Home » Science » Microbiology

Category Archives: Microbiology

DNA Metabarcoding: A Rapid Method for Biodiversity Assessment

DNA-metabarcoding2-2a

DNA metabarcoding refers to the automated identification of multiple species from a single bulk sample containing entire organisms. This offers unprecedented scientific and operation opportunities in order to understand biodiversity distribution and dynamics in a better way. Managing the health of global ecosystems requires detailed inventories of species and a good understanding of the patterns and trends of biodiversity. Evolutionary and ecological studies often rely on our ability to identify the species involved in the process under investigation or our capacity to provide robust biodiversity estimates. For about three centuries, the acquisition of biodiversity data was based on morphological characterization of plants and animals. The idea of identifying species on the basis of molecular markers emerged soon after the advent of molecular biology. Early methods involved the use of hybridization, restriction enzyme digestion or other molecular probes. DNA-based species identification was introduced by Arnot et al. and further development, standardized and advanced by Hebert et al. The ability to extract and store DNA for prolonged periods of time provides a unique opportunity to assess the evolution of biodiversity over time in relation to global change and to develop concrete measures to reserve these features. For more details, please click here.
DNA Metabarcoding

Advertisements

Opening Black Box of Soil Microbial Diversity through Molecular Techniques

tree_of_life

Biodiversity is generally defined as the variety and variability of living organisms and the ecosystems in which this occurs. The variability of life in the soil encompasses not only plants and animals but also the invertebrates and microorganisms that are interdependent on one another and the higher plants they support. Biodiversity is composed of three interrelated elements: genetic, functional and taxonomic diversity as shown in Figure 1. Taxonomic diversity i.e. the number of species forms an important part of an ecosystem’s diversity and is controlled by the genetic diversity. Genetic diversity can be much more than the number of recognized species. Hence, several species may have the same functions, resulting in functional redundancy. Some species may also interact to perform functions not possible by any single species. Therefore, biodiversity is the interaction of all these elements.

Soil biodiversity is more extensive than any other environment on the globe when all living forms are considered. The soil biota contains representations of all groups of microorganisms, fungi, bacteria, algae and viruses, as well as the microfauna such as protozoa and nematodes. The total diversity is equal to greater than any coral reef or rain forest. Soil algae and protozoa, like higher plants and animals, can be identified by their morphology. Fungi and bacteria, however, require more extensive biochemical and genetic analysis to enable identification.

It has been estimated that only between 1 and 5% of all microorganisms on the earth have been named and classified. A large proportion of these unknown species is thought to reside in the soil. The possible numbers of existing species of different groups are 1.5 million species of fungi, 300,000 species of bacteria, 400,000 species of nematodes and 40,000 species of protozoa. New molecular techniques have been used to estimate that single gram of soil probably contains several thousand bacterial species.

 Opening Black Box of Soil Microbial Diversity through Molecular Techniques

 

 

Intelligent Nano-Fertilizers

Many of anthropogenic activities modified the nutrient cycles of major and micro nutrients of worlds. The scale of these changes has massively accelerated since the industrial revolution throwing the equilibrium into disarray. Mineral nutrients  such as nitrogen, phosphorous potassium, calcium, magnesium, sulphur, and other micronutrients are essential for plant growth and crop production.  Presently, we face a glaring contrast of insufficient use of nutrients on one hand and excessive use on another. Nutrients Use efficiency (NUE) represents a key indicator to assess progress towards better nutrient management. Fertilizers are chemical compounds applied to promote plant growth. It is applied either through the soil or by foliar feeding. Artificial fertilizers are inorganic fertilizers formulated in approximate concentration to supply the nutrients. Nitrogen is an important source which is essential for the growth of plant. Urea is the most wildly used water soluble plant nitrogen source. Due to leaching the nitrogen content in the soil get decreased leading to low nitrogen utilization efficiency. Nitrogen-use efficiency for most crops ranges from 30 to 50 percent, so researchers are developing intelligent nano-fertilizers to reduce the amount of nitrogen lost during the crop production.  The plant needs different amount of nitrogen depending on its growth stage. A new generation of fertilizers will increase this efficiency from 30 percent to upwards of 80 percent. The idea is to develop a product that will release nitrogen only when the plant needs it and in the amount the plant needs. The plants communicate their surroundings environment by producing all kinds of chemical signals. A plant synthesizes specific compounds to communicate with specific microbes. The microbes then go to work and free nitrogen that the plant uses to grow. Thus, roots send out signal that ask microbes to transform nitrogen in the soil into a chemical form the plant can use. Many chemical compounds that are associated  with nitrogen uptake have been identified. These compounds can be used to synchronize the release of fertilizer with nitrogen uptake by the crop. Similarly, a plant under attack by insects or soil pathogen triggers defense mechanisms that synthesize alkaloids or antibiotics emitted into the surrounds soil to defense itself. A biosensor is a device that combines a biological recognition element with a physical or chemical transducer to detect a biological product. In other words, it is a probe that integrates a biological one with an electronic component to yield a measurable signal. Several biosensors are being developed for different applications. Typically a biosensor consists of three components: the biological recognition element, the transducer and the signal processing electronics. Nano-biosensors that will bind to these compounds can be developed so as to control of the release of fertilizers. The polymers coatings that protects the fertilizers from the elements contains nano-sized biosensors which are made up of very specific chemical compounds that allow the fertilizers to be released into the soil when the plant needs it. These biosensors know when to release nitrogen because they are able to detect chemical signals released from the roots of the plant to the soil. Biosensors can detect when a plant requires more nitrogen and allow microbes access to the fertilizer-nitrogen inside the polymer protected particles.  As mentioned earlier that each plant species sends out its own variety of chemical signals. Keeping this concept in mind, an intelligent nano-fertilizer product could be tailored to respond differently to the needs of different crops. For instance, the nitrogen particles could be designated to become available to wheat, but not to the canola growing in the same field because of different compounds emitted by different crops. We can prepare different biosensors using different compounds and tailor the fertilizers to each different crop for different climatic zones and soils. Dr. Carlos Montreal of Agriculture and Agri-Food Canada in Ottawa is one of the several research scientists developing a fertilizer that responds to organic compounds emitted by a plant’s roots. The research team is trying to make  intelligent fertilizers with the biodegradable three-dimensional polymer coating less than 100 nm  thick. Nitrogen-use efficiency for most crops ranges from 30 to 50 percent. Intelligent nano-fertilizers could be used to reduce the amount of nitrogen lost during the crop production.  The plant needs different amount of nitrogen depending on its growth stage. A new generation of smart fertilizers will increase this efficiency from 30 percent to upwards of 80 percent. Smart biosensors and smart delivery systems will help in enhancing productivity in agriculture. Hence, in coming years farmers could have access to an intelligent nano-fertilizer  that synchronizes the release of nitrogen with crop uptake.

intelligentnanofertm

%d bloggers like this: