Roseobacter
Roseobacter | |
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Roseobacter strain HIMB11 [1] | |
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Genus: | Roseobacter Shiba 1991
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Species
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Description
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.[4]
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.[5] Roseobacter are similar to phytoplankton in that both of them colonize surfaces, scavenge iron and produce bioactive secondary metabolites.[4]
Common Clusters
Name | Habitats | Distribution |
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OCT cluster | 90% nonredundant clone is from polar region | 55% clone sequences; 45% isolate sequences |
CHAB-I-5 cluster | 56% nonredundant clone is from coastal seawater | 100% clone sequences |
DC5-80-3 cluster | 79% are from planktonic habitats (surface and deep water) | 86% clone sequences |
RGALL cluster | Symbiotic relationship with eukaryotic marine organisms | 68% cultivated strains |
OBULB and SPON clusters | 32% nonredundant clone are from coastal seawater;
29% nonredundant clone are from seafloor environments |
70% clone sequences |
NAC11-7 cluster | 60% nonredundant clone is from near-shore seawater | 88% clone sequences |
DG1128 cluster | From macroalgae and phytoplankton | |
AS-21 cluster | From coastal seawater or sediment | |
TM1040 cluster | ||
AS-26 cluster | ||
ANT9093 cluster | From polar sea ice, sponges, sediments, |
Genomic features
Size
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.[6]
Plasmids
Plasmids are common to be seen in Roseobacters. The size of plasmids range from 4.3 to 821.7 Kb.[6] They can make up 20% of the genome content.[6] 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.[6]
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.[6]
Importance of genome study
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.[7]
Ecology
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.
Evolution
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.
Cultivated Roseobacters
It is predicted that the Roseobacter ancestor dates back to around 260 million years ago. They underwent a net
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.[8] 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.[8] 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.
Uncultivated Roseobacters
Diversity
The Roseobacter clade displays success in multiple marine habitats because of their expansive metabolic capabilities. There is enormous
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.[7]
Functions
Members of the Roseobacter clade play an important role in the ecosystem.[5]
Global carbon/sulfur cycle
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.[10] 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).[11]
Aromatic compound degradation
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[12]
Trace metal uptake
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.[13] 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.[13]
Symbiotic and pathogenic relationships
The Roseobacter clade can establish symbiotic and pathogenic relationships.[14] 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.[15] In addition, Roseobacters can develop close relationship with Pfiesteria, where they are found to be within or attached to these dinoflagellates.[16]
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.[5]
Applications
Bioactive compounds
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).[17] 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).
Larviculture
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.[18] 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.[19] 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.[20]
Quorum sensing
Most bacteria have chemical communication systems.
References
- .
- ^ a b Köpke, Beate (2007). Verteilung, Zusammensetzung und Aktivitäten mikrobieller Gemeinschaften in Wattsedimenten von der Oberfläche bis in mehrere Meter Tiefe [Distribution, composition and activity of microbial communities in tidal flats from the surface to a depth of several meters] (PDF) (PhD). Universität Oldenburg.
- ^ See the NCBI webpage on Roseobacter. Data extracted from the "NCBI taxonomy resources". National Center for Biotechnology Information. Retrieved 2007-03-19.
- ^ ISBN 978-3-319-47933-0.
- ^ PMID 16204474.
- ^ S2CID 206894192.
- ^ S2CID 206894192.
- ^ PMID 25428935.
- PMID 17526795.
- S2CID 85208716.
- PMID 16719716.
- PMID 11055908.
- ^ PMID 26729720.
- PMID 20021642.
- PMID 10877801.
- PMID 11472503.
- ISBN 978-3-319-47933-0.
- ISBN 9788792763723.
- PMID 27552638.
- PMID 27441104.
- ^ PMID 24402124.
Further reading
- Buchan A, Hadden M, Suzuki MT (December 2009). "Development and application of quantitative-PCR tools for subgroups of the Roseobacter clade". Applied and Environmental Microbiology. 75 (23): 7542–7. PMID 19801463.
- Martens T, Heidorn T, Pukall R, Simon M, Tindall BJ, Brinkhoff T (June 2006). "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". International Journal of Systematic and Evolutionary Microbiology. 56 (Pt 6): 1293–304. PMID 16738106.
- Shiba, T (1991). "Roseobacter litoralis gen. nov., sp. nov., and Roseobacter dentrificans sp. nov., aerobic pink-pigmented bacteria which contain bacteriochlorophyll a". Syst. Appl. Microbiol. 14 (2): 140–145. .
- Garrity GM, Holt JG (2001). "Taxonomic Outline of the Archaea and Bacteria". In DR Boone, RW Castenholz (eds.). Bergey's Manual of Systematic Bacteriology Volume 1: The Archaea and the deeply branching and phototrophic Bacteria (2nd ed.). New York: Springer Verlag. pp. 155–166. ISBN 978-0-387-98771-2.