Pea plant shapes its rhizosphere microbiome for nutrient uptake and combating stress

-By Kranti Karande

Legume crops like Pea are used as rotation crops along with rice cultivation in long term conservation agriculture experiments in the acidic soils of the North East region of India. Rhizosphere microbiomes present in the soil have significant influence on plant growth and productivity. The study aims at understanding the bacterial composition of microbiomes present in bulk soil as compared to the rhizosphere. It also aims to understand how the pea plant influences the bacterial communities present in soil and the rhizosphere microbiome in order to improve nutrient uptake and stress improvement. Pea cultivation is a practice used in conservation agriculture which strives to preserve and enrich the environmental resources to sustain and improve crop productivity. The study conducted will help devise future strategies to expand pea cultivation and improve soil health in the region. 

Crop rotation is an important and effective strategy as part of conservation agriculture practices. The North East region of India is a fragile, marginal, inaccessible and diverse ecosystem. Generally a mono-cropping system of rice is followed in this region.  Zero tillage (without disturbing the soil) cultivation of pea (Pisum sativum L.) has been considered beneficial to enhance the cropping intensity in the region. The majority of soils in North-East India are acidic in nature. The pH of soil among many other environmental factors has a significant influence on the type of nutrients and microorganisms present in the soil which in turn have an influence on the productivity of crops. Similarly, nutrient and residue management practices like the application of chemical fertilizers often influence the endogenous microbial communities. 

Sample collection for the study was done from experimental fields of the ICAR Research Complex for NEH Region, Umiam, Meghalaya, located in Eastern Himalayan region. Different tillage and residue management treatments were maintained in these fields for the last eight years by alternatively cultivating rice followed by pea cultivation. For microbial community analysis, bulk soil and pea rhizosphere samples were collected from each treatment plot. All the samples were processed for community DNA extraction. Analysis of the chemical properties of the soil samples was done using available methods. Rhizosphere soils were harvested from roots of pea plants. 

Soil pH (1:2.5) was found to be influenced by tillage and nutrient management practices at depth  0-15 cm. The combined effect of tillage and nutrient management practices on available N, P and K content and SOC,TOC of soil were significant. The rhizosphere showed higher diversity indices in comparison to the bulk soil samples. A total of 71 bacterial phyla were detected in the bulk soil and rhizosphere samples. A higher abundance of Firmicutes was recorded in bulk soil (~41.7%) in comparison to the rhizosphere (~17.8%). On the contrary, Proteobacteria were highly abundant in the rhizosphere (~43.9%) in comparison to bulk soil (~18.6%) samples. Significantly higher abundance of Proteobacteria and Bacteroidetes was observed in pea rhizosphere samples in comparison to bulk soil. 

Impact of residue management practices on abundance of specific microbial communities was observed across both rhizosphere and bulk soil samples. The impact of tillage history was also observed on the enrichment of specific OTUs in the bulk soil and rhizospheric soil. Differences in the abundance of 11 genera were recorded in the rhizosphere sample across the history of different tillage treatment. All these genera showed higher abundance in the conventional tillage fields. The correlation between soil properties and microbial community structure was also studied as part of the study. Significant correlations were observed between relative abundance of few bacterial phyla & genera and soil properties in both bulk soil and rhizospheric soil samples. However, the number of significant correlations was low in rhizosphere samples, in comparison to bulk soil samples. 

The study was designed to investigate the effect of long-term exposure to various tillage and residue management practices on the bacterial community structures of the bulk soils and how pea plant (a rotation crop) shapes the rhizosphere communities. A higher species diversity and evenness was observed in rhizospheric samples. There was no significant difference in bacterial richness and evenness among different tillage and residue management treatments in both rhizospheric and bulk soil samples. This is an indication that the plant rhizosphere effect (a plant’s ability to alter microbial communities in rhizospheric soil) is the key driver of alpha diversity. Plants can alter the microbial communities by secreting a variety of nutrients and bioactive molecules into the rhizosphere. Enrichment of specific OYUs in the Pea rhizosphere were also confirmed which can be attributed to the selection pressure of the Pea root. The results of the Pea rhizosphere and bulk soils were consistent with the fact that the majority of members of microbial communities in the host plant are horizontally acquired from the surrounding environment, and the soil is the main reservoir of a plant rhizosphere microbiome. The genus Nitrobacter was at higher abundance in pea rhizosphere samples than bulk soils, suggesting its enrichment by the host plant as Nitrobacter converts nitrite to nitrate making nitrogen more readily available to the host plant. Higher abundance of genes related to nitrogen fixation, phytohormone and siderophore production, phosphate solubilization in the rhizosphere soil substantiate the conclusion that the selection of bacterial communities is always based on plant growth promoting potential in the rhizosphere. 

The study concluded that pea plant is the most dominating selection factor shaping the microbial communities under diverse residue management and tillage treatments. The rhizospheric soil was found to be enriched with bacterial taxa known for plant growth promotion which indicates that the plant plays a role in selecting the rhizospheric communities to meet its requirement of nutrient uptake and combating stress.


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.

Description of a novel species isolated from the surface of tomato

-By Kranti Karande

A new bacterial strain designated as TOUT106T was isolated from the tomato surface. Though there were many bacterial species isolated from various fruits and vegetables like sweet potato, banana, tomato, lettuce and cucumber, TOUT106T was found to represent a novel species. This study was aimed at providing a detailed taxonomic description of this novel strain TOUT106T isolated from tomato surface. A novel strain is a micro organism which hasn’t been identified earlier.

The strain was isolated by washing the outer surface of a tomato collected from a local vegetable market in Pune, India. Colonies grown on a trypticase soy agar turned out to be 1-3 mm in diameter, circular, raised with an entire margin, and translucent opacity. The identification was done using MALDI-TOF MS technique. After extracting high quality genomic DNA from the strain, the 16s rRNA sequence was amplified. The similarity search for the 16S rRNA gene sequence of strain TOUT106T was performed against the type strains of prokaryotic species in the EzBioCloud’s database. 

Genome sequencing was performed and from the concatenated sequences of 92 core genes extracted, a possible phylogenetic tree was inferred. The Average Nucleotide Identity (ANI) was determined between strain TOUT106T and closely related strains of the Enterobacteriaceae family. Analysis of chemotaxonomic features (based on fatty acids and cell proteins)was done after harvesting cell biomass from culture grown on TSA at 28°C.  Antibiotic susceptibility was determined using the disc diffusion method. The susceptibility to antibiotics was interpreted based on the Clinical and Laboratory Standards Institute (CLSI) guidelines determined for members of the family Enterobacteriaceae

A search of the 16S rRNA gene sequence of strain TOUT106T showed the highest similarity to Salmonella enterica subsp. arizonae strain NCTC 8297T (98.4 %) . The phylogenetic tree constructed based on the 16S rRNA gene sequence placed the strain TOUT106T within the Salmonella clade. The genomic DNA content of strain TOUT106T was well within the specifications of genus Klebsiella. Comparative analysis of ANI value and dDDH relatedness of Enterobacteriaceae strains suggested that the strain TOUT106T is a novel species.  A comparison of MALDI-TOF MS spectra based dendrogram showed that the strain TOUT106T separated from the type strains of Salmonella and was placed along with Klebsiella variicola DSM 15968T and Raoultella terrigena DSM 2687T, corroborating well with the results of genome-based analysis. Colony morphology, as examined on blood agar medium, were mucoid and translucent.

Based on different methods of identification, scientists reported that the strain TOUT106T is a member of genus Klebsiella. However, it differs from closely related species of the genus Klebsiella in several aspects, such as biochemical features, physiological features, protein profile, and overall genome relatedness indices. Thus, it represents a novel species in the genus Klebsiella, for which the name Klebsiella indica sp. nov. is proposed.

Klebsiella indica (in’ L. fem. adj. indica, of or belonging to India, where the type strain was isolated from the outer wash of a tomato collected from the vegetable market in India). Cells are Gram-negative, straight rods with round ends (0.7-0.9×2-3 μm), and non-motile. Colonies grown on trypticase soy agar are 1-3 mm in diameter, circular, and with translucent opacity. The optimal temperature for growth is 28 °C, and the optimal pH is 7.0. Growth occurs in the absence of NaCl with up to 2% tolerance in trypticase soy broth. It is weakly positive for catalase and negative for oxidase activity. It is susceptible to the majority of antibiotics. 

Reference :

Microbiome of indian patrilineal families reveal association with age

-By Kranti Karande

The human microbiome plays an important role in maintaining stable health conditions. It is influenced by age, geography, diet and other factors. This study was aimed at understanding the association of composition of the human microbiome with age in Indian joint families formed through paternal descendants. Oral, skin and stool microbiome of a total of 54 healthy individuals from 6 joint families with three generations were studied and characterized using 16S rRNA gene based methodology. The study population had matching dietary, social habits, hygiene and sanitation habits, economic status and geographic position.  This study highlights that precise and perceptible association of age with microbiome can be drawn when other causal factors are kept constant. 

Human microbiome has evolved with the host and its ancestors for millions of years and it plays an important role in maintaining a good health by performing various functions such as digestion, protection against pathogen colonization to host immunity and regulation of central nervous system. The human microbiome is affected by various factors such as ethnicity, age, diet etc. Hence, it is important to study the same population for the exploration of a precise association of age and microbiome. This study of genetically linked individuals of different generations having similar diet, ethnicity and location will help to understand the ability of microbiome to persevere with increasing age and how they progress with the age. 

Approximately 99% of the gut microbiome was constituted of 5 bacterial phyla. Total of 174 bacterial genera were noted to be present out of which 5 contributed to 77% of the gut microbiome. The oral microbiome showed comparatively higher abundance of some specific bacterial phyla.  Bacterial genera prevalent in 95% of the study population with more than 0.1% abundance were considered as a part of the core microbiome. Gut, Oral and skin microbiome had 3, 13 and 2 core microbiome genera present in the samples respectively. 

Microbiome community structure of gut, oral and skin samples was investigated across three generations (age groups). Gut microbiome of each generation had a unique set of bacterial genera present in abundance out of the prevalent genera for the specific age group. High abundance of few bacterial taxa was recorded in particular age groups in the skin microbiome samples also. Comparative microbiome analysis in three age groups did not show significant difference in abundance of bacterial genera in the gut and skin microbiome. However, the oral microbiome showed significant variations in the abundance of genera Dialister, Fusobacterium, Streptococcus, Selenomonas, Filifactor and Treponema. 

Age-associated changes in the microbiome were further analyzed based on differentially abundant OTUs (a methodology). After performing a correlation analysis it was revealed that phylum Proteobacteria in gut microbiome and phylum Fusobacteria in oral microbiome showed higher abundance with increasing age. However, in the skin microbiome, no such statistically significant correlations were noted. Amongst the total 171 bacterial genera in the gut microbiome, only genus Bacteroides showed age-associated changes. Decreased abundance of Bacteroides was noted with increasing age.

Dietary information of the study population was collected using the food frequency questionnaire (FFQ) and this information is subsequently translated into the daily intake of carbohydrates, proteins, fats, lipids, fibers and calories with the help of a nutritionist. Detailed analysis showed that carbohydrates provide about 74%, 81% and 80% calories in the first, second and third generation members, respectively. Further analysis showed no significant correlation across generations suggesting similar microbiome structure and dietary pattern. This emphasizes the fact that overall homogeneity in the diet helps in maintaining the microbial state.

Bacteria with high fiber degrading potential were found highly abundant in first generation members while the second generation members showed an abundance of metabolism boosting gut microbiome. Early gut colonizers and Bacteroides were higher in the third generation members. The skin microbiome also showed age related changes in abundance of bacterial taxa present. With the increasing age, physiological changes occur in the skin structure which explains the association of key bacterial taxa in the members of the respective age groups. Similarly, in the oral microbiome, Fusobacteria was found to increase with increasing age. It was observed that a negative correlation in the abundance of Bacteroides with age; this is in contrast to previous studies demonstrating the higher abundance of genus Bacteroides with increasing age. Age related changes in oral microbiome could be associated with physiological changes occurring with increasing age in the oral cavity. 

In conclusion, this study particularly highlights the precise and perceptible association of age with the microbiome. The findings suggest that core taxa constitute more than 75% of the gut and oral microbiome, while only 67% of the skin microbiome, indicating a larger variability of the microbiome present on the skin. The baseline data presented from a healthy Indian sub-population can be used as reference for further studies including diabetes, obesity and inflammatory diseases. 


Phytoplasma: A tiny microbe affecting multiple plant species

By Kranti Karande

Phytoplasma is a group of extremely small bacteria (mollicutes). They don’t have a cell wall and any particular shape (pleomorphic). Phytoplasma was first identified by a Japanese scientist Yoji Doi as ‘mycoplasma-like-organisms’ in 1967. They are bacterial parasites of plants and insects. Phytoplasmas reside in plant’s phloem tissue while insects serve as vectors for the transmission of infection from plant to plant. Once disease caused by phytoplasma is established, entire fields of crops might be wiped out. Indian sandalwood production has been drastically reduced due to phytoplasma infection during the last few decades.

The major characteristic symptom of phytoplasma-caused disease is abnormal growth of the floral organ,green flowers development (phyllody) and numerous growth of tree branches which appears like ‘Witches’ boom’ and reduction in leaf size called ‘little leaf’. Phytoplasma infection also causes curling and yellowing of the leaves (virescence). Disease caused by phytoplasma is called Sandalwood Spike Disease (SSD) in sandalwood plants, as leaves show growth in ‘spike-like’ structure. In few species of plants, such as onion and bamboo, the symptoms of witches’ broom and shortening of plant height (stunting) are observed due to phytoplasma infection.

Some plant pathogens produce virulence factors (effectors) that modulate or interfere with normal host processes for the pathogen’s benefit. Phytoplasma is reported to express secretory proteins including SAP proteins. The major obstacle limiting research in phytoplasma disease is that the organism is difficult to cultivate in vitro (laboratory cultivation).

Dr. Amit Yadav’s research group at NCMR, NCCS Pune is interested in understanding these pathogenic microbes which cause disease in over a thousand species of plants and affect agricultural productivity around the world. They’re interested in understanding genetic factors related to pathogenicity and phytoplasma transmission. They study phytoplasma taxonomy and the role of insect gut micro biome in vectoring ability of the insects.

It’s important to study the genome of this organism to understand how this tiny microbe causes infection in plants and gets transmitted through insect vectors. Phytoplasma DNA is difficult to isolate and then sequence it further, as researchers have not yet been active in this organism’s laboratory cultivation. Dr. Yadav’s research group is currently working on 40-45 symptomatic plants associated with phytoplasma infection. Recently, the group was successful in isolating and sequencing sugarcane phytoplasma. Dr. Yadav’s group is interested in studying other phytoplasma species that are prevalent in India; mainly associated with diseases in economically important pulse crops, sandalwood and weed species; and will be the first to publish phytoplasma genome sequence from India.

There is no cure yet available for this infection. Phytoplasmas are transmitted from plants to plants via the insect vectors. Weeds are also known to be secondary phytoplasma carriers. The weeds around the field are not eradicated by farmers, insects introduce phytoplasma to these weeds and then again to the new crop transmitting phytoplasma infection. Dr. Yadav’s group is also interested in studying the insects’ vector families and mechanism involved in the transmission of infection with Phytoplasma.

Some researchers are trying to understand if phytoplasma are beneficial for the insect vectors transmitting phytoplasma, and why some insects act as transmitters and some not.

Phytoplasmas have one of the smallest genomes as compared to other common bacteria. They completely rely on their host for nutrient supply, growth, spread and reproduction. “How organism with such a small genome affects over 1000 plant species is a curious question that drives me in this study,” said Kiran Kirdat, researcher from Dr. Yadav’s group. She also commented that “Dr. Yadav has been a great motivator for me”.

Dr. Yadav’s group has reported novel species of phytoplasma from various economically important plants like from Mango, Sandalwood, Sugarcane, Tamarind etc. Along with taxonomy study their research focus is also on understanding role of insect gut microbiome in the vectoring ability of these insects. They are interested in understanding the diversity of microbiota in the gut of insect vectors. The Wikipedia page of ‘Sugarcane Grassy Shoot Disease’ has been created by Dr Yadav and he has contributed significantly in other phytoplasma related article on Wikipedia.

Dr. Yadav said that, “People are more aware of phytoplasma associated diseases than a decade ago, when I started working on this notorious bacterium. However, much needs to be done further. Many crops like Sugarcane, Sesame, Sandalwood, coconut in India are facing great challenge to sustain due to phytoplasma infection. We are working on two different aspect to study phytoplasma; one is to understand how this pathogen spread the disease from one plant to other through insect vector and other is to study the genome of this organism to find out disease biology. We are also working on development of reliable and robust detection of phytoplasmas to help on field workers.”

Phytoplasma affects many economically important plant species and thus is a major threat to agriculture economy. Understanding the epidemiology of the phytoplasma diseases, pathogen and genomics of this tiny microorganism will help to cure the infection in future.  

Scientists report that delay in sample processing affect the cell viability

Dr. Avinash Sharma
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.


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.