms, 20-30% of the prokaryotic community are Roseobacter.{{cite book | title = Bioprospecting | last1 = Bentzon-Tilia | first1 = Mikkel | last2 = Gram | first2 = Lone | chapter = Biotechnological Applications of the Roseobacter Clade |author-link2=Lone Gram| name-list-style = vanc | date = 2017 | publisher = Springer, Cham | isbn = 978-3-319-47933-0 | series = Topics in Biodiversity and Conservation | volume = 16 | pages = 137–166 | doi = 10.1007/978-3-319-47935-4_7 }}

Members of Roseobacter clade display diverse physiologies, and are commonly found to be either free living, particle associated, or in commensal relationships with marine phytoplankton, invertebrates, and vertebrates.{{cite journal | vauthors = Buchan A, González JM, Moran MA | title = Overview of the marine roseobacter lineage | journal = Applied and Environmental Microbiology | volume = 71 | issue = 10 | pages = 5665–77 | date = October 2005 | pmid = 16204474 | doi = 10.1128/AEM.71.10.5665-5677.2005 | pmc = 1265941 | bibcode = 2005ApEnM..71.5665B }} Roseobacter are similar to phytoplankton in that both of them colonize surfaces, scavenge iron and produce bioactive secondary metabolites.

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Most of the Roseobacters analyzed so far have large genomes: ranging from 3.5Mbp to 5.0Mbp. The smallest found is the genome of Loktanella vestfoldensis SKA53 with 3.06 Mbp, the largest that of Roseovarius sp. HTCC2601 with 5.4 Mbp. In Jannaschia sp. CCS1, Silicibacter pomeroyi DSS-3, and Silicibacter sp. TM1040, the fraction of non-orthologous genes form 1/3 of the genomes.{{Cite journal|last1=Brinkhoff|first1=Thorsten|last2=Giebel|first2=Helge-Ansgar|last3=Simon|first3=Meinhard|date=2008-06-01|title=Diversity, ecology, and genomics of the Roseobacter clade: a short overview|url=https://doi.org/10.1007/s00203-008-0353-y|journal=Archives of Microbiology|language=en|volume=189|issue=6|pages=531–539|doi=10.1007/s00203-008-0353-y|pmid=18253713|s2cid=206894192|issn=1432-072X|url-access=subscription}}

{{Unreferenced section|date=January 2021}}

Plasmids are common to be seen in Roseobacters. The size of plasmids range from 4.3 to 821.7 Kb. They can make up 20% of the genome content. Ecologically relevant genes can be found encoded on plasmids. Genome plasticity could be a reason to explain the diversity and adaptability of Roseobacters, which is supported by the high number of probably conjugative plasmids.

Linear conformation can be exhibited by plasmids, which is common for Roseobacters. In some strains, plasmid borne take place in a large proportion in genome content. Even though the mobility of plasmid has not yet been examined in the strains, they might contribute to the physiological diversity of Roseobacter.

Comparison and analyzation of genomes of Roseobacter clade organisms is important because it can give insight into horizontal gene transfer and specific adaptation processes. As the Roseobacter population is widely distributed worldwide with distinct types of habitats, the success of Roseobacter clade can not be explained by only investigating one single population. Hence, the key to understand why this clade is so abundant is to study the genetic as well as the metabolic diversity of organisms of the whole clade.{{cite journal | vauthors = Brinkhoff T, Giebel HA, Simon M | title = Diversity, ecology, and genomics of the Roseobacter clade: a short overview | journal = Archives of Microbiology | volume = 189 | issue = 6 | pages = 531–9 | date = June 2008 | pmid = 18253713 | doi = 10.1007/s00203-008-0353-y | s2cid = 206894192 }}

The Roseobacter clade is mostly found in the marine environment. The various species of Roseobacter each have their own ecological niche. Several isolates have been captured from a vast number of ecosystems in coastal areas and open oceans. Roseobacters are a significant part of bacterial communities connected to phytoplankton, macroalgae, and several marine animals. Different lifestyles such as mutualistic and pathogenic have been proposed. Members of the clade are spread all over temperate and polar oceans, and are also considerable in sea ice ecosystems. They are suggested to be extensive within coastal sediments, deep pelagic ocean, and deep sea sediments. The Roseobacter clade has immense diversity of metabolic proficiency and regulatory circuits, which can be credited to their prosperity in a vast number of marine ecosystems.{{cite journal | vauthors = Luo H, Moran MA | title = Evolutionary ecology of the marine Roseobacter clade | journal = Microbiology and Molecular Biology Reviews | volume = 78 | issue = 4 | pages = 573–87 | date = December 2014 | pmid = 25428935 | pmc = 4248658 | doi = 10.1128/MMBR.00020-14 }}

The Roseobacter clade can be found in coastal areas living freely in bulk seawater or in coastal sediments. In these coastal ecosystems, the Roseobacter clade interact with phytoplankton, macro algae and various marine animals living both mutualistic and pathogenic life styles. The Rosebacter clade can also be found in the deep pelagic ocean, deep-sea sediments and even the polar ocean. The reason why they are abundant in various marine habitats is because they have diverse metabolic capabilities and regulatory circuits.

It is predicted that the Roseobacter ancestor dates back to around 260 million years ago. They underwent a net genome reduction from a large common ancestral genome followed by two episodes of genome innovation and expansion through lateral gene transfer (LGT).

The first predicted episode of genome expansion was predicted to be around 250 million years ago. It was suggested that the genome expansion was most likely due to new ecological habitats provided by the rise of eukaryotic phytoplankton groups like the dinoflagellates and coccolithophorids. This theory is backed up by the fact that modern lineages of Roseobacters are abundant components of the phycosphere of these two phytoplankton groups. Genes related to mobility and chemotaxis in the ancestor of the Roseobacter clade would have potentially allowed Roseobacter to sense and swim towards these phytoplankton. Later on it was found that some lineages of Roseobacter are also associated with diatoms. All dinoflagellates, coccolithophorids and diatoms are red-plastid-lineage phytoplankton, and the coincidence of the red-plastid radiation and Roseobacter genome innovation is consistent with adaptive evolution. However the mechanism of the genome change is still not identified. Two theories are proposed: that the genome change is either dominated by exaptation where the change occurred prior to the environmental change or positive selection where environmental change is followed by the lateral gene transfer event, which were then selectively favoured.

The second genome innovation is believed to be more recent. It is predicted that the basal lineage with reduced genomes escaped both episodes of genome innovations and become streamlined directly from the common ancestor. Therefore, not all Roseobacter are descendants of the lineages that underwent genome innovation. It is suggested that gene gains appears in favour of genes such as transcriptional genes, repair genes and defence mechanism genes to help Roseobacter to compete with concurring microbial populations on particles and living surfaces in the marine environment.

De novo assembly from deeply sequenced metagenomes and single-cell genome sequencing are the two best ways for studying uncultivated Roseobacters without producing an unacceptable level of false positive results. It is found that genomic analyses focusing on cultured Roseobacters can potentially bias our view of the lineage's ecology. A recent study obtained four uncultivated roseobacters from surface waters of the North Pacific, South Atlantic, and Gulf of Maine. This clade appears to represent up to 35% of the Roseobacter sequences in samples from surface ocean waters. These Roseobacters have low G+C content, a reduced percentage of noncoding DNA and are predicted to have streamlined genomes.

The Roseobacter clade displays success in multiple marine habitats because of their expansive metabolic capabilities. There is enormous genomic and physiological diversity throughout the major clades, which refer to different size, gene content, GC content, ecological strategy, and trophic strategy. The diversity makes an impact in ecology because of the roles that bacterial lineages play in oceanic elemental cycles, and their connections with marine eukaryotes. The Roseobacter clade represents up to 20% of bacterial cells in certain coastal areas and 3 to 5% in open ocean surface waters.{{cite journal | vauthors = Moran MA, Belas R, Schell MA, González JM, Sun F, Sun S, Binder BJ, Edmonds J, Ye W, Orcutt B, Howard EC, Meile C, Palefsky W, Goesmann A, Ren Q, Paulsen I, Ulrich LE, Thompson LS, Saunders E, Buchan A | title = Ecological genomics of marine Roseobacters | journal = Applied and Environmental Microbiology | volume = 73 | issue = 14 | pages = 4559–69 | date = July 2007 | pmid = 17526795 | pmc = 1932822 | doi = 10.1128/AEM.02580-06 | bibcode = 2007ApEnM..73.4559M }}

Largely expanding amounts of genus and species characterizations in the clade shows the physiological and genetic diversity of these organisms. The designations of new strains solely based on the 16s rRNA gene sequences causes increasing difficulty. Some species are considered to be incorporated in one genus, but others argue that the different characteristics should cause the two species to be kept separate. Several bunches of clones and undefined strains have been determined within the Roseobacter clade. This clade is notable for potential genome correlations of closely related strains.

Members of the Roseobacter clade play an important role in the ecosystem.

Roseobacters are essential in the global carbon and sulfur cycles as well as the climate. Because of its large proportion in the total microbial community, the Roseobacter clade are major contributors to global {{CO2}} fixation. Previous studies indicate that within the Roseobacter clade, some members belong to a group named Aerobic Anoxygenic Phototrophs (AAPs), while other members are non-phototrophic. AAPs is the only known organisms that requires oxygen for photosynthesis, but does not produce it. Non-phototrophic members can be used for CO oxidation, while AAPs can conduct {{CO2}} fixation as Roseobacters can generate energy through aerobic anoxygenic photosynthesis.{{cite journal | last1 = Moran | first1 = Mary Ann | last2 = González | first2 = José M. | last3 = Kiene | first3 = Ronald P. | name-list-style = vanc | title = Linking a Bacterial Taxon to Sulfur Cycling in the Sea: Studies of the Marine Roseobacter Group | journal = Geomicrobiology Journal | date = July 2003 | volume = 20 | issue = 4 | pages = 375–388 | doi = 10.1080/01490450303901 | s2cid = 85208716 }} Roseobacter has the ability to degrade dimethylsulfoniopropionate (DMSP), an organic sulfur compound produced in abundance by marine algae. Through the degradation of algal osmolytes, they can also produce the climate-relevant gas dimethyl sulfide (DMS).{{cite journal | vauthors = Wagner-Döbler I, Biebl H | title = Environmental biology of the marine Roseobacter lineage | journal = Annual Review of Microbiology | volume = 60 | pages = 255–80 | date = 2006 | pmid = 16719716 | doi = 10.1146/annurev.micro.60.080805.142115 | hdl = 10033/15373 | hdl-access = free }}

Roseobacter can degrade aromatic compounds, and are capable of using aromatic compounds as primary growth substrates. Previous research found that Roseobacter degrade lignin-related compounds in a same way. In Roseobacter isolates, the presence of ring cleavage dioxygenases and associated genes of the β-ketoadipate pathway can be important for comparative studies on the ecology of aromatic compound degradation{{cite journal | vauthors = Buchan A, Collier LS, Neidle EL, Moran MA | title = Key aromatic-ring-cleaving enzyme, protocatechuate 3,4-dioxygenase, in the ecologically important marine Roseobacter lineage | journal = Applied and Environmental Microbiology | volume = 66 | issue = 11 | pages = 4662–72 | date = November 2000 | pmid = 11055908 | pmc = 92364 | doi = 10.1128/AEM.66.11.4662-4672.2000 | bibcode = 2000ApEnM..66.4662B }}

Roseobacter clade uptakes trace metal. Generally, larger Roseobacter genomes have greater trace metal uptake versatility and greater plasticity, which might lead to phylogenetically similar genomes having greatly differed capabilities.{{cite journal | vauthors = Hogle SL, Thrash JC, Dupont CL, Barbeau KA | title = Trace Metal Acquisition by Marine Heterotrophic Bacterioplankton with Contrasting Trophic Strategies | journal = Applied and Environmental Microbiology | volume = 82 | issue = 5 | pages = 1613–24 | date = January 2016 | pmid = 26729720 | doi = 10.1128/AEM.03128-15 | pmc = 4771312 | bibcode = 2016ApEnM..82.1613H }} The acquisition of both organically complexed and inorganic metals of Roseobacter strains can go through multiple diverse pathways, which indicates that roseobacters are able to adapt to and occupy a range of trace metal niches in the marine environment. It also means that the availability of trace metal resources may influence Roseobacter genome diversification. For some members of the Roseobacter clade, trace metal streamlining is also a valuable ecological strategy.

The Roseobacter clade can establish symbiotic and pathogenic relationships.{{cite journal | vauthors = Piekarski T, Buchholz I, Drepper T, Schobert M, Wagner-Doebler I, Tielen P, Jahn D | title = Genetic tools for the investigation of Roseobacter clade bacteria | journal = BMC Microbiology | volume = 9 | pages = 265 | date = December 2009 | pmid = 20021642 | pmc = 2811117 | doi = 10.1186/1471-2180-9-265 | doi-access = free }} Roseobacter strains can form symbiotic relationships with varies eukaryotic marine organisms. Roseobacter phylotypes has been identified in the species of the marine red alga Prionitis.{{cite journal | vauthors = Ashen JB, Goff LJ | title = Molecular and ecological evidence for species specificity and coevolution in a group of marine algal-bacterial symbioses | journal = Applied and Environmental Microbiology | volume = 66 | issue = 7 | pages = 3024–30 | date = July 2000 | pmid = 10877801 | doi = 10.1128/AEM.66.7.3024-3030.2000 | pmc = 92106 | bibcode = 2000ApEnM..66.3024A }} In addition, Roseobacters can develop close relationship with Pfiesteria, where they are found to be within or attached to these dinoflagellates.{{cite journal | last1 = Alavi | first1 = Mohammad | last2 = Miller | first2 = Todd | last3 = Erlandson | first3 = Karn | last4 = Schneider | first4 = Rachel | last5 = Belas | first5 = Robert | name-list-style = vanc |date=2001-06-01|title=Bacterial community associated with Pfiesteria-like dinoflagellate cultures |journal=Environmental Microbiology|language=en|volume=3|issue=6|pages=380–396|doi=10.1046/j.1462-2920.2001.00207.x | pmid = 11472503 }}

Pathogenic relationships, even though little studied and much less common than symbiotic relationships, have also been found in Roseobacter strains. For example, Roseobacter clade members and phylotypes have been indicated to be one of the causes of juvenile oyster disease in the Eastern oyster as well as of black band disease in scleractinian corals.

The Roseobacter clade can produce varies types of bioactive compounds. These compounds including algal growth promoters (i.e. auxins) and algaecidal compounds (i.e. the Roseobactides).{{Cite book |title=Bioprospecting |last1=Bentzon-Tilia|first1=Mikkel|last2=Gram|first2=Lone |chapter=Biotechnological Applications of the Roseobacter Clade | name-list-style = vanc |date=2017|publisher=Springer, Cham | isbn = 978-3-319-47933-0 |series=Topics in Biodiversity and Conservation|volume=16 |pages=137–166 | doi=10.1007/978-3-319-47935-4_7 }} There are also antimicrobial compounds, toxins, and algaecidal compounds. These compounds have the potential to be used for pharmaceutical or other industrial applications. In addition, with the genome mining of the Roseobacter, it was believed that Roseobacter are also capable of producing other compounds, which could be used as the source of novel bioactive compounds (e.g. novel antibiotics).

While juvenile and adult fish have a mature immune system and can be vaccinated, the larvae of marine fish and invertebrates are prone to bacterial infections. Marine bacteria from the Roseobacter clade (alpha-proteobacteria) have shown potential as probiotic bacteria to provide an alternative to the use of antibiotics for preventing bacterial diseases.{{cite book | url = http://orbit.dtu.dk/en/publications/aquaculture-application-and-ecophysiology-of-marine-bacteria-from-the-roseobacter-clade(f6886506-1923-47d6-a792-3fdffc2ee6a2)/export.html | title = Aquaculture application and ecophysiology of marine bacteria from the Roseobacter clade|last=D'Alvise|first=Paul | name-list-style = vanc |date=2013|publisher=DTU Food| isbn = 9788792763723}} Not only can Roseobactor be used among fish and invertebrate larvae, they can also be used to antagonize fish-pathogenic bacteria without harming the fish or their live feed.{{cite journal | vauthors = Sonnenschein EC, Nielsen KF, D'Alvise P, Porsby CH, Melchiorsen J, Heilmann J, Kalatzis PG, López-Pérez M, Bunk B, Spröer C, Middelboe M, Gram L | title = Global occurrence and heterogeneity of the Roseobacter-clade species Ruegeria mobilis | language = En | journal = The ISME Journal | volume = 11 | issue = 2 | pages = 569–583 | date = February 2017 | pmid = 27552638 | pmc = 5270555 | doi = 10.1038/ismej.2016.111 }} Since Roseobacter has such high abundances, accounting for 15 to 20% of oceanic bacterio-plankton communities, they can be used for establishment of synthetic biology chassis for bio-geoengineering activities such as bioremediation of oceanic waste plastic.{{cite journal | vauthors = Borg Y, Grigonyte AM, Boeing P, Wolfenden B, Smith P, Beaufoy W, Rose S, Ratisai T, Zaikin A, Nesbeth DN | title = Open source approaches to establishing Roseobacter clade bacteria as synthetic biology chassis for biogeoengineering | journal = PeerJ | volume = 4 | pages = e2031 | date = 2016-07-07 | pmid = 27441104 | pmc = 4941783 | doi = 10.7717/peerj.2031 | doi-access = free }}

Most bacteria have chemical communication systems. Quorum sensing (QS) is a process by which bacteria sense and perceive their own population density through diffusible signals. In the members of the Roseobacter clade, Acyl-homoserine lactone (AHL)-based quorum sensing is widespread: over 80% of available Roseobacterial genomes encode at least one luxI homologue.{{cite journal | vauthors = Zan J, Liu Y, Fuqua C, Hill RT | title = Acyl-homoserine lactone quorum sensing in the Roseobacter clade | journal = International Journal of Molecular Sciences | volume = 15 | issue = 1 | pages = 654–69 | date = January 2014 | pmid = 24402124 | pmc = 3907830 | doi = 10.3390/ijms15010654 | doi-access = free }} This shows the significant role of QS controlled regulatory pathways plays in adapting to the relevant marine environments. Among all the available Roseobacterial AHL-based QS, three are most well studied: Phaeobacter inhibens DSM17395, the marine sponge symbiont Ruegeria sp. KLH11 and the dinoflagellate symbiont Dinoroseobacter shibae. However, to understand more fully the ecological role of QS mechanisms, further studies on QS and the signalling process in a greater diversity of Roseobacters is needed.

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• {{cite journal | vauthors = Buchan A, Hadden M, Suzuki MT | title = Development and application of quantitative-PCR tools for subgroups of the Roseobacter clade | journal = Applied and Environmental Microbiology | volume = 75 | issue = 23 | pages = 7542–7 | date = December 2009 | pmid = 19801463 | pmc = 2786420 | doi = 10.1128/AEM.00814-09 | bibcode = 2009ApEnM..75.7542B }}
• {{cite journal | vauthors = Martens T, Heidorn T, Pukall R, Simon M, Tindall BJ, Brinkhoff T | title = Reclassification of Roseobacter gallaeciensis Ruiz-Ponte et al. 1998 as Phaeobacter gallaeciensis gen. nov., comb. nov., description of Phaeobacter inhibens sp. nov., reclassification of Ruegeria algicola (Lafay et al. 1995) Uchino et al. 1999 as Marinovum algicola gen. nov., comb. nov., and emended descriptions of the genera Roseobacter, Ruegeria and Leisingera | journal = International Journal of Systematic and Evolutionary Microbiology | volume = 56 | issue = Pt 6 | pages = 1293–304 | date = June 2006 | pmid = 16738106 | doi = 10.1099/ijs.0.63724-0 | doi-access = free }}
• {{cite journal | last = Shiba | first = T | date = 1991 | title = Roseobacter litoralis gen. nov., sp. nov., and Roseobacter dentrificans sp. nov., aerobic pink-pigmented bacteria which contain bacteriochlorophyll a | journal = Syst. Appl. Microbiol. | volume = 14 | issue = 2 | pages = 140–145 | doi=10.1016/s0723-2020(11)80292-4}}
• {{cite book | vauthors = Garrity GM, Holt JG | date = 2001 | chapter = Taxonomic Outline of the Archaea and Bacteria | title = Bergey's Manual of Systematic Bacteriology Volume 1: The Archaea and the deeply branching and phototrophic Bacteria | edition = 2nd | editor1 = DR Boone | editor2 = RW Castenholz | pages = [https://archive.org/details/bergeysmanualofs00boon/page/155 155–166] | publisher = Springer Verlag | location = New York | isbn = 978-0-387-98771-2 | chapter-url-access = registration | chapter-url = https://archive.org/details/bergeysmanualofs00boon | url = https://archive.org/details/bergeysmanualofs00boon/page/155 }}

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• [http://www.roseobase.org/ Roseobase: a genomic resource for marine Roseobacters]

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Category:Bacteria genera

Category:Rhodobacteraceae

Category:Marine microorganisms