Meet Dr. Neetha Joseph- Scientist at NCMR-NCCS Pune

Dr. Neetha Joseph’s research interest is in microbial systematics, ecology and community analysis. She is affiliated with NCMR-NCCS Pune from last 8 years. She is in-charge of FAME analysis service and curator of Firmicutes. It was a great pleasure to interact with Dr. Neetha and to know more about her as a person and her work.

Kranti: Dr. Neetha, you have worked with coastal environment micro-organisms during your PhD. At a personal level, what motivated you to enter into microbiology research?
Dr. Neetha: Kranti, my native place is in Kerala, a beautiful coastal area in India. Kochi is a lovely place with lot of Backwaters and Estuaries. When I finished my post-graduation, I got an opportunity to join at National Institute of Oceanography (NIO) where most of the research work is related to Ocean and Estuaries. Nutrient enrichment due to various anthropogenic activities is the most widespread problem in estuaries around the world. Significant spatial and temporal variability of physico-chemical and geochemical characteristics and productivity patterns are the important characteristics of estuaries. Microbial communities are involved in mineralization of organic matter; therefore, I was interested in understanding the response of these sedimentary microbial communities to these regional and seasonal changes using signature biomolecules (Phospholipid Fatty Acids – PLFA) as a means of identifying the specific group of microorganisms in the natural ecosystems .

Kranti: Everybody has someone in their life who inspires them to achieve something. Who is your inspiration in science?
Dr. Neetha: My PhD guide at NIO, Kochi is my inspiration in Science. She inspired me a lot! She encouraged me in various aspects of science and helped in boosting my confidence.

Kranti: Which methods and tools you use in your research?
Dr. Neetha: Microbial communities are involved in mineralization of organic matter in estuarine sediment. To understand the response of these microbial communities to various physiochemical and geochemical factors using signature biomolecules (Phospholipid Fatty Acids – PLFA) as a means of identifying the specific group of microorganisms in the natural ecosystems. Phospholipids are mainly found in the cell membrane, not in storage lipids and have a rapid turnover in aquatic sediments. So it provides a measure of viable cellular biomass in an ecosystem.  Different physiological and functional groups of microorganisms in sediments were described using PLFA analysis.
The extracted PLFAs were analyzed using gas chromatography (Agilent 7890 Series, USA) with a cross-linked phenyl – methyl siloxane capillary column (25 m, 0.2 mm) and FID. Identification of the FAMEs was carried out by comparison of retention time and equivalent chain length with known standards like Eukary calibration mixture – 1201A (Eukary6 method, Version: 3.7) and MIDI peak identification software (MIDI Inc., Newark, DE).

Kranti: You are contributing to microbiology related services offered at NCMR Pune. What are those services ?
Dr. Neetha: I am in – charge for FAME analysis service and curator of Firmicutes at NCMR. Under FAME analysis, the bacterial (aerobic and anaerobic) or yeast samples are identified based on their cell membrane fatty acids. Also cell membrane fatty acids are analyzed for novel taxa along with their closely related type strains for publication.

Kranti: Are journals necessary in the age of internet? Don’t you think research should be done not just to publish a paper but also to have real life impacts?  
Dr. Neetha: We know that nowadays we can extract all the information we require via internet. But we cannot compare the beauty of reading a book or journal with internet. Yes, I totally agree that we should do research not only to publish a paper but also to have real life impacts.

Kranti: Being a woman in science, what are the challenges that you’ve faced?
Dr. Neetha: Being a woman in science, the major challenge I face is to manage family, children and their education along with my research work. Another challenge is to get time to spend for research along with my routine services and other commitments.

Kranti: How do you maintain the balance of your family and work-life?
Dr. Neetha: For that I should thank my husband and children for their co-operation and moral support throughout my career.

Kranti: What advice would you like to give to young women who want to pursue research?
Dr. Neetha: If you have an actual interest in science along with sincerity, dedication and hardworking nature, you will be able to succeed in your research career. As a woman, you should be able to manage your time and having patience is also equally important to succeed in your life.

Kranti: Would you share with us any memorable incident/moment of your research life?
Dr. Neetha: In the year 2000, I got an opportunity to participate in Cochin – Alleppey – Mangalore Cruise on board CRV Sagar Paschimi, under DOD, COMAPS Programme. It was a rare experience and golden memory in my research life.

Kranti: Most of the scientist’s children opt for career in science. Do you want your child to become a scientist too? 
Dr. Neetha: Yes, if they are showing real interest in science and research, definitely I will encourage him or her to opt for career in Science.



Meet Dr. Om Prakash Sharma: Microbiologist at NCMR-NCCS Pune

You must have heard that ‘Oxygen is essential for Life!’ But what if I tell you that some organisms hate oxygen, and they cannot survive in presence of oxygen? Surprising! Isn’t it? There is a group of microorganisms called anaerobes who does not require oxygen for their survival. Dr. Om Prakash Sharma’s group at NCMR-NCCS Pune is interested in studying fascinating area of anaerobic microbiology. Dr. Sharma’s research interests also include environmental microbiology, microbial physiology, taxonomy etc. It was a great pleasure to interact with Dr. Sharma and know more about him as a person and as a researcher.

Kranti: What makes you most excited about working with anaerobes?
Dr. Sharma: Anaerobes are the provider of most of the anaerobic services like key components of clean-energy, global climate change, waste to energy generation, solid waste management, waste water treatment, bio-toilets, Human-gut-microbiome, anaerobic probiotics, fecal-microbiota-transplantation (FMT), fecal microbiome banking and emerging threat of anaerobic infection. However, they are less explored in comparison to aerobes as they are tough to cultivate and difficult to preserve. In India very few laboratories are working with anaerobes. I feel excited and energetic to think about the development of the biobank/ seedbank of obligate anaerobes and archaea  contributing to Indian academia and industries. This feeling pushes me to work with this group of microorganisms.

Kranti: How has your journey been from being a PhD student at Delhi University, Post-doctoral researcher at Florida State University, Georgia Institute of Technology to a Scientist at NCMR- NCCS Pune? How does research life change from being a student to being a faculty?
Dr. Sharma: My journey from DU to NCMR-NCCS Pune is same in terms of my feeling for microbes. I still feel like a student and have the same enthusiasm to explore the microbes. The best thing I feel is that I haven’t changed my field from last 20 years and it is helping me a lot to understand the field easily.  In terms of change, I am everyday learning about the feelings of students, colleagues and collaborators and try my level best not to hurt anyone in terms of ethics and benefit sharing. My 5 years’ postdoctoral experience was very fair about whom to give credit for what without hurting others and I try to implement that with my group too.

Kranti: We all are inspired or influenced by someone or something in life. Who or what is your inspiration in life?
Dr. Sharma: According to Hindu philosophy anyone who teaches you anything is a Guru and inspires your attitude and activities up to some extent. Although I appreciate the contribution of all my teachers but the work ethics, honesty and attitude of my postdoc advisor influenced me a lot. During my 4-5 years of postdoc duration, I always found him happy, smiling, well behaved, caring and learnt how to teach and appreciate your peers and subordinate without hurting or demoralizing  them.

Kranti: You grew up in a rural household, has it ever been a problem to achieve your dreams of becoming a scientist? 
Dr. Sharma: I can say yes in terms of money sometimes for essential books and application purposes but internally I never felt it as a problem. Fortunately, I got very good support from my teachers at each and every step of life that made me strong internally.

Kranti:  You are mentoring students for 10 years now. Every mentor has a unique way of training students. How do you train students? What is the most challenging part of training students?
Dr. Sharma: Till date I have only mentored students for their short period of dissertation but this number is quite good (40) and gives me the view of feeling of students. I would like to say getting good student is fortunate part of mentoring. During last 10 years some students were so nice in terms of knowledge and attitude that I realized that I was lucky to work with them. In addition, I never feel that I am mentor and more knowledgeable. I too learn from their observation, enthusiasm and way of working and writing and try to share what I have learnt.

Kranti: The major part of your research is focused on identification of Clostridium species, anaerobic infections, testing antimicrobial resistance and antimicrobial susceptibility of anaerobes. Could you elaborate on this part?
Dr. Sharma: I want to develop the culture bank of Clostridium of ecological and clinical significance and working on characterization of Clostridia available at NCMR . Anaerobic infection in humans is of developing interest among the clinicians and dentists and how the antibiotics behave in anaerobic vs anaerobic conditions have its own interest but availability of obligate anaerobes for all these purposes is of utmost importance. Cultivation and preservation of obligate anaerobes is a major challenge. Therefore according to mandate of NCMR we are reviving and developing long term preservation protocols that maintain the viability and functionality of the organisms for this purpose.

Kranti: Which methods and tools do you use in your research?
Dr. Sharma: It is really a very good question. Collecting anaerobic sample for cultivation of obligate anaerobic bacteria and Archaea is challenging. We use Hungate method of pre-reduced media preparation and handling. But for purification and cultivation of strict anaerobes availability of anoxic chamber and knowledge nutritional requirement, physiological nature and redox condition is a must. Considering the need of researchers working with strict anaerobes, we recently published a book Entitled Anaerobes and anaerobic process . Details of handling and techniques are given in that.

Kranti: You have received many recognition’s in your research career. Could you share your memory about any of the recognition?
Dr. Sharma: Till date I have received young achiever award from BHU, Best mentor Award from FAMU-USA, INSA-Visiting Fellow in Microbial Ecology, ICMR-DHR fellowshi in foreign laboratory and Members of Subcommittee of Methanogenic Archaea of ICSP. I was most thrilled during my visit to Israel as an INSA-Visiting Fellow in Microbial Ecology, my host prof. Ediie Cynrrun and myself worked together on same bench and I was influenced by him and learned how to treat and respect our guest when anyone visit our lab or facility.

Kranti:  Could you shed some light on where India stands today in Anaerobic microbiology research?
Dr. Sharma: Due to time consuming nature of handling of strict anaerobes very few researchers and student are inclined towards anaerobes. Most of the culture coming from Indian laboratories for deposit purpose on name of anaerobes are either facultative or aerotolerants. Due to increasing importance of anaerobes in gut research and biogas, Indian researchers are focusing on cultivation, characterization and biobanking.

Kranti: How do you maintain the balance of your family life and work life?
Dr. Sharma : It is a very difficult question to answer. I am waiting for my  kids to grow.

Kranti: Would you share with us any memorable incident/moment of your research life?
Dr. Sharma: I always have a fascination to work on weekends for half a day. Once I was working in Florida State University alone on Saturday and melting the agar-medium inside the tightly closed serum vials. When I picked the vials in hand from the water bath it blasted like a bomb. Fortunately, I was following the safety protocols and wore PPE. After that I immediately came home and never planned a risky experiment on the weekend when I am alone.

Kranti: Does science become hectic sometimes? What do you do to relax?
Dr. Sharma: Yes; It is  very natural. When I feel saturated I watch old movies, listen to gazals, write some poems and read literature.

Kranti: Are journals necessary in the age of the internet? Don’t you think research should be done not just to publish a paper but also to have real life impacts? 
Dr. Sharma: Publications of finding are an integral part of research but it depends what you are publishing and what is your ultimate aim and how your peers evaluate you. Number of publications depends on the type of work. But I agree research should not be done only for publication.

Kranti: Being a rational person, what do you think about the state of scientific temperament in the current times? 
Dr. Sharma: Scientific temperament is an individual property but it also very much depends on institute, laboratory environment, group leaders, individual interest, scientific ethics and honesty.

Kranti: What advice would you give to the young generation who want to pursue research?
Dr. Sharma: In my view honesty, ethics and interest matters for science and if anyone has all the three he/she will definitely enjoy it.

Kranti: How will you brief about your research if you want to communicate it to a layman?
Dr.Sharma: I am working with tiny unseen creatures of life. We cultivate, nourish and preserve them. They do not need oxygen for survival.  They, themselves, reside in dark and extreme pain but give light and energy to others. They are responsible for global climate change and global warming. Generate waste to energy, produce biogas and bio-fertilizer from waste. Essential component of gut-heath, bio-toilets and sewage treatment plant but also responsible for infection of deeper part of human-body.

Kranti: Where do you think India stands today in science communication? How can scientists contribute to effective science communication?
Dr. Sharma: The ultimate aim of science is to serve society. It will be only possible with more communication. We need more work in this area. Spreading science to the layman in popular form is also the responsibility of scientists. In my view it can be in any form cartoon, model, poems, scientific talks and popular writing etc. It should be promoted by funding agencies as well as at institutional and personal laboratory levels. Communication will also incline new generation scientists for doing better science.

Scientists report that delay in sample processing affect the cell viability

Dr. Avinash Sharma
NCMR, NCCS Pune
Wellcome Trust DBT
Indian Alliance Fellow

-By Kranti Karande

Sambhar Lake, located in the Rajasthan district, is the largest inland salt lake in India. It is a Ramsar site, a saline wetland of international importance because of the spectacular diversity of birds it attracts. The salt production from the lake is approximately 0.2 million tons per annum. Apart from this it is also considered as a hypersaline ecosystem because of high salinity which provides a great opportunity for microbial ecologists to understand halophiles. Over the last many years there are very few reports on the microbial diversity of halophiles, in particular archaea from Sambhar Lake.

Dr. Avinash Sharma’s group at NCMR-NCCS Pune cultivated diverse group of bacteria and archaea from Sambhar Lake. Archaea are very difficult to culture and not many research groups are working on this domain of life. Looking at the percentage of description of novel taxa belonging to bacteria and archaea, one can easily make out how poorly archaea are being studied.  13 genera were identified as archaeal while 12 genera belonging to bacteria were isolated in the current study. The authors also claim that there are 13 novel strains of archaea and bacteria isolated during study based on 16S rRNA gene sequencing and currently the group is working on genome analysis which is mandatory for the description of a novel taxa.   

        The reason behind capturing such a vast diversity was because of the multiple cultivation approaches used in the study.  The cultivation of microorganisms was done using two used approaches: onsite enrichment and sediment dilution in the laboratory. In the first method of cultivation, soil samples were inoculated in different growth media onsite. The same media and salt concentrations were also used for isolation in the second approach. That is same growth conditions were used in both approaches. Interestingly besides common found genera in both cultivation methods: AlteribacillusHalobacillusHalorubrumLentibacillusNatronorubrum
Piscibacillus and Thalassobacillus were found only in onsite cultivation whereas only three genera AliidiomarinaNatrinema and Natronolimnobius were found in laboratory processing.

Dr. Avinash Sharma said “Although both the approaches used for isolation are classical, but they provide better understanding to device sampling strategies. From our results we can conclude that it is important to use multiple cultivation approaches as these approaches help capturing vast group of organisms. Imagine if we would not have done the onsite enrichment we would have lost majority of the organisms we isolated in this study. We have also observed in the study how delay in sample processing effect the cell viability, although it is not possible to isolate each and every organism residing in the ecosystem but immediate sample processing is recommended to isolate majority of the organisms before they lose their viability”.

   The microorganisms isolated in this study are known for the production of bio technologically important compounds like halocines, bacteriorhodopsins, exopolymer, hydrolytic enzymes and possessing the anti-proliferative, anti-oxidant and anti-hemolytic activity.

Conservation of such unique organisms at NCMR-NCCS enrich the culture collection and provide better resources for future studies/research.

Reference: https://www.ncbi.nlm.nih.gov/pubmed/31912221

A new bacterial species described from the salt water lake in India

-By Kranti Karande

A bacterial strain ( MEB193T )was isolated from the Lonar lake which is a notified national Geo-heritage monument situated in Buldhana district of Maharashtra, India .

As researchers collected the sample water, the water had a pH of 9.8 and a temperature of 28ºC. This bacterial strain represented as MEB193T was isolated on modified sea water agar.The strain was described as rod-shaped, motile and non-spore forming.

Dr. Amaraja Joshi, NCMR Pune
Dr. Amaraja Joshi NCMR, NCCS Pune

Dr. Amaraja Joshi’s group at NCMR, with Dr. Yogesh Shouche identified the taxonomy of this strain.

Based on draft genome sequence on the Illumina MiSeq platform, 16S rRNA gene sequencing and observable characteristics , they found that the strain MEB193T represents a new species of the genus Nitrincola . The strain name is proposed as Nitrincola tapanii sp. nov. , in the honour of Dr. Tapan Chakrabarti for his enormous contribution in the field of microbial taxonomy and systematics. Five species of the genus Nitrinicola were described before this research. In conclusion, a new species surviving in an alkaline environment was described by researchers.

Reference: https://www.ncbi.nlm.nih.gov/pubmed/31751193