Roseobacter
In taxonomy, Roseobacter is a genus of the Rhodobacteraceae. The Roseobacter clade falls within the -3 subclass of the class Alphaproteobacteria. The first strain descriptions appeared in 1991 which described members Roseobacter litoralis and Roseobacter denitrificans, both pink-pigmented bacteriochlorophyll a-producing strains isolated from marine algae. The role members of the Roseobacter lineage play in marine biogeochemical cycles and climate change cannot be overestimated. Roseobacters make up 25% of coastal marine bacteria and members of this lineage process a significant portion of the total carbon in the marine environment. Roseobacter clade plays an important role in global carbon,sulphur cycle. It can also degrade aromatic compounds, uptake trace metal, and form symbiotic relationship. In term of its application, Roseobacter clade produce bioactive compounds, has been used widely in aquaculture, quorum sensing.
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.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. Roseobacter are similar with phytoplankton in ways of living. Both of them colonize surface, scavenge iron and produce bioactive secondary metabolites.
Common Clusters
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.Plasmids
s 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. 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.
Importance of genome study
Comparison and analyzation of genomes of Roseobacter clade organisms are important because it can give insight in 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.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. 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.Evolution
The Rosebacter clade can be found in coastal areas living freely in bulk seawater or in coastal sediments. In these coastal ecosystems, Rosebacter clade interact with phytoplankton, macro algae and various marine animals living both mutualistic and pathogenic life styles. Rosebacter clade can also be found quite abundant in deep pelagic ocean, deep-sea sediments and even polar ocean. The reason why they are abundant in various marine habitats is because they have a diverse metabolic capabilities and regulatory circuits.Cultivated Roseobacters
It is predicted that 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.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 reseobacter 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’s 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’s 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.
Uncultivated Roseobacters
from deeply sequenced metagenomes and single-cell genome sequencing are two best ways for studying uncultivated Roseobacters without producing an unacceptable level of false positive results. And it is found that genomic analyses focusing on cultured roseolacters 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.Diversity
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.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.
Functions
Members of the Roseobacter clade play an important role in the ecosystem.Global carbon/sulfur cycle
Roseobacters are essential in the global carbon, sulfur cycle as well as the climate. Because of its large proportion in the total microbial community, roseobacter clade are major contributors to global CO2 fixation. Previous studies indicates that within the Roseobacter clade, some members belong to a group named Aerobic Anoxygenic Phototrophs, while other members are non-phototrophic. AAPs is the only known organisms that requires oxygen for photosynthesis, but no produces. Non-phototrophic members can be used for CO oxidation, while AAPs can conduct CO2 fixation as Roseobacters can generate energy through aerobic anoxygenic photosynthesis. Roseobacter has the ability to degrade dimethylsulfoniopropionate, 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.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 degradationTrace 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. 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 roseobacter clade, trace metal streamlining is also a valuable ecological strategy.Symbiotic and pathogenic relationships
Roseobacter clade can establish symbiotic and pathogenic relationships. 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. In addition, Roseobacters can develop close relationship with Pfiesteria, where they are found to be within or attached to these dinoflagellates.Pathogenic relationship, even though has little studys and much less common than symbiotic relationship, has 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.