Roseobacter | |
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Roseobacter strain HIMB11 [1] | |
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Genus: | Roseobacter Shiba 1991 |
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In taxonomy, Roseobacter is a genus of the Rhodobacteraceae. The Roseobacter clade falls within the {alpha}-3 subclass of the class Alphaproteobacteria. The first strain descriptions appeared in 1991 which described members Roseobacterlitoralis and Roseobacterdenitrificans, 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. [3] Roseobacter clade plays an important role in global carbon and sulphur cycles. It can also degrade aromatic compounds, uptake trace metal, and form symbiotic relationship. In term of its application, Roseobacter clade produces bioactive compounds, has been used widely in aquaculture and quorum sensing.
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]
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 SPONclusters | 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, |
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 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]
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]
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. [7] 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. [8]
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). [8]
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. [8] 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. [8] The Roseobacter clade represents up to 20% of bacterial cells in certain coastal areas and 3 to 5% in open ocean surface waters. [9]
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]
Members of the Roseobacter clade play an important role in the ecosystem. [5]
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]
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]
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]
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]
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).
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]
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. [21] 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. [21] 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. [21]
Alphaproteobacteria is a class of bacteria in the phylum Pseudomonadota. The Magnetococcales and Mariprofundales are considered basal or sister to the Alphaproteobacteria. The Alphaproteobacteria are highly diverse and possess few commonalities, but nevertheless share a common ancestor. Like all Proteobacteria, its members are gram-negative, although some of its intracellular parasitic members lack peptidoglycan and are consequently gram variable.
Pseudomonas citronellolis is a Gram-negative, bacillus bacterium that is used to study the mechanisms of pyruvate carboxylase. It was first isolated from forest soil, under pine trees, in northern Virginia, United States.
Pseudomonas stutzeri is a Gram-negative soil bacterium that is motile, has a single polar flagellum, and is classified as bacillus, or rod-shaped. While this bacterium was first isolated from human spinal fluid, it has since been found in many different environments due to its various characteristics and metabolic capabilities. P. stutzeri is an opportunistic pathogen in clinical settings, although infections are rare. Based on 16S rRNA analysis, this bacterium has been placed in the P. stutzeri group, to which it lends its name.
The class Zetaproteobacteria is the sixth and most recently described class of the Pseudomonadota. Zetaproteobacteria can also refer to the group of organisms assigned to this class. The Zetaproteobacteria were originally represented by a single described species, Mariprofundus ferrooxydans, which is an iron-oxidizing neutrophilic chemolithoautotroph originally isolated from Kamaʻehuakanaloa Seamount in 1996 (post-eruption). Molecular cloning techniques focusing on the small subunit ribosomal RNA gene have also been used to identify a more diverse majority of the Zetaproteobacteria that have as yet been unculturable.
Alteromonas macleodii is a species of widespread marine bacterium found in surface waters across temperate and tropical regions. First discovered in a survey of aerobic bacteria in 1972, A. macleodii has since been placed within the phylum Pseudomonadota and is recognised as a prominent component of surface waters between 0 and 50 metres. Alteromonas macleodii has a single circular DNA chromosome of 4.6 million base pairs. Variable regions in the genome of A. macleodii confer functional diversity to closely related strains and facilitate different lifestyles and strategies. Certain A. macleodii strains are currently being explored for their industrial uses, including in cosmetics, bioethanol production and rare earth mining.
Roseobacter litoralis is a species of aerobic pink-pigmented bacteria. It contains Bacteriochlorophyll a. It contains spheroidenone, does not synthesize bacteriochlorophyll anaerobically, but shows aerobic phototrophic activity. It is also considered a photosynthetic marine bacterium. Cells are ovoid or rod-shaped and motile by subpolar flagella. R. litoralis does not reduce nitrate, while R. dentrificans does. R. litoralis can be found in marine seaweed.
Roseobacter denitrificans is a species of aerobic pink-pigmented bacteria. It contains Bacteriochlorophyll a. It contains spheroidenone, does not synthesize bacteriochlorophyll anaerobically, but shows aerobic phototrophic activity. Cells are ovoid or rod-shaped and motile by subpolar flagella. R. litoralis does not reduce nitrate, while R. denitrificans does.
Desulfitobacterium dehalogenans is a species of bacteria. They are facultative organohalide respiring bacteria capable of reductively dechlorinating chlorophenolic compounds and tetrachloroethene. They are anaerobic, motile, Gram-positive and rod-shaped bacteria capable of utilizing a wide range of electron donors and acceptors. The type strain JW/IU-DCT, DSM 9161, NCBi taxonomy ID 756499.
Desulfitobacterium hafniense is a species of gram positive bacteria, its type strain is DCB-2T..
Ruegeria pomeroyi is a species of Gram-negative, rod-shaped, aerobic dimethylsulfoniopropionate-demethylating bacterium. Its type strain is DSS-3T. Its genome has been sequenced.
Salinispora is a genus of obligately aerobic, gram-positive, non-acid-fast bacteria belonging to the family of Micromonosporaceae. They are heterotrophic, non-motile, and obligately grow under high osmotic/ionic-strength conditions. They are the first identified genus of gram-positive bacteria which has a high osmotic/ionic-strength requirement for survival. They are widely abundant in tropical marine sediments and were first identified in 2002. This genus of bacteria has potential biotechnological significance due to their production of novel secondary metabolites which can be used pharmaceutically.
Congregibacter litoralis KT71 is a gram-negative Gammaproteobacteria part of the NOR5/OM60 Clade discovered in seawater from Heligoland, an island in the North Sea by H. Eilers from the Max Planck Institute for Microbiology. C. litoralis KT71 is described as a pleomorphic bacterium and has a size of 2 x 0.5 μm. When grown in culture, C. litoralis KT71 has a generation time of 4.5 hours and prefers to grow on complex substrates where the sole carbon source is undefined, though it can utilize some sole carbon sources because they are most likely used by the organism for its central metabolism.
Mary Ann Moran is a distinguished research professor of marine sciences at the University of Georgia in Athens. She studies the role of bacteria in Earth's marine nutrient cycles, and is a leader in the fields of marine sciences and biogeochemistry. Her work is focused on how microbes interact with dissolved organic matter and the impact of microbial diversity on the global carbon and sulfur cycles. By defining the roles of diverse bacteria in the carbon and sulfur cycles, she connects the biogeochemical and organismal approaches in marine science.
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.
Dinoroseobacter shibae is a facultative anaerobic anoxygenic photoheterotroph belonging to the family, Rhodobacteraceae. First isolated from washed cultivated dinoflagellates, they have been reported to have mutualistic as well as pathogenic symbioses with dinoflagellates.
Methylophaga thiooxydans is a methylotrophic bacterium that requires high salt concentrations for growth. It was originally isolated from a culture of the algae Emiliania huxleyi, where it grows by breaking down dimethylsulfoniopropionate from E. hexleyi into dimethylsulfide and acrylate. M. thiooxydans has been implicated as a dominant organism in phytoplankton blooms, where it consumes dimethylsulfide, methanol and methyl bromide released by dying phytoplankton. It was also identified as one of the dominant organisms present in the plume following the Deepwater Horizon oil spill, and was identified as a major player in the breakdown of methanol in coastal surface water in the English channel.
Marine viruses are defined by their habitat as viruses that are found in marine environments, that is, in the saltwater of seas or oceans or the brackish water of coastal estuaries. Viruses are small infectious agents that can only replicate inside the living cells of a host organism, because they need the replication machinery of the host to do so. They can infect all types of life forms, from animals and plants to microorganisms, including bacteria and archaea.
Lone Gram is Danish microbiologist known for her work in bacterial physiology, microbial communication, and biochemicals that originate from bacterial cultures. She is an elected member of the Royal Danish Academy of Sciences and Letters and has received the Order of the Dannebrog.
Chromids, formerly secondary chromosomes, are a class of bacterial replicons. These replicons are called "chromids" because they have characteristic features of both chromosomes and plasmids. Early on, it was thought that all core genes could be found on the main chromosome of the bacteria. However, in 1989 a replicon was discovered containing core genes outside of the main chromosome. These core genes make the chromid indispensable to the organism. Chromids are large replicons, although not as large as the main chromosome. However, chromids are almost always larger than a plasmid. Chromids also share many genomic signatures of the chromosome, including their GC-content and their codon usage bias. On the other hand, chromids do not share the replication systems of chromosomes. Instead, they use the replication system of plasmids. Chromids are present in 10% of bacteria species sequenced by 2009.
Alison Buchan is the Carolyn Fite Professor at the University of Tennessee. She is known for her work on bacteria in natural environments, especially bacteria within the Roseobacter group. In 2022 she was named as a fellow of the American Academy of Microbiology.