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#microorganisms

19 public questions tagged with this topic.

Bioremediation

Bioremediation is defined as:

Bioremediation encompasses deliberate application of biological agents including bacteria, archaea, fungi and plants to neutralize, transform, degrade or immobilize environmental pollutants, ultimately converting hazardous organics into less harmful end products such as carbon dioxide, water, chloride and inorganic salts. Indigenous genera Pseudomonas, Sphingomonas, Rhodococcus harbor catabolic plasmids TOL encoding toluene degradation, OCT for octane, NAH for naphthalene, and chromosomal genes nahAc non-heme iron dioxygenase, alkB integral membrane alkane hydroxylase, xylE catechol 2,3-dioxygenase that initiate oxidative attack. Mycoremediation using Phanerochaete chrysosporium exploits lignin peroxidase to oxidize recalcitrant polycyclic aromatic hydrocarbons. Unlike chemical precipitation requiring lime addition producing sludge, incineration generating dioxins with high energy cost, or physical removal via excavation, bioremediation exploits natural metabolic pathways under ambient temperature, operates in situ minimizing disturbance or ex situ with control, and can be enhanced via bioaugmentation, biostimulation or engineered strains expressing expanded substrate ranges. Applications span oil spills, chlorinated solvents, heavy metals via biosorption and radionuclides via bioprecipitation, representing sustainable ecosystem restoration strategy.

Ref: EPA Bioremediation overview https://www.epa.gov/remedy/bioremediation; Vidali I J Green Chem 2001; NCERT Environmental Biotechnology.

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Basic Applied Biology

Which organism is used in coffee bean fermentation?

Coffee bean processing requires removal of pectin-rich mucilage layer surrounding parchment after pulping, a task accomplished through controlled microbial fermentation lasting 12 to 36 hours. Erwinia dissolvens, now taxonomically revised as Pantoea agglomerans, along with other enterobacteria such as Erwinia herbicola, initiates mucilage depolymerization by secreting extracellular polygalacturonase, pectin lyase and pectin methylesterase that hydrolyze alpha-1,4-linked D-galacturonic acid residues and methyl esters in pectic polysaccharides. This enzymatic breakdown drastically reduces viscosity, liberates simple sugars like glucose and fructose subsequently utilized by yeasts Saccharomyces and lactic acid bacteria producing organic acids that modestly lower pH from 6.5 to 4.2 facilitating washing and preventing germination. Aroma precursors generated during this phase influence final cup quality, while prolonged over-fermentation risks formation of butyric and propionic off-flavors from Clostridia. Wet-processed arabica relies heavily on bacterial pectinolysis for uniform bean drying, representing classic example of natural plant waste bioconversion for beverage quality improvement. Ecological succession later includes Bacillus, Pseudomonas putida and yeast Debaryomyces providing additional pectinolytic, cellulolytic enzymes that further clean bean surface, reduce water usage during washing and contribute to disease suppression in nursery seedlings.

Ref: Avallone et al. Applied Microbiology Biotechnology 2002 Coffee fermentation; Haile & Kang Int J Food Microbiol 2019.

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