Dickeya lacustris

General Information

Dickeya lacustris is a fascinating microorganism primarily known for its role as a plant pathogen. This bacterium belongs to the family Pectobacteriaceae and is notable for its ability to cause soft rot diseases in a variety of plant hosts. One of the most intriguing aspects of D. lacustris is its production of plant cell wall-degrading enzymes, such as pectinases, cellulases, and proteases. These enzymes break down the structural components of plant cells, leading to tissue maceration and the characteristic soft rot symptoms. Another unique feature of Dickeya lacustris is its adaptation to aquatic environments. Unlike many other plant pathogens that are primarily soil-borne, D. lacustris can thrive in water bodies, which makes it a significant concern for crops grown in or near aquatic systems. This adaptability also provides a valuable model for studying bacterial survival and virulence in diverse environmental conditions. From a research perspective, D. lacustris is particularly valuable for studying host-pathogen interactions and the molecular mechanisms underlying plant disease. Its genome has been sequenced, providing insights into the genetic basis of its pathogenicity and environmental adaptability. Researchers are also interested in exploring the potential for developing biocontrol strategies to mitigate the impact of D. lacustris on agriculture. In summary, Dickeya lacustris stands out due to its enzymatic arsenal, environmental versatility, and impact on plant health, making it a critical subject of study in plant pathology and microbial ecology.

Dickeya lacustris is a fascinating bacterium that belongs to the family Pectobacteriaceae. This organism is particularly notable for its role as a plant pathogen, primarily affecting aquatic and semi-aquatic plants. One of the most interesting aspects of D. lacustris is its ability to cause soft rot in various plant species, which can lead to significant agricultural losses. This characteristic makes it a subject of interest for researchers studying plant diseases and their management. The bacterium is known for its enzymatic capabilities, particularly the production of pectinases, which enable it to degrade pectin in plant cell walls. This enzymatic activity not only facilitates the infection process but also provides insights into the mechanisms of plant-microbe interactions. Understanding these interactions can lead to the development of more effective strategies for controlling plant diseases caused by D. lacustris and related pathogens. Moreover, Dickeya lacustris has been isolated from various freshwater environments, highlighting its ecological significance. Its presence in aquatic ecosystems raises questions about its role in nutrient cycling and its interactions with other microorganisms. This aspect makes it a valuable organism for studies in microbial ecology and environmental microbiology. In summary, Dickeya lacustris stands out due to its pathogenicity, enzymatic prowess, and ecological relevance, making it a compelling subject for ongoing research in plant pathology and microbial ecology.

Taxonomy

Superkingdom: Bacteria

Phylum: Pseudomonadota

Class: Gammaproteobacteria

Order: Enterobacterales

Family: Pectobacteriaceae

Genus: Dickeya

Species: Dickeya lacustris

NCBI ID

2259638

Genome Info

FTP Path:
ftp.ncbi.nlm.nih.gov/genomes/all/GCF/029/635/795/GCF_029635795.1_ASM2963579v1

File for sequence-based predictions:
GCF_029635795.1_ASM2963579v1_genomic.fasta

Descriptions

Clinical Implications and Relevance

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

The bacterium Dickeya lacustris 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 not as well-documented as those of other pathogens. There have been limited reports suggesting that Dickeya lacustris may be associated with infections in immunocompromised individuals, although these cases are rare and not fully characterized. Pathogenicity in humans is not well established, and further research is needed to clarify its potential role in human disease. In terms of antimicrobial resistance, there is currently insufficient data to determine the resistance mechanisms of Dickeya lacustris against common antibiotics, which is a significant area of concern for many bacterial pathogens. The organism's interaction with the human body remains largely unexplored, and its immune evasion strategies are not well understood. While Dickeya lacustris is not recognized as a major human pathogen, its relevance in agricultural contexts highlights the importance of monitoring plant-associated bacteria that may have the potential to affect human health indirectly through food supply chains. Overall, the clinical implications of Dickeya lacustris remain largely speculative and warrant further investigation to establish any definitive links to human health.

Habitat and Ecological Niches

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

Dickeya lacustris is a bacterium commonly associated with freshwater environments, particularly in lakes and ponds. This microorganism thrives in nutrient-rich waters, often found in areas with abundant organic matter, such as decaying plant material and sediments. Its presence is typically linked to the degradation of plant tissues, where it plays a significant role in the nutrient cycling process within these aquatic ecosystems. In terms of ecological niches, D. lacustris is known to inhabit the rhizosphere of aquatic plants, where it can engage in symbiotic relationships. This interaction can enhance nutrient availability for the plants while the bacterium benefits from the organic compounds released by the roots. Such relationships are crucial for maintaining the health of aquatic ecosystems, as they contribute to the overall productivity and stability of the biome. Furthermore, D. lacustris can also be found in biofilms on submerged surfaces, where it interacts with other microorganisms. These biofilms are essential for the biodiversity of freshwater habitats, providing a complex community structure that supports various life forms. The bacterium's ability to adapt to varying environmental conditions, such as changes in temperature and nutrient levels, allows it to thrive in diverse freshwater habitats, making it a key player in the ecological dynamics of these biomes.

Industrial Application

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

The bacterium Dickeya lacustris has shown potential in various industrial applications, particularly in the fields of biotechnology and waste management. This organism is known for its ability to degrade complex organic compounds, making it a candidate for biodegradation processes in contaminated environments. Its enzymatic activity allows it to break down pollutants, which can be harnessed for effective waste treatment solutions. In the realm of biofuel production, Dickeya lacustris may contribute to the fermentation processes that convert biomass into biofuels. By utilizing its metabolic pathways, this microorganism can potentially enhance the efficiency of fermentation processes, leading to higher yields of bioethanol or biogas from organic waste materials. Moreover, the unique properties of Dickeya lacustris could be explored in pharmaceutical development. Its ability to produce specific enzymes may be leveraged for the synthesis of bioactive compounds, which are crucial in drug formulation and development. The organism's role in enzyme production can facilitate the creation of novel pharmaceuticals with enhanced efficacy. Overall, Dickeya lacustris presents a promising avenue for innovation in environmental biotechnology, renewable energy, and healthcare, showcasing its versatility and importance in sustainable industrial practices.

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: 10

LLM predicted phenotypes: 3

Phenotype	High-quality annotation	anthropic/claude-3.5-sonnet	anthropic/claude-3-haiku:beta	mistralai/mixtral-8x7b-instruct:nitro	google/palm-2-chat-bison-32k	perplexity/llama-3-sonar-small-32k-chat	meta-llama/llama-3-70b-instruct:nitro	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	google/gemini-flash-1.5	google/gemini-flash-1.5	meta-llama/llama-3-8b-instruct:nitro	meta-llama/llama-3-8b-instruct:nitro	google/gemma-7b-it	google/gemma-7b-it	openchat/openchat-7b	openchat/openchat-7b	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 ✓	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	false ✗	false ✗	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	facultatively anaerobic	facultatively anaerobic ✓	N/A	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 ✓	facultatively anaerobic ✓	facultatively anaerobic ✓	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 ✓	true ✗	true ✗	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	true ✗	true ✗	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 ✓	true ✗	false ✓	true ✗	true ✗	false ✓	false ✓	false ✓	true ✗	true ✗	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	true ✗	true ✗	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓
Biosafety level	biosafety level 1	biosafety level 1 ✓	biosafety level 2 ✗	biosafety level 2 ✗	biosafety level 2 ✗	biosafety level 2 ✗	biosafety level 1 ✓	biosafety level 2 ✗	biosafety level 1 ✓	biosafety level 2 ✗	biosafety level 2 ✗	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 2 ✗	biosafety level 2 ✗	biosafety level 1 ✓	biosafety level 1 ✓
Health association	N/A	true	true	true	true	true	true	true	false	false	false	true	true	true	true	true	true	true	true	false	false	true	true	true	true	true	true	true	true
Host association	TRUE	false ✗	true ✓	true ✓	false ✗	true ✓	false ✗	true ✓	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	true ✓	true ✓	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 ✓	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	N/A	beta	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 ✓	bacillus ✓	bacillus ✓	bacillus ✓	bacillus ✓

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