Update data/rag/knowledge_base/Azotobacter/genus.json

data/rag/knowledge_base/Azotobacter/genus.json

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+{
+  "genus": "Azotobacter",
+  "taxonomy": {
+    "family": "Azotobacteraceae",
+    "order": "Pseudomonadales",
+    "class": "Gammaproteobacteria"
+  },
+  "overview": "Azotobacter is a genus of large, Gram-negative, free-living nitrogen-fixing bacteria commonly found in soil and aquatic environments. They are obligate aerobes and known for producing thick-walled cysts and abundant extracellular polysaccharides. Azotobacter species protect nitrogenase from oxygen through respiratory protection and melanin-like pigment production.",
+  "key_traits": [
+    "Large ovoid Gram-negative rods",
+    "Strict aerobes",
+    "Nitrogen fixation under free-living conditions",
+    "Produce cysts with thick walls (distinctive)",
+    "Motile with peritrichous flagella (often lost in cysts)",
+    "Pigment production (brown/black melanins in some species)",
+    "Catalase positive",
+    "Oxidase positive",
+    "Do not grow in 6.5% NaCl",
+    "ONPG negative"
+  ],
+  "ecology": "Common in neutral to alkaline soils, compost, rhizospheres, freshwater surfaces, and nutrient-rich sediments. Important contributors to nitrogen cycling in terrestrial ecosystems. Their ability to form cysts allows survival under desiccation or nutrient stress.",
+  "pathogenicity": "Azotobacter species are not human or animal pathogens. Their significance is ecological and industrial (biofertilizers). Any clinical isolation should be interpreted as environmental contamination.",
+  "genus_level_biochemistry": {
+    "general_tendencies": [
+      "Catalase and oxidase positive.",
+      "Non-fermentative aerobic metabolism.",
+      "Nitrogenase activity measurable under N-free conditions.",
+      "Production of melanin-like pigments in some species.",
+      "ONPG negative.",
+      "No growth in 6.5% NaCl."
+    ],
+    "non_definitive_tests": [
+      "Carbohydrate oxidation patterns vary and do not define the genus.",
+      "Pigment production differs by species and growth phase."
+    ]
+  },
+  "genus_differentiation": {
+    "from_close_genera": [
+      "Azomonas species do not produce cysts, unlike Azotobacter.",
+      "Pseudomonas species are smaller, non-cyst-forming, and do not fix nitrogen aerobically.",
+      "Alcaligenes and Achromobacter are oxidase positive but lack nitrogen fixation and cyst formation.",
+      "Bacillus is Gram-positive and forms endospores, not cysts."
+    ],
+    "key_rag_filters": [
+      "Large Gram-negative rods + cyst formation → strongly favors Azotobacter.",
+      "Environmental soil isolate + pigment production → push toward Azotobacter.",
+      "Nitrogen-free medium growth → nearly exclusive to Azotobacter among aerobes."
+    ]
+  },
+  "diagnostics": {
+    "typical_lab_findings": [
+      "Large Gram-negative rods with vacuolated appearance",
+      "Cyst formation under nutrient limitation",
+      "Pigmented colonies (brown/black in some species)",
+      "Growth on nitrogen-free media",
+      "Motility in vegetative cells"
+    ],
+    "important_tests": [
+      "Nitrogen-free growth test",
+      "Cyst formation on microscopy",
+      "Pigment production assessment",
+      "Catalase and oxidase tests"
+    ],
+    "confirmation_methods": [
+      "16S rRNA sequencing",
+      "Species-level biochemical profiles",
+      "Whole-genome sequencing for industrial strains"
+    ]
+  },
+  "notes": "Azotobacter is used in agriculture for nitrogen biofertilization. Clinical laboratories should treat isolates as environmental contaminants.",
+  "references": [
+    "Soil Microbiology and Biochemistry literature",
+    "Manual of Environmental Microbiology",
+    "Azotobacter nitrogen fixation research reviews"
+  ]
+}