Environmental biotechnology and metagenomics

By MICHAEL JOHN UGLO THIS is our lecture number 11 and the second last on the series on biotechnology. A warm welcome to you all. You see, in the technology world, I am saddened that technology remains inconceivable and might even sound ludicrous for the majority of our people. That is why I try to explain the ideas about science and technology to the nation for free and I am contented that my aim is achieved with the fact that every Friday you read something on science and technology. Now let me make this point clear to you that, if you are a student currently, you have to read a lot of books and not spend so much of your time on mobile phones and computer games. You will not become somebody that you dream of becoming if you do not read. If you are a student, please always carry a book around with you to read. The breakthrough innovations as contained in the study of environmental biotechnology fare well to become so paramount. It uncovers the totality of genetic materials that are out there in the natural environment, an interesting field to tap into. It opens up so much in ideas and information into the discovery of newer pathways for biochemical reactions as well as newer enzymes for cellular metabolisms. Such areas look at the entirety of the community of the microorganisms from the natural environment. This realm comprises of the plasmids that form as adjuncts to the main chromosomes of the cell. Other areas include viruses, viroids, free DNAs and the DNAs from a mixture of organisms. This is all studied in the discipline called metagenomics which provides opportunities for researchers as well as scientists to come up with these new innovations with transcending scientific findings and concomitantly newer biochemical reactions that are not currently known to the scientific community.

Metagenomics and genetic engineering The information gathered in metagenomics enables genetic engineers to manipulate and culture new genetic materials on bacterial vector cells. It can be used for cloning to obtain replicas of such genes as cloned genes. It has exposed to the people’s knowledge for our understanding of the unknown information that is out there in the natural environment. This study will help us to know the complexity of the microbial communities with their innate microbial ecosystems and this gives insights into the free DNAs. Hence, it exposes the undiscovered metabolisms out there in nature fueled by unknown biocatalysts to form the respective metabolites. This will also lead us into the discovery of any biomolecule’s presence. The entire genome can be mapped from this particular natural environment to get one directly into studying the morphology of the environment. It will also be applicable as a derivative from this research applied to the other areas apart from the place where it is found implying implementation in situ as well as other areas. Metagenomics points to the study of environmental biotechnology to be an overarching area in terms of the genomes of the natural environment. New genes as well as the varied forms of life with their biocatalysts can be discovered that were not previously known.

Unknown microbes Such is known with the fact that the varied physiology of the microorganism population in that environment is able to expose the genetics of the unknown microbes. This will then greatly affect the way in which the environment is being used having known the enzymes together with the new proteins that form from it. Concurrently, it will lead to the identification of the respective biochemical pathways for very specific enzyme activities and the associated by products such as the antibiotic productions. The identification of undiscovered microorganisms is an overwhelming finding that can be potentially used to clean up environmental pollutants using stable isotopic probing. In here a sample of the soil, water or part of a vegetation is used to expose it to contaminants like phenol, ammonia, chlorides or carbonate and methanol or even butanol or sulphates. These precursors can be labelled with detectable isotopes such as Oxygen -18 (18O), Nitrogen-15 (15N) or Carbon-13 (13C). When there are presences of microbes which ingest and metabolise these substances then, these will be included into their genomes. Microbes that consume the chemicals are then isolated if there are any by the method of centrifugation based on the understanding that if the precursor materials are metabolised, their DNAs will be heavier and can be isolated. These follow a gradient inclination from a cesium chloride centrifugation extractive method. Cloned DNAs These DNAs can be cloned into vectors as a finding to be a remedy for the chemical clean-up effort in the environment for very specific environmental contaminants. Hence, these form part of the metagenomic library. Herein, new microbes can be identified to be applied in the bio-reclamation exercise as an innovation in this area of biotechnology. The microorganisms soar to be very helpful in the earth’s problematic pollution obliteration wrangles. They transform hazardous environmental contaminants into eco-friendly substances. As an example, in the developed and undeveloped nations alike and at the specific sites of gasoline stations, there are leakages into the soil beneath it. These leakages can be able to contaminate the soil as well as further seepage and infiltration can contaminate the ground water below it. For instance, in the United States, the major source of the drinking water is groundwater which is obtained from below the ground. It is surprisingly found that the microbes living in the soil below those gas stations are able to develop the appropriate mechanisms and in particular are modifications made to their digestive enzymes to ingest and metabolise those pollutant chemicals. These pollutants are from gasoline from those stations and are composed of so many different types of chemical substances. Those chemical substances will require a variety of microorganism populations to digest and eradicate them from becoming a health threat to the people. Some microbes such as bacteria have the capability to consume dissolved oxygen (DO) in the water making the water devoid of DO. It has to be noted here that dissolved oxygen is necessary for aquatic organisms to thrive because when they are in the water, they extract the DO for their breathing.

Respiration This respiration takes place through their thin filament of their gill structures and their cellular respiration for metabolism to keep them alive. Dissolved oxygen is found trapped within the interstices of the water molecule (H2O). When some species of bacteria deplete oxygen, the other microbes with different specialised niches are able to do other works such as degrading the gasoline by obtaining their energy from using plant nutrients. Such plant nutrients will include the nitrates (NO4) that have a minus combining power of one (1) so called the oxidative power of negative one (1) written as (NO4)-. This nutrient radical is degraded by some bacterial species while the others will degrade iron (Fe), manganese (Mn) and then sulphate (SO4)2-. As can be seen from the chemical names, these chemical substances are not the same. Hence, there are correspondingly a lot of different groups of microbes working together to degrade these pollutants in the environment. It can be specifically noted that the entire microbial community work collaboratively together to break down these contaminants in metagenomics. The waste these interactions produce as byproducts as mentioned earlier amount to water and carbon dioxide. These products are ecologically sound and environment friendly. Specifically, water is very important for the survival of both plants and animals and the microbes to keep them hydrated as the medium for the much-needed biochemical reactions to take place in their bodies. In photosynthesis, it contributes hydrogen for the synthesis of carbohydrate. The other byproduct being carbon dioxide is also ecofriendly because it is the reagent needed by the plants diffused through their palisade mesophyll chloroplasts via stomata. It is regulated by the guard cells as the main gas required to donate the element carbon to build the carbohydrates like the glucose as a monosaccharide. Also being environmentally sensitive on the heat and light on the surrounding humidity and light’s sensitivity apart from its intensity the guard cell also regulates the transpiration stream with the molecular forces of adhesion and cohesion of water as a suspension to transport the salts and minerals up the plant. The entire physiology owes to the presence of the microbial community that filter what is the best they can offer the ecosystem and this has to take precedence to determine how we should be using our natural environment as a point of insinuation with metagenomics. Next week: Industrial biotechnology My Prayer for PNG today is: “Sweet the rains new fall, sunlit from Heaven. Like the first dewfall on the first grass. Praise for the sweetness of the wet garden. Sprung in completeness where His feet pass”