Bio-prospecting – micro-organisms and plants as a source of novel enzymes

 Bioprospecting consists of the systematic identification, evaluation, and exploitation of the diversity of life in a certain place. It explores genetic resources for commercial purposes. In case of microorganisms, it  exploits culturable and nonculturable  microbial biodiversity. The in silico prospecting of genome sequences of microorganisms that are already available in databases can alos be studied to identify microorganisms, genes, enzymes, and/or metabolic pathways for further biotechnological applications in industry or in research itself

    There is a growing need for new bioactive compounds in the pharmaceutical (e.g. antibiotics against multi-resistant pathogens) and the agro- and food industries (e.g. agrochemicals, biocontrol products, food additives). Bio-resources have great potential to hold a manifold of promising compounds for biotechnological application.

An example is the search for heat-tolerant industrial enzymes. As most enzymes are destroyed by heat, some industrial processes would be greatly enhanced if heat-tolerant enzymes were discovered. The microbial biodiversity of thermal springs gave a solution to the question of where heat-tolerant enzymes would occur. These habitats revealed microbes with heat-stable enzymes that are being applied to a variety of industrial processes, including paper and pulp manufacturing, biotechnology, commercial cleaning, and forensic science, with each generating important benefits or major revenues. A possible new source of industrial enzymes of this type is the recently discovered bacterium Pyrodictium, which inhabits hydrothermal vents and can grow at temperatures between 85 and 121⁰C.

Plant-associated microbes epecially, endophytes which are microbes growing inside the plants, present an attractive and promising source but are nearly unexploited. Therefore, bioprospecting of plant microbiomes is gaining more and more attention. Due to their highly specialized and co-evolved genetic pool, plant microbiomes host a rich secondary metabolism.

Plants have been described as one of the richest sources of valuable bioactive natural products. Each plant is colonized by more than 1,000 microbial species, which are to a high degree not cultivable. Plants are divided into specific niches for microorganisms (rhizosphere, phyllosphere, endosphere), where biotic and abiotic factors shape specific microbial communities. Each plant microbiome has a specific composition due to the plant-specific secondary metabolism and physiology. This depends on the plant family, for instance dicotyledonous plants have developed a richer secondary metabolism than monocotyledonous plants. 

The microbiome fulfils multiple functions for the host health, like pathogen defense and contribution to stress tolerance under adverse environmental conditions and further supports growth and nutrient supply. The potential of the microbiome to influence the host is well-recognized however, the diversity of metabolites that are synthetized by the microbiota is largely unexplored.

Metagenomics is one means that facilitates examination of the entire genetic pool comprised by (plant) microbiomes, thereby providing access to the potential of the high share of uncultivable microbes. Metagenomics is the study of the unculturable- it studies the genomes of all the organisms present at an area without culturing them first. The extraction of the total environmental DNA is done, followed by examination at the sequence level or  based on the functions (gene expression). 

Sequence based analysis  requires the DNA to be sequenced but when expressed, the metagenome can be screened for certain, desired activities by specifically designed screening assays. 

Given the fact that more than 98% of the microbial diversity is not readily cultivable under current lab conditions, a search in metagenomes is a promising approach in bioprospecting. Bioprospecting towards novel enzymes and bioactive compounds has been frequently performed using environmental samples originated from soil, marine environments and microbiota associated to mammals (e.g. the human gut microbiome). 

Enzymes: Enzymes with novel activities are classical targets in microbial screenings that aim for an industrial application. 

Microbiota adapted to extreme conditions are especially interesting. Reactions as carried out during industrial processes require enzymes with high activty, specificity and high stability at particular conditions such as high salt content, cold or elevated temperature and low or increased pH.

Examples of such enzymes include, novel salt-tolerant chitibiosidase for potential degradation of seafood waste, new alkaline and thermostable esterase and lipase that exhibits high stability at elevated temperatures and in the presence of organic solvents. 

Plant associated microbes, may produce new enzymes for industrial applications. There are reports of  isolation of thermophilic endoglucanase and xylanase from sugarcane bagasse.  Several novel glycoside hydrolase genes (GHases) were identified in naturally occurring microbial biomass decay communities from poplar wood chips, after enrichment in an anaerobic bioreactor.

Enzyme discovery screenings  have been carried out by analyzing metagenomic libraries from soil and marine environments or the human gut. Cell-wall degrading or lytic enzymes, like cellulases, glucanases, proteases, xylanases and chitinases have been detected in plant associated microorganisms, especially in endophytic fungi and bacteria. 

Despite the increasing number of novel enzymes detected in metagenomes in the last decades, only a very small fraction has been expressed and fully characterized to evaluate further utilization in industrial processes.