In
taxonomy
Taxonomy is the practice and science of categorization or classification.
A taxonomy (or taxonomical classification) is a scheme of classification, especially a hierarchical classification, in which things are organized into groups or types. ...
, ''Roseobacter'' is a
genus
Genus ( plural genera ) is a taxonomic rank used in the biological classification of extant taxon, living and fossil organisms as well as Virus classification#ICTV classification, viruses. In the hierarchy of biological classification, genus com ...
of the
Rhodobacteraceae
The Rhodobacteraceae are a family of Pseudomonadota in the order Rhodobacterales within the alpha subgroup.See the NCBIbr>webpage on Rhodobacteraceae Data extracted from the Like all Pseudomonadota, they are gram-negative. It contains chemo ...
. 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
Marine biogeochemical cycles are biogeochemical cycles that occur within marine environments, that is, in the saltwater of seas or oceans or the brackish water of coastal estuaries. These biogeochemical cycles are the pathways chemical substanc ...
and climate change cannot be overestimated. Roseobacters make up 25% of coastal
marine bacteria
Marine prokaryotes are marine bacteria and marine archaea. They are defined by their habitat as prokaryotes that live in marine environments, that is, in the saltwater of seas or oceans or the brackish water of coastal estuaries. All cellular ...
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 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.
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
Physiology (; ) is the scientific study of functions and mechanisms in a living system. As a sub-discipline of biology, physiology focuses on how organisms, organ systems, individual organs, cells, and biomolecules carry out the chemical an ...
, and are commonly found to be either free living, particle associated, or in commensal relationships with marine phytoplankton, invertebrates, and vertebrates.
Roseobacter are similar to phytoplankton in that both of them colonize surfaces, 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
Plasmid
A plasmid is a small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently. They are most commonly found as small circular, double-stranded DNA molecules in bacteria; how ...
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.
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.
Importance of genome study
Comparison and analyzation of genomes of Roseobacter clade organisms is important because it can give insight into
horizontal gene transfer
Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between Unicellular organism, unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offsprin ...
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
Phytoplankton () are the autotrophic (self-feeding) components of the plankton community and a key part of ocean and freshwater ecosystems. The name comes from the Greek words (), meaning 'plant', and (), meaning 'wanderer' or 'drifter'.
Ph ...
,
macroalgae
Seaweed, or macroalgae, refers to thousands of species of macroscopic, multicellular, marine algae. The term includes some types of ''Rhodophyta'' (red), ''Phaeophyta'' (brown) and ''Chlorophyta'' (green) macroalgae. Seaweed species such as k ...
, and several marine animals. Different lifestyles such as
mutualistic and
pathogen
In biology, a pathogen ( el, πάθος, "suffering", "passion" and , "producer of") in the oldest and broadest sense, is any organism or agent that can produce disease. A pathogen may also be referred to as an infectious agent, or simply a germ ...
ic 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
The pelagic zone consists of the water column of the open ocean, and can be further divided into regions by depth (as illustrated on the right). The word ''pelagic'' is derived . The pelagic zone can be thought of as an imaginary cylinder or wa ...
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 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
genome reduction
Genome size is the total amount of DNA contained within one copy of a single complete genome. It is typically measured in terms of mass in picograms (trillionths (10−12) of a gram, abbreviated pg) or less frequently in daltons, or as the total ...
from a large common ancestral genome followed by two episodes of genome innovation and expansion through
lateral gene transfer
Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offspring ( reproduction). ...
(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
A microorganism, or microbe,, ''mikros'', "small") and ''organism'' from the el, ὀργανισμός, ''organismós'', "organism"). It is usually written as a single word but is sometimes hyphenated (''micro-organism''), especially in olde ...
populations on particles and living surfaces in the marine environment.
Uncultivated Roseobacters
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.
Diversity
The Roseobacter clade displays success in multiple marine habitats because of their expansive metabolic capabilities. There is enormous
genomic
Genomics is an interdisciplinary field of biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, three-dim ...
and
physiological
Physiology (; ) is the scientific study of functions and mechanisms in a living system. As a sub-discipline of biology, physiology focuses on how organisms, organ systems, individual organs, cells, and biomolecules carry out the chemical ...
diversity throughout the major clades, which refer to different size, gene content,
GC content
In molecular biology and genetics, GC-content (or guanine-cytosine content) is the percentage of nitrogenous bases in a DNA or RNA molecule that are either guanine (G) or cytosine (C). This measure indicates the proportion of G and C bases out o ...
, 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
eukaryote
Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bacte ...
s.
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
Genus ( plural genera ) is a taxonomic rank used in the biological classification of extant taxon, living and fossil organisms as well as Virus classification#ICTV classification, viruses. In the hierarchy of biological classification, genus com ...
and
species
In biology, a species is the basic unit of classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of the appropriate s ...
characterizations in the clade shows the physiological and genetic diversity of these organisms. The designations of new
strains solely based on the
16s rRNA 16S rRNA may refer to:
* 16S ribosomal RNA
16 S ribosomal RNA (or 16 S rRNA) is the RNA component of the 30S subunit of a prokaryotic ribosome ( SSU rRNA). It binds to the Shine-Dalgarno sequence and provides most of the SSU structure.
The g ...
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
In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ge ...
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 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.
Roseobacter has the ability to degrade dimethylsulfoniopropionate (DMSP), an organic sulfur compound produced in abundance by marine algae. Through the degradation of algal
osmolyte
Osmolytes are low-molecular weight organic compounds that influence the properties of biological fluids. Their primary role is to maintain the integrity of cells by affecting the viscosity, melting point, and ionic strength of the aqueous solution. ...
s, they can also produce the climate-relevant gas
dimethyl sulfide
Dimethyl sulfide (DMS) or methylthiomethane is an organosulfur compound with the formula (CH3)2S. Dimethyl sulfide is a flammable liquid that boils at and has a characteristic disagreeable odor. It is a component of the smell produced from cook ...
(DMS).
Aromatic compound degradation
Roseobacter can degrade
aromatic compound
Aromatic compounds, also known as "mono- and polycyclic aromatic hydrocarbons", are organic compounds containing one or more aromatic rings. The parent member of aromatic compounds is benzene. The word "aromatic" originates from the past grouping ...
s, 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
Trace metal uptake
Roseobacter clade uptakes
trace metal
Trace metals are the metals subset of trace elements; that is, metals normally present in small but measurable amounts in animal and plant cells and tissues and that are a necessary part of nutrition and physiology. Many biometals are trace me ...
. 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 the Roseobacter clade, trace metal streamlining is also a valuable ecological strategy.
Symbiotic and pathogenic relationships
The 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 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.
Applications
Bioactive compounds
The Roseobacter clade can produce varies types of
bioactive compound
A bioactive compound is a compound that has an effect on a living organism, tissue or cell, usually demonstrated by basic research in vitro or in vivo in the laboratory. While dietary nutrients are essential to life, bioactive compounds have not ...
s. These compounds including algal growth promoters (i.e.
auxin
Auxins (plural of auxin ) are a class of plant hormones (or plant-growth regulators) with some morphogen-like characteristics. Auxins play a cardinal role in coordination of many growth and behavioral processes in plant life cycles and are essenti ...
s) and algaecidal compounds (i.e. the Roseobactides). 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. 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. 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
Bioremediation broadly refers to any process wherein a biological system (typically bacteria, microalgae, fungi, and plants), living or dead, is employed for removing environmental pollutants from air, water, soil, flue gasses, industrial effluent ...
of oceanic waste plastic.
Quorum sensing
Most bacteria have chemical communication systems.
Quorum sensing
In biology, quorum sensing or quorum signalling (QS) is the ability to detect and respond to cell population density by gene regulation. As one example, QS enables bacteria to restrict the expression of specific genes to the high cell densities at ...
(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.
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.
References
Further reading
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External links
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Roseobase: a genomic resource for marine Roseobacters
{{Taxonbar, from=Q7368622
Bacteria genera
Rhodobacteraceae
Marine microorganisms