Ruegeria pomeroyi

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Silicibacter pomeroyi
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Ruegeria pomeroyi

(González et al. 2003) Yi et al. 2007
Synonyms
  • Silicibacter pomeroyiGonzález et al. 2003

Ruegeria pomeroyi is a species of Gram-negative, rod-shaped, aerobic dimethylsulfoniopropionate-demethylating bacterium. Its type strain is DSS-3T (=ATCC 700808T =DSM 15171T). [1] Its genome has been sequenced. [2]

Contents

Discovery

Ruegeria pomeroyi was discovered off the coast of the Eastern United States in the laboratory of Mary Ann Moran, Ph.D. [3] at the University of Georgia.

R. pomeroyi was named after Lawrence "Larry" Pomeroy, the marine microbial ecologist who notably established in 1974 that marine bacteria play a substantial and pivotal role in ocean food web dynamics. [4] Pomeroy was also a researcher at the University of Georgia.

Genome

The genome of the Ruegeria pomeroyi type strain (DSS-3) was completed in 2004. The genome is 4,109,442 base pairs long with a megaplasmid that is 491,611 base pairs long. [5]

Ecology

Ruegeria pomeroyi is a coastal ocean bacterium in a lineage of bacteria commonly considered ecological "generalists." [5] The relatively large genome of R. pomeroyi, as compared to other marine bacterial species, supports this concept. In line with this, R. pomeroyi has a highly versatile ability to utilize and sequester carbon and energy. [6]

R. pomeroyi also has the ability to degrade dimethylsulfoniopropionate (DMSP), a sulfur-containing algal osmolyte and use the sulfur to synthesize sulfur-containing amino acids. Although many marine bacteria are capable of degrading DMSP, the genes and proteins used to do so were elusive to researchers for many years. It was in R. pomeroyi that Howard and colleagues discovered the first gene that degrades DMSP. [7] This gene (dmdA) [7] codes for a protein (DmdA) that removes a methyl group (-CH3) from DMSP. The DmdA protein has since been further characterized from R. pomeroyi, [8] as well as the transcriptional response of the dmdA gene to the presence of DMSP [9] and the sequence diversity of the dmdA gene. [10] This demethylation process is the first step in the highly sought-after demethylation pathway of DMSP degradation in marine bacteria. Following the discovery of the dmdA gene, the gene sequence was used to establish that over half of marine bacteria, including both open-ocean and coastal bacteria, are capable of demethylating DMSP. [11]

Following the discovery of the demethylation pathway of DMSP degradation in R. pomeroyi, an alternative pathway of DMSP degradation was discovered in which DMSP is cleaved in half instead of demethylated, a process which R. pomeroyi also is capable. [12]

Related Research Articles

In taxonomy, Ruegeria is a genus of the Rhodobacteraceae. This genus was formerly known as the marine Agrobacterium before they were reclassified in 1998. It bears in fact the name of Hans-Jürgen Rüger, a German microbiologist, for his contribution to the taxonomy of marine species of Agrobacterium.

<span class="mw-page-title-main">Dimethylsulfoniopropionate</span> Chemical compound

Dimethylsulfoniopropionate (DMSP), is an organosulfur compound with the formula (CH3)2S+CH2CH2COO. This zwitterionic metabolite can be found in marine phytoplankton, seaweeds, and some species of terrestrial and aquatic vascular plants. It functions as an osmolyte as well as several other physiological and environmental roles have also been identified. DMSP was first identified in the marine red alga Polysiphonia fastigiata.

<span class="mw-page-title-main">Brine pool</span> Large area of brine on the ocean basin

A brine pool, sometimes called an underwater lake, deepwater or brine lake, is a volume of brine collected in a seafloor depression. The pools are dense bodies of water that have a salinity that is three to eight times greater than the surrounding ocean. Brine pools are commonly found below polar sea ice and in the deep ocean. Those below sea ice form through a process called brine rejection. For deep-sea brine pools, salt is necessary to increase the salinity gradient. The salt can come from one of two processes: the dissolution of large salt deposits through salt tectonics or geothermally heated brine issued from tectonic spreading centers.

Nitrospira translate into “a nitrate spiral” is a genus of bacteria within the monophyletic clade of the Nitrospirota phylum. The first member of this genus was described 1986 by Watson et al. isolated from the Gulf of Maine. The bacterium was named Nitrospira marina. Populations were initially thought to be limited to marine ecosystems, but it was later discovered to be well-suited for numerous habitats, including activated sludge of wastewater treatment systems, natural biological marine settings, water circulation biofilters in aquarium tanks, terrestrial systems, fresh and salt water ecosystems, and hot springs. Nitrospira is a ubiquitous bacterium that plays a role in the nitrogen cycle by performing nitrite oxidation in the second step of nitrification. Nitrospira live in a wide array of environments including but not limited to, drinking water systems, waste treatment plants, rice paddies, forest soils, geothermal springs, and sponge tissue. Despite being abundant in many natural and engineered ecosystems Nitrospira are difficult to culture, so most knowledge of them is from molecular and genomic data. However, due to their difficulty to be cultivated in laboratory settings, the entire genome was only sequenced in one species, Nitrospira defluvii. In addition, Nitrospira bacteria's 16S rRNA sequences are too dissimilar to use for PCR primers, thus some members go unnoticed. In addition, members of Nitrospira with the capabilities to perform complete nitrification has also been discovered and cultivated.

<span class="mw-page-title-main">Gammaproteobacteria</span> Class of bacteria

Gammaproteobacteria is a class of bacteria in the phylum Pseudomonadota. It contains about 250 genera, which makes it the most genus-rich taxon of the Prokaryotes. Several medically, ecologically, and scientifically important groups of bacteria belong to this class. All members of this class are Gram-negative. It is the most phylogenetically and physiologically diverse class of the Pseudomonadota.

<i>Roseobacter</i> Genus of bacteria

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. 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.

Alcanivorax borkumensis is an alkane-degrading marine bacterium which naturally propagates and becomes predominant in crude-oil-containing seawater when nitrogen and phosphorus nutrients are supplemented.

<span class="mw-page-title-main">Bacterial phyla</span> Phyla or divisions of the domain Bacteria

Bacterial phyla constitute the major lineages of the domain Bacteria. While the exact definition of a bacterial phylum is debated, a popular definition is that a bacterial phylum is a monophyletic lineage of bacteria whose 16S rRNA genes share a pairwise sequence identity of ~75% or less with those of the members of other bacterial phyla.

<span class="mw-page-title-main">Zetaproteobacteria</span> Class of bacteria

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.

"Candidatus Scalindua" is a bacterial genus, and a proposed member of the order Planctomycetales. These bacteria lack peptidoglycan in their cell wall and have a compartmentalized cytoplasm. They are ammonium oxidizing bacteria found in marine environments.

Variovorax paradoxus is a gram negative, beta proteobacterium from the genus Variovorax. Strains of V. paradoxus can be categorized into two groups, hydrogen oxidizers and heterotrophic strains, both of which are aerobic. The genus name Vario-vorax and species name para-doxus (contrary-opinion) reflects both the dichotomy of V. paradoxus metabolisms, but also its ability to utilize a wide array of organic compounds.

Alcanivorax dieselolei is a species of alkane-degrading bacteria. Its genome has been sequenced. It is halophilic, aerobic, Gram-negative, non-spore-forming, catalase- and oxidase-positive, motile and rod-shaped. Its type strain is B-5T.

Roseovarius nubinhibens is a species of Gram-negative, rod-shaped, aerobic dimethylsulfoniopropionate-demethylating bacteria. Its type strain is ISMT.

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.

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.

Endozoicomonas is a genus of Gram-negative, aerobic or facultatively anaerobic, chemoorganotrophic, rod-shaped, marine bacteria from the family of Endozoicomonadaceae. Endozoicomonas are symbionts of marine animals.

Vertical transmission of symbionts is the transfer of a microbial symbiont from the parent directly to the offspring. Many metazoan species carry symbiotic bacteria which play a mutualistic, commensal, or parasitic role. A symbiont is acquired by a host via horizontal, vertical, or mixed transmission.

Ann Patricia Wood is a retired British biochemist and bacteriologist who specialized in the ecology, taxonomy and physiology of sulfur-oxidizing chemolithoautotrophic bacteria and how methylotrophic bacteria play a role in the degradation of odour causing compounds in the human mouth, vagina and skin. The bacterial genus Annwoodia was named to honor her contributions to microbial research in 2017.

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.

References

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  3. "Moran Lab". moranresearch.uga.edu. Retrieved 2016-07-29.
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Further reading