Agar-Degrading (agarolytic) Bacteria is physiological class of bacteria capable of utilising agar as a sole carbon source. This ability is made available by the use of agarases - enzymes which break down agarose into oligosaccharides. This physiological class branches through genii, regardless of Gram Stain status or morphology. Through a review of scientific literature we can find identification methods, optimum conditions and the general function and location of agarolytic bacteria, as well as methods to culture them in vitro for study and experimentation.
Agar is a gelatinous substance derived from algae and seaweed that has found considerable use in laboratories as a medium for bacterial growth. Seaweed is fairly common in oceans, with Gelidium amansii (a species of red algae heavily used for agar) usually found in East and Southeast Asian coasts. Coupled with differing nutrients, inhibitors and indicators, Agar plates can be utilised as both a selective and differentiating medium by allowing only bacteria with the required properties to flourish(2).
By preparing a nutrient agar plate that has agar as its only carbon source, it is possible to screen for agar-degrading bacteria, as they are the only ones that may survive. The key of their ability to obtain carbon from agar alone is their capability of synthesizing agarase, the first enzyme in the agar catabolic pathway(8).
Agarases are classified as either α-agarases or β-agarases based upon whether they degrade α or β linkages in agarose, breaking them into oligosaccharides. α-agarases yield oligosaccharides with 3.6 anhydro-L-galactose at the reducing end whereas β-agarases result in D-galactose residues. (3) While the optimal pH of agarase is 5.5, it is stable at a tolerant range, from 4.0 to 9.0.(1)
The above diagram serves as a model of enzyme activity which agarase (as an enzyme) should behave similarly too. While not an exact representation, it does deliver a rough approximation suitable for demonstrating the enzymatic activity where agarose (green) is broken down into oligosaccharides (blue and red). The agarase is not affected by the catalysis reaction, merely resuming its original state. Due to this the same molecule of agarase can catalyse many reactions. However, radically differing temperatures or pH values may denature the enzyme permanently, destroying its capacity to catalyse reactions.
A recent paper (5) suggested the use of β-agarases to prepare large homogenous quantities of oligosaccharides by breaking down agarose. This article emphasises the use of enzyme activity over acid hydrolysis because “the hydrolysis product is not homogenous and the hydrolysing reaction is not easily controllable”(5). Due to the enzyme’s natural ability to “degrade [these] polysaccharides with high specificity and under mild conditions” by breaking down β-linkages, agarose is degraded both efficiently and reliably. This technique relies on the production of extracellular agarase from strains of E. coli modified to carry AgaA or AgaB (different types of β-agarases) encoding genes and is the same way the process is carried out in nature, with bacteria releasing agarase to break down agar outside of the cell gradually until it is in a form suitable to be utilized by the bacteria. It can be seen that agarase defines agar-degrading bacteria, as its namesake function is not possible without it.
Environment and Nutrients
As could be expected, many species of agar-degraders are marine micro-organisms – an adaptation to their environment which would be wasted in the majority of other micro-organisms such as those that exist on land (although there are such examples, including a species of Paenibacillus in the Rhizosphere of Spinach (4)). From species within genus Vibrio (1) to Alteromonas (6), the presence of agarase allows agar-degrading bacteria an abundant food source...