Dickeya parazeae

General Information

Dickeya parazeae is a fascinating bacterium primarily known for its role as a plant pathogen. This organism is part of the Dickeya genus, which includes several species notorious for causing soft rot diseases in a variety of crops. What makes D. parazeae particularly interesting is its ability to produce a wide array of plant cell wall-degrading enzymes, such as pectinases, cellulases, and proteases. These enzymes break down the plant's structural components, leading to tissue maceration and the characteristic soft rot symptoms. Another unique aspect of D. parazeae is its genetic adaptability. The bacterium has a highly plastic genome, which allows it to rapidly acquire and lose genes through horizontal gene transfer. This genetic flexibility enables D. parazeae to adapt to different environmental conditions and host plants, making it a versatile and resilient pathogen. From a research perspective, D. parazeae is valuable for studying plant-microbe interactions, particularly the mechanisms of pathogenicity and host specificity. Understanding how D. parazeae interacts with its host plants at the molecular level can provide insights into developing effective disease management strategies. Additionally, the enzymes produced by D. parazeae have potential applications in biotechnology, such as in the degradation of plant biomass for biofuel production. In summary, Dickeya parazeae is a notable bacterium due to its role as a plant pathogen, its genetic adaptability, and its production of plant cell wall-degrading enzymes. These characteristics make it a significant subject of study in both agricultural and biotechnological research.

Dickeya parazeae is a fascinating plant pathogenic bacterium that belongs to the family Pectobacteriaceae. This organism is particularly notable for its role in causing soft rot diseases in a variety of economically important crops, including potatoes and other members of the Solanaceae family. Its ability to degrade pectin, a key structural polysaccharide in plant cell walls, allows D. parazeae to effectively invade and cause tissue maceration, leading to significant agricultural losses. One of the unique aspects of D. parazeae is its genetic diversity, which can influence its pathogenicity and host range. This diversity is a subject of interest for researchers aiming to understand the mechanisms of plant-pathogen interactions and to develop effective control strategies. The bacterium's virulence factors, including various exoenzymes and toxins, are also under investigation, as they play a crucial role in its ability to cause disease. Furthermore, D. parazeae has been studied for its potential use in biocontrol applications, as understanding its interactions with other microorganisms could lead to innovative methods for managing plant diseases. The organism's adaptability to different environmental conditions makes it a valuable model for studying microbial ecology and evolution in agricultural settings. Overall, Dickeya parazeae stands out not only for its impact on crop health but also for its contributions to our understanding of microbial pathogenesis and plant-microbe interactions.

Taxonomy

Superkingdom: Bacteria

Phylum: Pseudomonadota

Class: Gammaproteobacteria

Order: Enterobacterales

Family: Pectobacteriaceae

Genus: Dickeya

Species: Dickeya parazeae

NCBI ID

2893572

Genome Info

FTP Path:
ftp.ncbi.nlm.nih.gov/genomes/all/GCA/017/897/605/GCA_017897605.1_ASM1789760v1

File for sequence-based predictions:
GCA_017897605.1_ASM1789760v1_genomic.fasta

Descriptions

Clinical Implications and Relevance

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

The bacterium Dickeya parazeae is primarily known for its role as a plant pathogen, particularly affecting crops such as potatoes and other members of the Solanaceae family. However, its clinical implications in human health are emerging, particularly in the context of infections associated with immunocompromised individuals. While not traditionally recognized as a human pathogen, there have been isolated reports of Dickeya parazeae causing soft tissue infections and wound infections, especially in patients with underlying health conditions. Pathogenicity is attributed to its ability to produce various virulence factors, including exoenzymes that degrade plant cell walls, which may also play a role in tissue degradation in human infections. In terms of antimicrobial resistance, there is limited data available, but like many Gram-negative bacteria, Dickeya parazeae may possess intrinsic resistance mechanisms that could complicate treatment options. The organism's interaction with the human body is not well-characterized, but its potential to evade the immune response through biofilm formation and secretion of virulence factors raises concerns about its management in clinical settings. Currently, there are no known medical applications such as probiotics or vaccines associated with Dickeya parazeae, but ongoing research may reveal more about its interactions with human health and potential therapeutic avenues. Overall, while Dickeya parazeae is primarily a concern in agriculture, its sporadic association with human infections highlights the need for further investigation into its clinical relevance.

Habitat and Ecological Niches

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

Dickeya parazeae is a bacterium primarily associated with agricultural ecosystems, particularly in the context of plant pathology. This microorganism is known to thrive in environments where it can interact with host plants, especially in the rhizosphere and phyllosphere of various crops, including potatoes and other members of the Solanaceae family. Its presence is often linked to conditions that favor plant stress, such as high moisture levels and nutrient-rich soils, which can enhance its pathogenicity. In the rhizosphere, Dickeya parazeae plays a significant role in the degradation of organic matter, contributing to nutrient cycling. However, it is also a notorious plant pathogen, causing diseases such as black leg in potatoes. This dual role highlights its importance in the ecosystem, where it can both support and challenge plant health. The bacterium exhibits notable interactions with its surroundings, including symbiotic relationships with certain soil microorganisms that may enhance its survival and virulence. Additionally, it has adapted to various environmental stresses, such as fluctuating temperatures and moisture levels, which allows it to persist in diverse habitats. Overall, Dickeya parazeae is a key player in the agricultural biome, influencing both plant health and soil dynamics, and its management is crucial for sustainable crop production.

Industrial Application

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

The microorganism Dickeya parazeae has shown potential in various industrial applications, particularly in the fields of biotechnology and waste management. This bacterium is known for its role in biodegradation, where it can break down complex organic materials, making it useful in the treatment of agricultural waste and other organic pollutants. Its ability to degrade plant materials can be harnessed in composting processes, enhancing the efficiency of organic waste recycling. In the realm of biofuel production, Dickeya parazeae can contribute to the conversion of biomass into biofuels through fermentation processes. By utilizing its metabolic pathways, this organism can help in the production of ethanol from plant-derived sugars, thus supporting the development of sustainable energy sources. Moreover, Dickeya parazeae has been studied for its potential in pharmaceutical development. Its enzymatic activities may lead to the discovery of novel compounds that could be used in drug formulation or as biocatalysts in various chemical reactions. The exploration of its metabolic products could yield valuable insights into new therapeutic agents. Overall, the applications of Dickeya parazeae in these industries highlight its versatility and importance in advancing sustainable practices and innovative solutions in biotechnology and environmental management.

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: 8

LLM predicted phenotypes: 4

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

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