National Science Day-2020 celebration at NCMR, NCCS Pune

-By Kranti Karande

On 24 February 2020, an event was organized at NCMR, NCCS Pune for celebrating National Science Day, which is celebrated every year all over India on 28 February to commemorate the discovery of Raman effect by Sir C.V. Raman on the same day in 1928.

24 February 2020, 9:30 am: A group of approximately 120 students from class 7th and 8th of four different schools (DSK, VIBGYOR, Vidya Valley, and Ryan International School) were sitting in the Raman Hall of National Centre for Microbial Resource. They were waiting for someone. All noise stopped as that person entered into the hall. Instead of giving a formal lecture, Dr. Yogesh Shouche (Head of NCMR) preferred chitchatting with the students. He started with a question, “Which virus is in news these days?” He introduced the students with different types of microbes, importance of microbiology research and beneficial and harmful microbes. He solved all the queries of students. Students were very enthusiastic and happy to interact with Dr. Shouche.

After interactive session with Dr. Shouche, students visited the microbiology exhibition in group of 10 individuals. The Bioluminiscent bacterial display was arranged in a dark room, this was the main attraction for students.

The displays were arranged for Cyanobacteria, Anoxic Photosynthetic bacteria, Fungus, Archaea, and Antimicrobial (AMR) Assay.

This one day event at NCMR ventured students into the world of microbiology and they were awe stuck to learn about all the displays. “We loved this exhibition, it was awesome”, said one of the students. NCMR was delighted to host this event and we are looking forward to organize more such events for popularizing science.

Meet Dr. Rohit Sharma: Mycologist at NCMR, NCCS Pune

Dr. Rohit Sharma is a fungal taxonomist working at NCMR, NCCS Pune. He has been working in this field from last 15 years. He has identified 2 novel genera and 11 novel species of fungi. It was a great pleasure to interact with Dr. Sharma and find out more about him and his work.

Kranti: What motivated you to enter into the research field of fungal taxonomy?
Dr. Sharma:
I think it all started quite early when I used to go for sampling with my father, a Plant Pathologist at J.N. Agriculture University, Jabalpur. I used to go on collection trips with him during my school and college days to collect fungi infecting crops and wild plants and initial interest developed from there. During this period, I also got an opportunity to meet Dr. Kalman Vanky, expert in smut fungi and got opportunity to see his dedication towards the field of smut taxonomy. However, the actual involvement started when I began my doctoral work under Dr. Akhilesh K . Pandey and Dr. Ram C. Rajak whose lab was known to work on diversity and taxonomy of fungi. Here, I could get experience on entomopathogenic fungi, pathogenic and saprophytic micro fungi, mushrooms and yeasts. I developed a lot of insight in the lab under their guidance. Regular interactions helped to understand basics and the lab was rich in literature (monographs, journals and manuals) which usually is a bottle neck in the morpho-taxonomy of fungi. In the present organization as a curator of fungi, I got an opportunity to handle many fungi (yeasts, mycelial fungi and mushrooms) that helped in the development of the expertise in fungal taxonomy and systematics including polyphasic taxonomy.

Kranti : Why it is important to study fungal taxonomy?
Dr. Sharma: Fungi are hyper-diverse group of organisms. So far, many have been discovered but many are still to be discovered. Till now, about 1,20,000 fungi are known and researchers are discovering many more with an annual rate of approx. 1000 fungi. Based on the environmental sequence/ metagnomic data, it is now estimated that 22-38 lakhs fungi are yet to be discovered which makes it important to study the fungal diversity and taxonomy. Moreover, since they play an important role in environment and industrial biotechnology, it is important to explore, identify and subsequently study for their bio prospecting. Moreover, human and plant pathogens are increasing day by day and many environmental opportunistic pathogens are causing infections. Hence, it becomes important to have their authentic identification and proper classification for better management. The fungal taxonomy is complex and includes species specific morphological and physiological characters and intraspecific variation. The DNA-based taxonomic studies have helped to resolve many taxonomic problems and describe several cryptic species and are considered more stable than morphological characters.

Kranti: How many fungi you have collected and identified till now?
Dr. Sharma: So far we have collected and identified more than one thousand fungi from Lonar lake-Maharashtra, Famlong Lho-Sikkim, Achanakmar Sanctuary- Chhattisgarh, and other sites of India. They have been isolated from soil, litter, insect gut, sediments, water and as plant endophytes. We at NCMR-NCCS have described 2 novel genera (Matsushimamyces and Alanomyces) and 12 novel species, viz., Naganishia indica, Coniochaeta dendrobiicola, Leucosporidium himalayensis, Aureobasidium tremulum, Matsushimamyces bohaniensis, Alanomyces indica, Nothophoma raii, Curvularia lonarensis, Arthrinium gutiae, Pyrenochaeta telephoniae, Chaetomium jatrophae and Arthrinium jatrophae.

Kranti: What is your contributing role in services at NCMR?
Dr. Sharma: At present, I have been working as Curator-Fungi and looking after more than 15,000 fungal cultures preserved at our collection. My earlier work mostly was related to development of fungal culture collection at NCCS-NCMR, development of protocols, training human resource and undertaking basic research. So far, we have processed more than 2500 fungal cultures deposited by researchers from academia and from industry and accessioned approximately one thousand of them. We also provide identification services by conventional (morphology and API kit) as well molecular method, customized services and contractual research to industries. I along with my technician and project staff have been able to deposit more than 500 cultures to the NCMR-NCCS culture collection and screened them for various potential industrial applications viz., enzymes, bio active metabolites, waste degradation, etc. During the period, I have handled 4 research projects focusing on fungal diversity and their bio prospecting which in turn contributed to enrich the culture collection and preserve fungal wealth of our country.

Kranti: How has your journey been from being a PhD student to a Scientist at prestigious national institute?
Dr. Sharma: It has been a nice learning process, from working on ectomycorrhizal mushrooms during doctoral thesis to working with micro-fungi and yeasts at NCMR-NCCS. It has state of the art facilities and I can now use advanced techniques for my work. Work culture is very nice in our institute and  freedom to work and pursue my research interest in the area of diversity and taxonomy.

Kranti: What are the challenges you face during a field trip?
Dr. Sharma: During my doctoral thesis, I have went for sampling in the forests of Madhya Pradesh and Chhattisgarh for collection of ectomycorrhizal mushrooms. There are several challenges faced due to lack of communication, remoteness of the forests, etc. Moreover, we used to collect mushrooms from 8 am in the morning to 5 pm in the evening with a small packed lunch. In the evening after arriving at the forest guest house, we used to complete the mushroom data sheets and then around 7-pm we used to start culturing the mushrooms before putting them for drying. Sometimes it used to get 2-3 am in the morning because the mushrooms might decompose as the time passes after their harvest from the field.

Kranti: Which is your favorite fungus?
Dr. Sharma: The whole group of fungi are fascinating and one cannot pinpoint a single fungus. These are morphologically diverse and each one is unique in their features viz., colony color, shape, conidial shape, size, etc. The sexual and asexual stage found in these groups of organism makes them more interesting. From microscopic mycelial fungi to multi-cellular mushrooms to single celled yeasts, all have uniqueness of their own. From exogenous spores to endogenous spores, from pycnidia to cleistothecia, all have different morphological structures.

Kranti: What are the storage methods used at NCMR?
Dr. Sharma: We at NCMR-NCCS preserve the culture by five methods viz., cryopreservation at -80oC and at -196oC (liquid nitrogen) and by freeze drying. Apart from this, we also preserve the fungal cultures in distilled water and mineral oil (at 4oC). 

Kranti: What is your support system?
Dr. Sharma: My family and friends are my support system at individual level and colleagues and my team working with me at the professional level.

Kranti: What would you have liked to become if not a scientist?
Dr. Sharma: I would have been involved in doing agriculture, preferably doing scientific and organic agriculture with little bit of teaching at some academic organization so that I can interact and dissipate knowledge to students.

Kranti: What are the current and future projects in your group?
Dr. Sharma: Currently, we are working on collecting fungi from various sites and bio prospecting them for various applications like antimicrobial activity and treatment of industrial effluent. In future, we would like to focus more on the industrial applications of the fungal resource preserved in our collection and develop biotechnological usage of them.

Kranti: What are you hobbies?
Dr. Sharma: I like to read general books. Gardening is one my favorite hobbies and like to grow flowering as well as vegetable plants.

Kranti: Does research sometimes becomes stressful? What do you do for relaxation?
Dr. Sharma: Yes, research sometimes is stressful as sometimes multiple things gets lined up at the same time. To relax, I listen to classical music or go for trekking at nearby Pashan Tekri.

Kranti: What are your thoughts on Science communication in India? How can scientist contribute for better Science communication?
Dr. Sharma: I remember during my childhood I used to read a magazine ‘Science Reporter’, it used to explain scientific discoveries in simple language. Science communication in India is developing over the years by means of audio-visual and writing medium. Scientists can contribute for better science communication by conducting science talks for undergraduates explaining their research in a simplified manner. It is better now than it used to be. There are more communication channels available now with online platforms like blogs and online articles as compared to earlier days. 

The Importance of Studying Soil Microbes and their Interactions

-By Kranti Karande

A large number of micro-organisms are present in the soil ecosystem. There is a popular phrase that, microbes in a handful of soil are more in number compared to the total number of human beings that have ever existed on this planet. Soil life consists of microbes, nematodes, earthworms, ants, other insects, etc. With an estimated 100 billion bacteria that can be found in a handful of soil, it is the largest group of organism in this life-sustaining ecosystem. It is an astonishing reality that this handful of soil contains about 500 individual species of fungi and its mycelium can run up to 50 km in length. Staggering, isn’t it!

Among microbes, bacteria are present in large number in soil. Soil bacteria are mainly responsible for nitrogen fixation. Actinomyecetes, a group of bacteria break large lignin molecules into small molecules. Although not as commonly abundant as bacteria, fungi also significantly contribute in soil health by decomposing organic matter and nutrient recycling. Microbes contribute to soil in various ways by increasing its fertility, aggregation ability and by fixing nitrogen.

Soil ecosystem plays an important role in cultivating high yielding crops. Microbes being the major community of the soil, it is important to study them in order to conserve and nurture soil ecosystem. Studying soil microbes will help in increasing soil fertility and indirectly will contribute for betterment of farmers’ lives and for betterment of society.

Isn’t it interesting to study how these tiny microbes contribute in overall plant health? The very first interaction between plants and microorganisms occurs in soil. Every plant is associated with a unique rhizosphere (root microbial community). The rhizosphere microbial community is selected from large number of microorganisms present in the soil. The symbiotic association (beneficial for both) between rhizosphere and plant leads to complex interactions contributing to plant growth.

The interactions between these three components: plants, microbes and soil system play a critical role in maintaining health of the plant. However, the complexity of these interactions is not yet clear. Research group led by Dr. Kamlesh Jangid at NCMR, NCCS Pune is trying to understand this complex interaction.

Animals call for help when in need, but can you imagine how bacteria might be communicating with each other, especially in the complex soil ecosystem? You may wonder whether they use mobile phones. Not really, but they do have a very advanced communication system. Bacteria produce and release signalling molecules called as Auto inducers (AIs), which are then sensed by neighbouring organisms enabling them to differentiate between self and non-self. Isn’t it fascinating? This mechanism of cell-to-cell communication is known as quorum sensing.

While the mechanism was first discovered in 1970s by the team of Kenneth Nealson, Terry Platt and J. Woodland Hastings, it was not until 1994 that the term “quorum” was associated with this density-dependant mechanism by Fuqua , Winans and Greenberg. Quorum is a mechanism by which bacteria plan and fine-tune their actions as a group rather than as individual cells, thus co-ordinating gene expression and overall microbial population behaviour. Dr. Jangid’s group is discovering the presence of this mechanism across the bacterial community in soils. Studying this mechanism will help the scientific community to better understand the gene regulation in the soil microbes and will answer the questions related to their functional roles.

While studying the most abundant bacteria in soil, affiliated with the phylum Actinobacteria, Dr. Jangid’s group discovered that quorum sensing is extremely under explored partly due to the lack of sensor systems that can detect the huge diversity of AI molecules secreted by this group of bacteria. Specifically, only nine out of the 342 genera in the phylum Actinobacteria are experimentally proven to have this communication mechanism. Dr. Jangid’s group is now developing sensor systems for detecting signalling molecules produced by these bacteria to better understand quorum sensing in this phylum. This research can likely contribute to agricultural, biotechnological, medical and ecological fields.

If we understand the distribution of quorum sensing in soil bacteria, we will be able to modulate soil communities to enhance soil health and increase overall crop productivity. In addition, this will facilitate our understanding of the communication between microbes present in the rhizosphere and why plants are associated with a unique rhizosphere (root microbial community).

It was a great pleasure to interact with Dr. Jangid. In the discussion, Dr. Jangid commented that, “Soil microbiology and bacterial quorum sensing are two separately followed niche fields and their interjection enables us to explore new paths for improving soil health and creating more sustainable agricultural practices. Quorum sensing is also being researched extensively for developing new synthetic analogues that block (or quench) this communication mechanism among pathogenic microbes rather than the conventional anti-microbial drugs in use. The advantage of quorum quenching is that unlike antimicrobial targets, we expect very little to none resurgence towards this approach”.

Link to Dr. Jangid’s lab webpage:

Dr. Kamlesh Jangid with his research team

First Phytoplasma whole genome sequence from India

-By Kranti Karande

Phytoplasma is a group of extremely small bacteria. They don’t have a cell wall and any particular shape. Phytoplasma was first identified by a Japanese scientist Yoji Doi as ‘mycoplasma-like-organisms’ in 1967. They are bacterial parasites of plants and insects. 

Sugarcane Grassy Shoot (SCGS) is a disease caused by phytoplasma and the disease leads to 5% to 20% crop loss. SCGS phytoplasma causes severe proliferation of tillers leading to the typical grassy appearance of sugarcane, hence the name grassy shoot is given. Another disease called Bermuda Grass White leaf (BGWL) disease is a destructive phytoplasma disease of Bermuda grass.

Research group of Dr. Amit Yadav at NCMR, NCCS Pune performed whole genome sequencing of two phytoplasma associated with these two diseases. This is the first whole genome sequence of phytoplasma published from India. This sequence data might help in taxonomical characterization of other phytoplasma belonging to the same group.

A sugarcane plant sample (strain SCGS) exhibiting grassy shoot symptoms and a Bermuda grass sample (strain LW01) showing white leaf symptoms were collected from Pune, Maharashtra, India. The presence of phytoplasma was confirmed by 16S rRNA gene sequencing. Researcher confirmed that these phytoplasma strains belonged to the 16SrXI and 16SrXIV phytoplasma groups, respectively. Both genomes were annotated using the NCBI Prokaryotic Genome Annotation Pipeline

The final SCGS assembly contained 29 scaffolds corresponding to 505,173 base pairs of DNA. The genome was found to be 95.43% complete and the GC content was 19.86%.The SCGS genome was predicted to have 404 protein-coding genes, 12 tRNA and two rRNA genes.

Similarly, the LW01 assembly contained 21 scaffolds corresponding to 483,935 base pairs of DNA. This genome was found to be 91.32 % complete and the GC content was 20.46 %. The LW01 genome was predicted to have 425 protein-coding genes, 13 tRNA and three rRNA genes.


How Idli- a traditional Indian food becomes soft and spongy? Know about the key players..

-By Kranti Karande

Idli is a staple Indian food. Have you seen how Idli is prepared?

Idli cannot be made just by mixing pulverized rice and lentil in a short time period. The cereals needed to make Idli must be soaked, milled and mixed to make a batter. The batter is then fermented properly to make dough rise to get Idli soft and spongy. Usually the fermentation period is overnight, however sometimes it takes longer for Idli batter to ferment and rise. What determines the Idli batter fermentation duration?

The length is dependent on how rapidly the microorganisms in the batter grow and ferment the batter. Some of you must have noticed that during hot and humid weather, Idli batter is fermented in short duration, while it takes longer during cold weather. It is because, in humid weather, the development of microorganisms is faster. But you may wonder which are the microorganisms that contribute to fermentation and how they bring about fermentation of Idli batter?

Dr. Milind Patole

Fermented foods are studied widely worldwide and food fermentation of a given geographical area is studied and popularized by native scientists of that region. To give an example, Kimchi, a fermented vegetable food, native to Korea is studied widely by Korean Scientists and has more than 1200 publications in international peer reviewed journals. Kimchi is very popular food in western world and even a Google doodle appeared in November, 2017 ‘Celebrating Kimchi’. However, the problem of Idli fermentation was initially addressed by a noted food microbiologist, Prof. K. H. Steinkraus at Cornell University, New York, USA in 1965. There are only 50 published articles on Idli although Idli has several beneficial health effects. Therefore, Dr. Milind Patole’s research group at NCMR, NCCS Pune revisited the Idli fermentation problem and curiously investigated microorganisms involved in Idli batter and their role in fermentation process.

They carried out this study using techniques of microbiology and molecular biology such as amplicon sequencing MiSeq, quantitative PCR etc. Both culturally dependent and independent experiments were conducted, i.e. 354 bacteria were isolated from Idli batter samples collected from two vendors in two geographically distant destinations and one fermented in laboratory.

Interestingly, they reported that Lactic Acid Bacteria (LAB) is the dominant bacterial strain contributing to fermentation, and other bacterial strains identified in the Idli batter are Bacillales and Enterobacteriales. LAB constituted 86% of the total population of bacteria. Results also highlighted that most microorganisms belonged to phylum Firmicutes (70%) and Proteobacteria (22%). Further analysis was carried out up to species level identifying strains that contribute to the fermentation of the Idli batter.

Idli fermentation closely resembles the sourdough in which the release of carbon dioxide action is carried out by bacteria rather than yeast. Dr. Patole’s group also studied the physio chemical properties and growth kinetics during Idli fermentation. They dealt with a question of how fermentation of Idli is different than other fermented compounds. They report that succession of bacterial population is observed in fermentation of Idli batter which is not so common in fermentation of other food items.

Researchers also reported that Weisella emerged as the major genus in fermentation of Idli batter. An experiment also reported that only Weisella isolates can independently ferment the Idli batter. The Weissella confusa isolates also showed beneficial phytase- and B12-producing activities, signifying the abundance and role of this organism in fermentation of Idli batter.

Do you know that fermentative microorganisms not only make Idli soft and spongy but also contribute to the taste and flavor of the final product Idli?

This study provided an analysis of Idli batter fermentation using modern molecular tools giving a detailed account of the bacterial diversity that makes it possible to ferment. Because of the succession of the bacterial population the Idli fermentation is more complex than other food fermentation. With microbiota understood in this study, we might be able to speed up the process of Idli fermentation and the beneficial properties of these microorganisms make this food item suitable for the delivery and supplementation of beneficial probiotic organisms. Further study should be done by isolating microorganisms from the Idli batter collected from all geographical locations in India.

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