Dickeya aquatica

General Information

Dickeya aquatica is a fascinating microorganism primarily known for its role in plant pathology. This bacterium belongs to the family Pectobacteriaceae and is a notable pathogen of aquatic plants. One of the most intriguing aspects of D. aquatica is its ability to cause soft rot diseases in a variety of plant hosts, which can lead to significant agricultural losses. The bacterium produces a suite of plant cell wall-degrading enzymes, including pectinases, cellulases, and proteases, which facilitate its invasion and colonization of plant tissues. What makes D. aquatica particularly unique is its adaptation to aquatic environments, distinguishing it from many other members of the genus Dickeya, which are typically associated with terrestrial plants. This adaptation suggests that D. aquatica has evolved specific mechanisms to survive and thrive in waterlogged conditions, making it an interesting subject for studies on microbial ecology and evolution. From a research perspective, D. aquatica is valuable for understanding the molecular mechanisms of plant-microbe interactions, especially in the context of waterborne plant diseases. Its genome has been sequenced, providing insights into the genetic basis of its pathogenicity and environmental adaptability. The study of D. aquatica can also contribute to the development of novel strategies for managing plant diseases in aquatic and semi-aquatic environments, which is crucial for protecting crops and natural ecosystems alike. In summary, Dickeya aquatica stands out due to its pathogenicity in aquatic plants, its enzymatic arsenal for plant tissue degradation, and its ecological niche, making it a significant organism for both basic and applied research in plant pathology and microbial ecology.

Dickeya aquatica is a fascinating species of bacteria that belongs to the family Pectobacteriaceae. This organism is particularly notable for its role in plant pathology, as it is known to cause soft rot in a variety of aquatic and semi-aquatic plants. Its ability to thrive in waterlogged environments makes it unique among its relatives, which are often associated with terrestrial plants. One of the most interesting aspects of D. aquatica is its enzymatic capabilities, particularly the production of pectinases and cellulases. These enzymes enable the bacterium to degrade plant cell walls, facilitating its invasion and colonization of host tissues. This characteristic not only highlights its potential as a model organism for studying plant-microbe interactions but also raises concerns in agricultural contexts, especially in crops that are grown in wet conditions. From a research perspective, D. aquatica serves as a valuable organism for understanding the mechanisms of pathogenicity in bacteria. Its genetic and biochemical pathways can provide insights into how bacteria adapt to specific environments and overcome plant defenses. Furthermore, studying this bacterium can contribute to the development of biocontrol strategies aimed at managing plant diseases, particularly in aquatic ecosystems. In summary, Dickeya aquatica stands out due to its specialized ecological niche, pathogenic potential, and enzymatic prowess, making it a significant subject of study in both microbiology and plant pathology.

Taxonomy

Superkingdom: Bacteria

Phylum: Pseudomonadota

Class: Gammaproteobacteria

Order: Enterobacterales

Family: Pectobacteriaceae

Genus: Dickeya

Species: Dickeya aquatica

NCBI ID

1401087

Genome Info

FTP Path:
ftp.ncbi.nlm.nih.gov/genomes/all/GCA/900/095/885/GCA_900095885.1_Daq1742

File for sequence-based predictions:
GCA_900095885.1_Daq1742_genomic.fasta

Descriptions

Clinical Implications and Relevance

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

The bacterium Dickeya aquatica is a member of the genus Dickeya, which is primarily known for its role as a plant pathogen, particularly in crops such as potatoes. However, its clinical implications in human health are emerging, particularly in relation to infections associated with immunocompromised individuals. While D. aquatica is not commonly recognized as a human pathogen, there have been isolated cases where it has been implicated in wound infections and soft tissue infections, especially in patients with underlying health conditions. Pathogenicity is thought to be linked to its ability to produce various virulence factors, including exoenzymes that can degrade plant cell walls, which may also contribute to tissue damage in human hosts. Furthermore, there is growing concern regarding antimicrobial resistance among members of the Dickeya genus, including D. aquatica. Resistance to commonly used antibiotics can complicate treatment options for infections, making it crucial for healthcare providers to be aware of this organism in clinical settings. In terms of immune evasion strategies, D. aquatica may utilize biofilm formation, which can protect it from both the host immune response and antibiotic treatment. This characteristic is particularly concerning in the context of chronic infections, where biofilms can lead to persistent and difficult-to-treat conditions. While research is still ongoing, the potential for Dickeya aquatica to act as an opportunistic pathogen highlights the need for further investigation into its clinical relevance, especially in the context of outbreaks or infections in vulnerable populations.

Habitat and Ecological Niches

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

Dickeya aquatica is a bacterium commonly associated with freshwater environments, particularly in lakes, rivers, and wetlands. This microorganism thrives in nutrient-rich waters, often found in areas with abundant organic matter, which provides a suitable environment for its growth and reproduction. Its presence is frequently linked to the decomposition of plant material, where it plays a crucial role in nutrient cycling and organic matter breakdown. In these aquatic biomes, D. aquatica can engage in symbiotic relationships with various aquatic plants, aiding in the breakdown of complex organic compounds and enhancing nutrient availability for plant uptake. This interaction not only supports plant health but also contributes to the overall productivity of the ecosystem. Furthermore, Dickeya aquatica is known to exhibit environmental adaptability, allowing it to thrive in varying conditions, including changes in temperature and nutrient levels. Its ability to form biofilms on submerged surfaces enhances its survival and competitiveness in these dynamic habitats. Overall, D. aquatica plays a significant role in maintaining the ecological balance within its freshwater habitats, contributing to both the decomposition processes and the health of aquatic plant communities.

Industrial Application

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

The microorganism Dickeya aquatica has shown potential in various industrial applications, particularly in the fields of biotechnology and waste management. This bacterium is known for its ability to thrive in aquatic environments, which makes it a candidate for biodegradation processes, particularly in the breakdown of organic pollutants in water bodies. Its enzymatic activity can facilitate the degradation of complex organic compounds, thus contributing to the purification of contaminated water. In the realm of biofuel production, Dickeya aquatica may play a role in the fermentation of biomass, converting organic materials into bioethanol or other biofuels. The bacterium's metabolic pathways can be harnessed to optimize the fermentation process, potentially increasing yield and efficiency. Moreover, in pharmaceutical development, the unique metabolic products of Dickeya aquatica could be explored for their bioactive compounds, which may have applications in drug formulation or as antimicrobial agents. The organism's ability to produce specific enzymes can also be utilized in enzyme production, which is crucial for various industrial processes, including food processing and bioremediation. Overall, Dickeya aquatica presents a multifaceted opportunity for innovation across several industries, leveraging its natural capabilities for sustainable practices and product development.

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

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