Ruegeria pomeroyi

General Information

Ruegeria pomeroyi is a fascinating marine bacterium that has garnered significant interest in the scientific community due to its unique metabolic capabilities and ecological roles. This organism is part of the Roseobacter clade, a group known for their diverse metabolic functions and widespread presence in marine environments. One of the most remarkable features of R. pomeroyi is its ability to degrade dimethylsulfoniopropionate (DMSP), a sulfur-containing compound produced by marine algae. The degradation of DMSP by R. pomeroyi leads to the production of dimethyl sulfide (DMS), a gas that plays a crucial role in the global sulfur cycle and has implications for climate regulation due to its influence on cloud formation. Additionally, R. pomeroyi possesses a versatile metabolism that allows it to utilize a wide range of organic compounds, making it an important player in the marine carbon cycle. This metabolic flexibility is supported by its large genome, which encodes a variety of enzymes and transport systems for the uptake and processing of different substrates. From a research perspective, R. pomeroyi serves as a model organism for studying marine microbial ecology and biogeochemical cycles. Its ability to interact with other marine organisms and its role in nutrient cycling make it a valuable subject for understanding the complex dynamics of marine ecosystems. In summary, Ruegeria pomeroyi is a key organism in marine environments due to its role in sulfur and carbon cycling, its metabolic versatility, and its ecological interactions. These characteristics make it an important focus for research aimed at unraveling the complexities of marine microbial communities and their impact on global biogeochemical processes.

Ruegeria pomeroyi is a fascinating marine bacterium that belongs to the family Rhodobacteraceae. This organism is particularly notable for its role in the marine ecosystem, where it contributes significantly to the cycling of organic matter and nutrients. One of the most interesting aspects of R. pomeroyi is its ability to degrade a variety of complex organic compounds, including those derived from phytoplankton and other marine organisms. This capability makes it a key player in the marine carbon cycle, helping to break down organic materials and recycle nutrients back into the ecosystem. Additionally, R. pomeroyi is known for its unique metabolic versatility. It can utilize a range of carbon sources, including dimethylsulfoniopropionate (DMSP), which is a compound produced by marine algae. The ability to metabolize DMSP is particularly significant because it is a precursor to dimethyl sulfide (DMS), a compound that plays a crucial role in cloud formation and climate regulation. Thus, R. pomeroyi not only contributes to nutrient cycling but also has implications for understanding climate processes. From a research perspective, R. pomeroyi serves as an excellent model organism for studying marine microbial ecology and biogeochemistry. Its genome has been sequenced, providing insights into the genetic basis of its metabolic capabilities and ecological functions. Researchers are particularly interested in its potential applications in biotechnology, such as bioremediation and the production of biofuels, due to its ability to degrade complex organic compounds efficiently. In summary, Ruegeria pomeroyi stands out as a valuable organism in marine science, with its unique metabolic pathways and ecological significance making it a subject of ongoing research and interest in the fields of microbiology and environmental science.

Taxonomy

Superkingdom: Bacteria

Phylum: Pseudomonadota

Class: Alphaproteobacteria

Order: Rhodobacterales

Family: Roseobacteraceae

Genus: Ruegeria

Species: Ruegeria pomeroyi

NCBI ID

89184

Genome Info

FTP Path:
ftp.ncbi.nlm.nih.gov/genomes/all/GCA/018/972/145/GCA_018972145.1_ASM1897214v1

File for sequence-based predictions:
GCA_018972145.1_ASM1897214v1_genomic.fasta

Descriptions

Clinical Implications and Relevance

Source: gpt-4o-mini-2024-07-18

The microorganism Ruegeria pomeroyi is a marine bacterium known for its role in the marine ecosystem, particularly in the cycling of organic matter and nutrients. While it is not primarily associated with human disease, its clinical relevance lies in its potential applications in biotechnology and environmental health. Ruegeria pomeroyi has been studied for its ability to degrade pollutants and its role in bioremediation, which can have indirect benefits for human health by improving water quality. Additionally, it has been investigated for its potential use in probiotics and biofertilizers, contributing to sustainable agricultural practices. However, there is limited documentation regarding its pathogenicity or direct associations with infections in humans. Its interactions with the human body are not well characterized, and it does not exhibit known antimicrobial resistance mechanisms that are clinically significant. Overall, while Ruegeria pomeroyi is not a pathogen, its ecological and biotechnological implications are noteworthy in the context of environmental health and sustainability.

Habitat and Ecological Niches

Source: gpt-4o-mini-2024-07-18

Ruegeria pomeroyi is a marine bacterium commonly found in coastal waters and estuaries, particularly in regions with high nutrient availability. This organism thrives in environments characterized by moderate salinity and temperature variations, often associated with the presence of organic matter from phytoplankton and other marine organisms. Its ecological niche is primarily linked to the microbial loop, where it plays a crucial role in the degradation of organic compounds, thus contributing to nutrient cycling in the marine ecosystem. In terms of interactions, R. pomeroyi is known for its symbiotic relationships with various marine organisms, including algae and corals. It can enhance nutrient availability for these hosts through its metabolic processes, which include the breakdown of complex organic materials. This bacterium is also involved in biogeochemical cycles, particularly the cycling of carbon and nitrogen, making it an essential player in maintaining the health of marine ecosystems. Furthermore, R. pomeroyi exhibits remarkable environmental adaptability, allowing it to thrive in varying conditions, such as changes in temperature and nutrient levels. Its ability to utilize different substrates for growth underscores its importance in marine microbiomes, where it contributes to the overall biodiversity and functionality of these habitats.

Industrial Application

Source: gpt-4o-mini-2024-07-18

The marine bacterium Ruegeria pomeroyi has shown significant potential in various industrial applications, particularly in the fields of biotechnology, waste management, and biofuel production. This organism is known for its ability to utilize a range of organic compounds, making it a valuable player in biodegradation processes. In biotechnology, Ruegeria pomeroyi is utilized for its unique metabolic pathways that allow it to degrade complex organic materials, which can be harnessed for waste treatment in marine environments. This capability is particularly important for the remediation of polluted waters, where it can help break down harmful substances, thus contributing to environmental sustainability. In the realm of biofuel production, Ruegeria pomeroyi has been studied for its potential in the conversion of marine biomass into biofuels. The bacterium's ability to ferment various substrates can be leveraged in fermentation processes to produce bioethanol and other biofuels, providing a renewable energy source that can reduce reliance on fossil fuels. Additionally, Ruegeria pomeroyi has been explored for its role in pharmaceutical development. The metabolites produced by this microorganism may have bioactive properties that can be investigated for new drug discoveries, particularly in the field of marine pharmacology. Overall, the diverse metabolic capabilities of Ruegeria pomeroyi position it as a promising candidate for various industrial applications, particularly in enhancing sustainability and efficiency in waste management, biofuel production, and biotechnology.

Phenotypes and Predictions

The table shows the phenotypes and predictions. Cell colors indicate the class of the value. When literature-based data is available, a checkmark (✓) indicates a correct prediction, while an ✗ indicates an incorrect prediction.

Literature-based phenotypes: 9

LLM predicted phenotypes: 4

Phenotype	High-quality annotation	openai/gpt-4o	anthropic/claude-3.5-sonnet	google/gemma-7b-it	meta-llama/llama-3-8b-instruct:nitro	anthropic/claude-3-haiku:beta	perplexity/llama-3-sonar-small-32k-chat	openchat/openchat-7b	mistralai/mixtral-8x7b-instruct:nitro	google/gemini-pro	openai/gpt-3.5-turbo-0125	openai/gpt-3.5-turbo-0125	google/gemini-pro-1.5	google/gemini-pro-1.5	openai/gpt-4	openai/gpt-4	microsoft/wizardlm-2-8x22b	microsoft/wizardlm-2-8x22b	google/palm-2-chat-bison-32k	google/palm-2-chat-bison-32k	google/gemini-flash-1.5	google/gemini-flash-1.5	meta-llama/llama-3-70b-instruct:nitro	meta-llama/llama-3-70b-instruct:nitro	microsoft/phi-3-mini-128k-instruct	microsoft/phi-3-mini-128k-instruct	mistralai/mistral-7b-instruct	mistralai/mistral-7b-instruct
Motility	N/A	true	true	true	true	true	true	false	false	true	true	true	true	true	true	true	true	true	true	true	true	true	true	true	false	false	false	false
Gram staining	gram stain negative	gram stain negative ✓	gram stain negative ✓	gram stain negative ✓	gram stain negative ✓	gram stain negative ✓	gram stain negative ✓	gram stain negative ✓	gram stain negative ✓	gram stain negative ✓	N/A	gram stain negative ✓	N/A	gram stain negative ✓	N/A	gram stain negative ✓	N/A	gram stain negative ✓	N/A	gram stain negative ✓	N/A	gram stain negative ✓	N/A	gram stain negative ✓	N/A	gram stain variable ✗	N/A	gram stain negative ✓
Aerophilicity	aerobic	aerobic ✓	aerobic ✓	N/A	N/A	N/A	N/A	N/A	N/A	N/A	aerobic ✓	aerobic ✓	aerobic ✓	aerobic ✓	aerobic ✓	aerobic ✓	aerobic ✓	aerobic ✓	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A
Extreme environment tolerance	TRUE	false ✗	false ✗	true ✓	true ✓	true ✓	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓
Biofilm formation	N/A	true	true	true	true	true	true	false	true	true	true	true	true	true	true	true	true	true	true	true	true	true	true	true	true	true	true	true
Animal pathogenicity	TRUE	false ✗	false ✗	true ✓	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗
Biosafety level	biosafety level 1	biosafety level 1 ✓	biosafety level 1 ✓	biosafety level 2 ✗	biosafety level 1 ✓	biosafety level 1 ✓	biosafety level 1 ✓	biosafety level 2 ✗	biosafety level 1 ✓	biosafety level 1 ✓	biosafety level 1 ✓	biosafety level 1 ✓	biosafety level 1 ✓	biosafety level 1 ✓	biosafety level 1 ✓	biosafety level 1 ✓	biosafety level 1 ✓	biosafety level 1 ✓	biosafety level 1 ✓	biosafety level 1 ✓	biosafety level 1 ✓	biosafety level 1 ✓	biosafety level 1 ✓	biosafety level 1 ✓	biosafety level 2 ✗	biosafety level 2 ✗	biosafety level 1 ✓	biosafety level 1 ✓
Health association	N/A	true	false	true	true	true	true	false	true	true	true	true	true	true	true	true	true	true	true	true	true	true	true	true	false	false	false	false
Host association	FALSE	false ✓	false ✓	true ✗	true ✗	false ✓	true ✗	false ✓	true ✗	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	true ✗	true ✗	true ✗	true ✗	true ✗	true ✗
Plant pathogenicity	TRUE	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗
Spore formation	FALSE	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓
Hemolysis	N/A	N/A	N/A	alpha	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A
Cell shape	bacillus	bacillus ✓	bacillus ✓	bacillus ✓	bacillus ✓	bacillus ✓	coccus ✗	bacillus ✓	bacillus ✓	bacillus ✓	bacillus ✓	bacillus ✓	bacillus ✓	bacillus ✓	bacillus ✓	bacillus ✓	bacillus ✓	bacillus ✓	bacillus ✓	bacillus ✓	bacillus ✓	bacillus ✓	bacillus ✓	bacillus ✓	coccus ✗	coccus ✗	bacillus ✓	bacillus ✓

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