Description of a novel genus and novel species isolated from the Rann of Kachchh.

Members of Rhizobiaceae are found in diverse ecosystems, including aquatic and marine ecosystems. Microbes belonging to genera Georhizobium, Hoefea, Lentilitoribacter, Martelella, Rhizobium, and Pseudorhizobium have been mainly reported from marine or aquatic environments. Rhizobium is one of the major genera in the family Rhizobiaceae. Currently, genus Rhizobium consists of 91 validly published species. The majority of Rhizobium species play key role in symbiotic fixation of nitrogen within the root nodules of leguminous plants. However, non-symbiotic and free living members of Rhizobium are found in various niches like soils, including the rhizosphere, bioreactor, lake water, arsenic-rich groundwater, and beach sand. Recently, different new genus names such as Allorhizobium, Pararhizobium, Neorhizobium, and Pseudorhizobium have been proposed in genus Rhizobium.

Rann of Kachchh (Google images)

Rann of Kachchh is the largest desert in the world and is a transitional area between marine and terrestrial ecosystems. This region experiences fluctuation in temperature. Due to the hot and hypersaline environment, there is a high probability of finding novel halophilic and halotolerant microorganisms with high economic and industrial potential in this region. The strain ADMK78T was isolated from the saline desert soil of Rann of Kachchh, it showed less than 98.7% 16S rRNA sequence similarity. The collaborative study conducted by the researchers at NCMR-NCCS Pune and UGC-Centre of Advanced Study, Sardar Patel University, Gujarat demonstrated the taxonomic position of strain ADMK78T through a polyphasic and genomic analysis.

The strain was isolated on Zobell Marine Agar following the serial dilution of the saline desert soil collected from the Rann of Kachchh, Gujarat. 16S rRNA phylogeny, whole genome sequencing and core-genes based phylogeny was studied. Physiology and chemotaxonomic analysis was also done.  The strain showed highest similarity to Rhizobium wuzhouense followed by Rhizobium ipomoeae. The sequence search resulted in more than 99% sequence similarity for two sequences. The first one was from an alpha-proteobacterium associated with Microcystis aeruginosa culture, and the second one was from Ciceribacter sp. isolated from low salinity lakes on the Tibetan plateau. Several species of Rhizobium were distantly placed from the core clade that contained the type species of the genus making it a non-monophyletic group. The genome size of this strain is 4,342,374 bp, which is smaller than the genome size of symbiotic members of Rhizobium and in the range of the sizes of the non-symbiotic strains of Rhizobium.

Phylogenetic analysis based on 92 core-genes extracted from the genome sequences and average amino acid identity revealed that the strain ADMK78T forms a distinct cluster including five species of Rhizobium, which is separate from the cluster of the genera Rhizobium and Ciceribacter. The study proposed re-classifcation of Rhizobium ipomoeae, R. wuzhouense, R. rosettiformans and R. rhizophilum into the novel genus Peteryoungia. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of ADMK78T were less than 82 and 81%, respectively, among all type strains included in the genus Peteryoungia. The strain ADMK78T showed differences in physiological, phenotypic, and protein profiles estimated by MALDI-TOF MS to its closest relatives. Based on the phenotypic, chemotaxonomic properties, and phylogenetic analyses, the strain ADMK78T represents a novel species, Peteryoungia desertarenae sp. nov. The strain is deposited at NCMR with accession number MCC 3400T. The study also proposed the reclassification of Rhizobium daejeonense, R. naphthalenivorans and R. selenitireducens, into the genus Ciceribacter, based on core gene phylogeny and AAI values.

Reference: https://pubmed.ncbi.nlm.nih.gov/33966089/

Antibiotic susceptibility study of human gut-derived facultative anaerobic bacteria

The human gastrointestinal tract is an ideal habitat for many microbes and obligate and facultative anaerobes are dominant microbes in the human-gut. The critical role of facultative anaerobes in host infections has been previously studied. The gut- microbiota is a key determinant in the defensive action of the host’s intestinal barrier, and in immunocompromised individuals, disruption of GIT homeostasis leads to gut dysbiosis. This changes the conditions which commensal microorganisms experience and can lead to a shift in microbial opportunistic pathogenicity. With few exceptions, most human pathogens are facultative anaerobes. Under oxic conditions facultative anaerobes respire oxygen and switch to anaerobic respiration or fermentation in oxygen-deprived conditions. Antibiotics are the best option to treat bacterial infections, and antimicrobial susceptibility testing is the method to determine the susceptibility of a pathogen to identify the appropriate antibiotic therapy. Generally, appropriate antibiotic concentrations for treatment are determined by AST and MIC testing under in vitro aerobic conditions. However, the possibility that the target pathogen may respond differently to antimicrobial compounds under anaerobic conditions has been neglected.

A study conducted by group of Dr. Om Prakash Sharma at NCMR-NCCS Pune reported that microorganisms isolated from human gut respond in different way to some antibiotic drugs in the presence or absence of oxygen, and the minimum inhibitory concentration values are significantly different between oxic and anoxic growth conditions. This study is highlighted in the Journal of Microbes and Infection. This was reported by analyzing 17 bacterial strains from 15 genera of facultative anaerobes isolated from the human-gut. Facultative anaerobes cause infections in anoxic parts of the human body like deep wound, gastrointestinal tract, lungs etc. Generally, antibiotic susceptibility tests for facultative anaerobes are performed under aerobic conditions due to ease of handling and rapid growth. However, variations in susceptibility of facultative anaerobes to antibiotics under aerobic and anaerobic conditions can lead to failure of antibiotic treatment. This study evaluated the susceptibility of facultative anaerobic microorganisms to antibiotics during growth under anaerobic or aerobic conditions.

A total of 17 facultative anaerobic bacterial strains from the feces of a healthy individual were selected for antibiotic susceptibility testing under aerobic and anaerobic conditions. The 17 strains belonged to 15 different genera and 3 different phyla and represent a broad phylogenetic range of organisms present in the human gastrointestinal tract. Of the tested strains, variable susceptibility to antibiotics under aerobic and anaerobic conditions was observed in 10 of 17.  As there are very few prior studies examining differential antimicrobial susceptibility under aerobic and anaerobic conditions, there is no equivalent susceptibility data for selected organisms and antibiotics combination in database for comparison.

Bacterial strains from the genera Streptococcus, Pellistega, Enterobacter, Lactococcus, Klebsiella, Bacillus and Arthrobacter showed similar resistance patterns for each antibiotic under aerobic and anaerobic conditions and did not meet the criteria for further analysis. Differential antimicrobial susceptibility was observed for at least one compound in bacterial strains from the genera Mixta, Weissella, Enterococcus, Micrococcus, Staphylococcus, Enterobacter, Bacillus (tequilensis), Kocuria, and Kluyvera. Significantly lower MIC values under aerobic conditions relative to anaerobic conditions were observed for Enterococcus faecalis and Enterobacter hormaechei subsp. steigerwaltii in the presence of cefixime. Similarly, significantly lower MIC values under aerobic conditions relative to anaerobic conditions were observed for Mixta calida, Staphylococcus hominis and Weissella cibaria when in the presence of cefpodoxime. Conversely, significantly higher MIC values in aerobic conditions relative to anaerobic conditions were observed for Kluyvera cryocrescens in the presence of ceftriaxone. The MIC of Kocuria indica was significantly higher for ceftriaxone in anaerobic conditions relative to aerobic conditions.

Researchers compared the resistance patterns of representative microbes from 15 bacterial genera isolated from the human- gastrointestinal tract against 22 different antibiotics from six classes under aerobic and anaerobic conditions. Preliminary results obtained by a disc diffusion method were verified using minimum inhibitory concentration (MIC) testing. The results demonstrated that 7 strains had a similar pattern of drug resistance under both conditions, while the remaining 10 strains had significant differences in resistance patterns between aerobic and anaerobic conditions for at least one antibiotic. The study concluded that successful antibiotic therapy requires proper analyzing of the oxygen condition of the growth environment and MIC testing of each pathogen under anaerobic and aerobic conditions.

Reference: https://www.sciencedirect.com/science/article/pii/S1286457921000691

Comparative study of 16S rRNA gene databases of known strain sequences

A collaborative study was conducted by researchers at SSBS Pune, NCMR Pune and Reliance Lifesciences Pvt Ltd Mumbai, benchmarking of 16S rRNA gene databases using known strain sequences. They used authentic and validly published 16S rRNA gene type strain sequences and analyzed them using a widely used QIIME open-source bioinformatics pipeline along with different parameters of OTU clustering and QIIME compatible databases. Limited differences were observed in the reference data set analysis using partial and full-length 16S rRNA gene sequences in microbiome studies. The analysis highlighted common discrepancies observed at various taxonomic levels using various methods and databases.

16S rRNA gene analysis is the most convenient and widely used method for microbiome studies. Inaccurate taxonomic assignment of bacterial strains might affect the results as all downstream analyses rely heavily on the accurate assessment of microbial taxonomy. A large number of databases and tools available for classification and taxonomic assignment of the 16S rRNA gene make it challenging to select the best-suited method for a particular dataset.  This study was done to benchmark the 16S rRNA gene databases using known strain sequences.

Next-Generation Sequencing (NGS) techniques are capable of generating high quality, comparable data. Different methods are used to overcome the limitations regarding 16S rRNA gene analysis. However, though mock microbial communities serve the purpose of estimating sequencing errors, they mostly represent minimal diversity. They thus cannot be used as a standard for taxonomic identification by analysis pipeline and databases. Thus it is necessary to have 16S rRNA gene analysis pipeline validated using a standard data set with known taxonomic identification.  

The sample dataset used in this study was obtained from an authentic database and the sample size that is the number of 16S rRNA sequences was 5395. In this study, researchers used authentic and validly published, type strain, full length and partial 16S rRNA gene sequences. These sequences were compared against various databases with QIIME pipeline, which incorporate various algorithms for quality control, clustering similar sequences, assigning taxonomy, calculating diversity measures and visualizing. They used 16S rRNA gene sequences of type strains obtained from the RDP database as it allows the option to download the bulk dataset. Three different databases were used for microbiome analysis, namely Greengenes, SILVA, and EzTaxon which are used for 16S rRNA gene-based microbiome studies.

Comparative analysis showed that higher numbers of OTUs were obtained for a 99% identity threshold compared to the 97% identity threshold for the respective combination of the database used. A total 18.78% and 10.53% discrepancy was observed at the genus level for the full length and partial sequences, respectively, which is a high amount of discrepancy. The discrepancy at each taxonomic level can be calculated, and the quality of data present in the database can be decided. It is crucial to select databases, pipelines, and algorithms very carefully considering discrepancies in taxonomic assignment and selection should be done based on the necessity of the study. Also, databases should be validated, and discrepancies should be corrected in successive updates of databases.

Primary goal of all microbial studies is to identify the bacteria that constitute the complex communities. A valid and reliable method is a must for identifying these complex communities. The purpose of this study was to validate widely used databases like EzTaxon,  SILVA, Greengenes and data analysis pipelines like QIIME .

Reference: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8131573/

Study of probiotic potentials of microbial communities associated with fermented foods of northeast India

Probiotics are described as “Live microorganisms which when administered in adequate amounts confer a health benefit on the host”. Probiotics are commonly consumed functional food. Probiotics are reported to improve the immunological and gastrointestinal functions, it also plays role in reducing the risk of cancer and cardiovascular diseases.

Ethnic fermented foods have been consumed since ancient times with the notion that they provide health advantages and could be a source of probiotics. We know very little about microorganisms involved in the fermentation process of these foods. A study was conducted by team of Dr. Avinash Sharma at NCMR-NCCS Pune to understand the microbial community associated with the ethnic fermented food from northeast part of India, using high throughput sequencing approach. Three ethnic fermented foods were chosen as samples: ‘Axone’, ‘Bastenga’ and ‘Chathur’. Food specific enrichment of bacterial genera was observed as Lactobacillus (90.7%) in ‘Axone’, Bacillus (62%) and Clostridium (15.9%) in ‘Bastenga’ and, Lactobacillus (47.8%) and Staphylococcus (36.3%) in ‘Chathur’, whereas Saccharomyces (98.7%) belonging to phylum Ascomycota predominates the fungal communities among all the samples.

Three different ethnic fermented food preparations were sampled in triplicates from a local household in Manipur and Nagaland, states of North East India. The ‘Axone’ or ‘Glycine max’, a preparation made of fermented Soybean and the ‘Bastenga’, a fermented bamboo shoot were collected from Dimapur, Nagaland, whereas ‘Chathur’ a locally brewed beer out of fermented rice was collected from Ukhrul, Manipur. Amplicon sequencing approach was employed by targeting V4 region of 16S rRNA and ITS gene to identify the consortia of bacteria, yeasts and molds. Further, the research team screened the probiotic potential of microbial communities associated with these food preparations by using approach of metagenomic imputation followed by mapping against set of known genes catering probiotic properties.

Bacterial diversity study revealed that ‘Axone’ have least diversity of microbes while ‘Chathur’ represents most diverse sample. Assessment of fungal communities indicated ‘Chathur’ being highly diverse while ‘Bastenga’ representing least diverse sample. Investigation of bacterial community composition revealed predominance of bacterial phylum Firmicutes followed by Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes and Fusobacteria accounting for 99.9% of bacterial communities. The samples Axone and Bastenga contain Firmicutes as the main phylum with relative abundance of 98.4% and 99.2%, respectively. In contrast, Chathur comprises of Firmicutes (81.1%) and Proteobacteria (10.1%) as the most abundant phyla.

Interestingly, Lactobacillaceae dominates in Axone , whereas Chathur harbors Lactobacillaceae , Clostridiaceae and Bacillaceae as the major constituents. Further, Bastenga comprised of Bacillaceae and Staphylococcaceae. Likewise, at genera level Lactobacillus out numbers other bacterial members for the Axone. Genera Lactobacillus and Bacillus were found to dominate in case of Chathur and Bastenga , respectively. Additionally, Chathur consists of Clostridium, Bacillus ,Pediococcus, Streptococcus, Geobacillus, Staphylococcus, Weissella whereas Bastenga comprises of Staphylococcus being the second most prevalent taxa.

The use of high throughput sequencing to investigate ethnic fermented foods gives key info on microbial community structure, especially major contributors associated to fermentation processes. The findings of this work indicate that integrating culture-dependent techniques and comparative genomics, it may be possible to identify indigenous probiotic candidates.

Reference: https://www.sciencedirect.com/science/article/pii/S0023643821007313

Study of skin microbiota in leprosy patients from India

Mycobacterium leprae (Wikipedia)

Leprosy is one among serious skin infection diseases present worldwide. Leprosy is associated with significant social stigma that renders the life of affected individuals difficult and isolated. Leprosy is caused by Mycobacterium leprae with a chronic granulomatous infection of the peripheral nerves along with the skin. The disease is characterized by damage of the peripheral nerves, mucous membranes, eyes and skin. Untreated skin especially on the face thickens because of dermal infiltration giving rise to the ‘leonine faces’. Skin is the primary organ affected in leprosy patients, though the role of skin microbiome in pathogenesis is not very well studied. One of the recent studies have shown that skin of leprosy patients harbors perturbed microbiota which grants inflammation and disease progression.

Researchers conducted a collaborative study in order to understand the lesional and non-lesional skin microbiota in leprosy patients. Different experimental techniques were used for conducting this study. DGGE is a molecular sequence dependent fingerprinting technique that allows characterization of the microbiota from large number of skin samples without pre-existing knowledge of its composition. In this study, nested PCR-DGGE and a comprehensive computational analysis for the microbial diversity exploration present in skin swab samples collected from LS and NLS sites was done. The overall objective of the study was to catalogue and compare the skin microbial communities present in healthy control with those in lesional skin (LS) and non-lesional skin (NLS) sites of Leprosy patients. According to the researchers, the results obtained from this study can potentially be used for generating preliminary hypotheses about interaction between disease causing microorganisms, microbial co-inhabitants and pathophysiology of the disease in leprosy patients.

A comprehensive analysis of 16S rRNA profiles was done, corresponding to skin samples from participants located in two geographical locations in India, Hyderabad and Miraj. Study participants were chosen from well-established leprosy research centers located in two geographically well-separated locations in India in order to understand if any variability occurs as a result of differences in food, climate and lifestyle. The genus Staphylococcus was one of the representative bacteria in healthy controls while it was underrepresented in skin microbiota of leprosy patients. Taxa affiliated to phyla Firmicutes and Proteobacteria were found in abundance in healthy controls and lesional skin, respectively.

While the NLS microbiota for LP from both Hyderabad and Miraj indicated the presence of similar microbiota with bacteria belonging to genus Canibacter, Corynebacterium, Cutibacterium, Janibacter, Moraxella and Staphylococcus, samples of LP from Miraj were observed to additionally harbour Bacillus, Methylobacterium, Microvirga, Paracoccus and Staphylococcus. Some of the important genera found in Hyderabad subjects were Canibacter, Corynebacterium, Cutibacterium, Janibacter, Moraxella and Staphylococcus while Miraj subjects had Bacillus, Methylobacterium, Microvirga, Paracoccus and Staphylococcus genera. Taxonomic analysis indicates presence of few taxa having distinct abundance trends between healthy control (HC) and leprosy patients (LP) : Acinetobacter, Corynebacterium, Kocuria, Micrococcus, Paracoccus, Propionibacterium, Staphlococcus were observed to be the most abundant common taxa in samples from both Hyderabad and Miraj.

Network analysis study reveals signature differences in microbial co-occurrence patterns in datasets corresponding to HC and LP. The skin lesions occurring on the lesional and non-lesional skin surface has analyzed some sort of abnormalities.  The abnormalities were structured to undergo through experimental sites that are lesional and non-lesional sites, and understand the severity of the disease.

Observed diversity level changes, shifts in core microbiota, and community network structure support the evident dysbiosis in normal skin microbiota due to leprosy. Insights obtained indicate the need for exploring skin microbiota modulation as a potential therapeutic option for leprosy.

In order to understand the detailed results in this study please refer: https://www.nature.com/articles/s41598-020-80533-5

Study of microbiota in biomass and tobacco smoke associated lung disease

Chronic Obstructive Pulmonary Disease (COPD) is a disease of public health concern globally. It is the third leading cause of death worldwide, and the second leading cause in India. Tobacco and biomass smoke are the main causes leading to different lung diseases. Chronic exposures to tobacco smoke and biomass smoke have been shown to be associated with the risk of developing COPD. In India, there is high prevalence of COPD due to biomass smoke and tobacco smoke exposure. Microbial diversity in tobacco-smoke associated COPD has been studied earlier, microbiota in biomass smoke associated COPD was not yet explored.

A collaborative study was conducted by researchers at KEM hospital Pune, NCMR Pune and Chest Research foundation Pune to understand the biomass and tobacco smoke associated microbiota in COPD. It was not well studied whether there is a difference in the microbiota between healthy subjects and biomass smoke-associated COPD (BMSCOPD) subjects and between BMSCOPD and tobacco smoke-associated COPD (TSCOPD) subjects. The aim of the study was to compare nasal and oral microbiota between healthy, TSCOPD and BMSCOPD from rural population in India. This study suggests that disruption or imbalance in microbial community happens which may further contribute to the progression of COPD.

Study subjects were recruited from the population of KEM Hospital research centre, Vadu, HDSS . Subjects who were diagnosed with COPD were randomly selected from the cohort of COPD subjects. Nasal swabs and oral washings were collected from all the 31 subjects. Amplicon sequencing of bacterial 16S rRNA gene, bioinformatics and statistical analysis was done.

Results indicated that microbial communities differed significantly between nasal and oral samples. Greater diversity and higher interindividual variations were observed in nasal samples as compared to oral samples. The findings also indicated that, not all but few specific taxa contribute to the alteration in microbial community structure from healthy to disease state.

To compare the microbial diversity between healthy and disease state, all the COPD samples (TSCOPD and BMSCOPD) were pooled together and compared with healthy subjects. In the nasal samples, researchers found significant increase in the abundance of Actinomyces, Actinobacillus, Megasphaera, and Selenomonas in COPD group, whereas Propionibacterium was significantly higher in the healthy subjects. In the oral samples, they noted a significant increase in the abundance of Corynebacterium, Selenomonas, and Actinomyces among COPD subjects compared to healthy subjects. In the nasal samples, they found a significantly higher abundance of the phyla Planctomycetes and Armatimonadetes in TSCOPD as compared to BMSCOPD, while Acidobacteria were significantly abundant in BMSCOPD as compared to TSCOPD in the oral samples. Between healthy and BMSCOPD, in nasal samples, they found that 15 genera were significantly different in their abundance between the healthy and BMSCOPD. In oral samples, they found 14 genera which were significantly diferent in their abundance between the healthy and BMSCOPD. A significant difference was found for Haemophilus in oral samples.

It is the first study that has examined differences in the nasal and oral microbiota between healthy, TSCOPD, and BMSCOPD subjects in an Indian rural population. Although there were no significant differences in the overall microbial community structure, they reported significant differences in the microbiota in some key taxa between healthy and COPD subjects and also between TSCOPD and BMSCOPD subjects. Between healthy and COPD subjects, they reported a significant increase in the abundance of Actinomyces, Actinobacillus, Megasphaera, and Selenomonas in the nasal samples of COPD subjects, while Corynebacterium, Selenomonas, and Actinomyces were found to be increased in the oral samples of COPD subjects. Between TSCOPD and BMSCOPD subjects, they reported that Gallibacterium and Methanosaeta were significantly higher in the nasal samples of BMSCOPD subjects, while Acinetobacter was significantly higher in the oral samples of TSCOPD subjects.

The difference in the bacterial communities in BMSCOPD and TSCOPD suggests difference in pathophysiology of the disease and also suggests clinical phenotypic differences between these two groups. Thus, the pathophysiology of TSCOPD and BMSCOPD may differ due to the differences in microbial communities and, this should be considered carefully before designing the treatment method for COPD.

Reference: https://link.springer.com/article/10.1007/s00203-020-02155-9#:~:text=Chronic%20exposures%20to%20tobacco%20smoke,cavities)%20(Charlson%20et%20al.

On the Occasion of upcoming National Science Day 2021!

National Science Day is celebrated in India every year on February 28. The day is celebrated to commemorate the discovery of Raman Effect by Sir C.V. Raman on the same day in 1928. Sir C.V. Raman was awarded the Nobel Prize in Physics in 1930 for this important discovery. The Government of India honored him with the highest civilian award, the Bharat Ratna in 1954. The very first National Science Day was celebrated on February 28, 1987.

The objective for celebration of this day is to inspire students about science, spreading the knowledge related to science, scientific activities and scientific achievements. Many events are organized on this day to popularize Science and Technology. The theme for the National Science Day 2021 is ‘ Future of STI: Impact on Education, skills and work.’

Every year NCMR-NCCS Pune arranges Microbial exhibition for school students to celebrate National Science Day, which is not possible this year due to covid-19 situation. On the Occasion of upcoming National Science Day, we are taking an opportunity to describe National Centre for Microbial Resource (NCMR), the largest culture collection of the world.

National Centre for Microbial Resource (NCMR) is a national microbial facility funded by Department of Biotechnology (DBT), Government of India and is affiliated with National Centre for Cell Science (NCCS) Pune. NCMR started as Microbial Culture Collection (MCC) in 2009 has an authorization to preserve and catalogue diversity of microorganisms collected from different ecological niches from all over India and to make them available for exploitation by researchers. NCMR supplies authentic cultures of archaea, bacteria, fungi and plasmids to both academic institutions and industry.

The aim of the Centre is to serve as a leading world-class Microbial Resource Repository and to provide authentic high-quality services for microbial preservation, characterization and authentication and supply to industry and academic institutions. The Centre is built on “Service for Science, Science for Service” model. It is serving the nation in biodiversity conservation, biotechnological research and education by providing services of the highest international standards and conducting research in the related areas of microbial ecology and systematics, and human resource development. The Centre is serving as an International Depositary Authority (IDA) under the Budapest Treaty and Designated National Repository under Ministry of Environment and Forests.

To know more about scientific activities of NCMR , visit: http://210.212.161.138/home

Happy National Science Day 2021!

A novel species isolated from Queen Maud Land, Antarctica

Scanning electron micrograph of Marisediminicola senii

-By Kranti Karande

Antarctica is Earth’s southernmost continent, which is beautifully covered by snow and ice. It is coldest continent with extreme environmental conditions. Antarctica was once thought to be frozen and lifeless, and is now known for its biodiversity where microbial life is thriving. Its important to understand the microbial diversity on this continent as microorganisms play an important role in the functioning of Antarctic ecosystems. A type strain was isolated from glacier sediment sample collected from the Queen Maud Land, Antarctica, during the 38th Indian Scientific Expedition to Antarctica in 2019. Research group of Dr. Avinash Sharma at NCMR-NCCS Pune studied the characteristics of the isolated strain.

Dr. Avinash Sharma collecting sample at Antarctica

Distinguishing characteristics based on the polyphasic analysis indicated the strain as a novel species of genus Marisediminicola for which the name Marisediminicola senii sp. nov., is proposed. The strain is named as Marisediminicola senii in the honor of late Mr. Subhajit Sen, a researcher from India who lost his life in an accident during the 37th Indian Scientific Expedition to Antarctica in 2017. Mr. Sen’s research in Antarctica was focused on fabric analysis of glacial deposits.

Marisediminicola senii sp. nov., with accession number MCC 4327 (Type strain) is now stored at NCMR along with other approximately two lakh microbes. The National Centre for Microbial Resource (NCMR) has an authorization to preserve and catalogue the diversity of microorganisms collected from various ecological niches in India and to make them available for research use.

Reference: https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.004641

Microbes sustaining climate change by oxidizing ammonia and sulfur in an Arctic Fjord

Microorganisms play an important role in the ecological balancing of extreme ecosystems. Over the last few years, polar regions have been affected by global warming and extinction of native species. The archaeal and bacterial communities have a very significant and interchangeable role in the nitrogen and sulfur cycling as they perform biological oxidation of ammonia and sulfur. A study was conducted to understand the microbial communities present at different oceanic depths of Krossfjorden with the help of high throughput sequencing methods. The aim of the study was also to decipher the role of microbial communities in the oceanic biogeochemical cycling with focus on ammonia and sulfur cycling.

The sediment samples were collected in triplicates from Krossfjorden (Norway) during the arctic summer. DNA extraction and further amplicon sequencing and analysis was done. The data suggested that bacterial communities are prevalent at the middle and lower sediments while archaeal communities are mainly present at the middle sediment. Thaumarchaeota population was predominant followed by Crenarchaeota, Euryarchaeota, Woesearchaeota and Marine Hydrothermal Vent Group. The study indicated major microbial biomass comprising of Proteobacteria, Bacteroidetes, Verrucomicrobia, Actinobacteria, Chloroflexi and Lentisphaerae, along with Marinicella, Desulfobulbus, Lutimonas, Sulfurovum and clade SEEP-SRB4 as major members of surface sediments. Interestingly, Bacteroidetes, Firmicutes, Verrucomicrobia and Lentisphaerae were found to be dominant members at lower depth (~180 m), while Proteobacteria, Actinobacteria and Planctomycetes showed more profusion at depth of ~250 m which can be related to its maximum activity at relatively higher depths in the Arctic. Similarly, Fusobacteria, Chloroflexi and Acidobacteria outnumbered other bacterial phyla at the depth of ~300 m. The genera Psychrilyobacter, Psychromonas, Marinifilum were observed in this study are likely to be involved in the hydrolysis and fermentation of spirulina forming volatile fatty acids, mainly acetate which is later utilized by sulfate-reducing bacteria. Sequences related to sulfate-reducing bacteria like Desulfobacteraceae and Desulfobulbaceae were detected in this study which are known for the acetate mineralization. Besides that, the abundant proportion of sulfur oxidizers Sulfurovum, Sulfurimonas from Epsilonproteobacteria was observed which could grow chemolithoautotrophically, which implies its ability to survive in nutrient-deprived conditions.

The study also indicated that archaeal communities across all depths of the fjord were found to engage in ammonia cycling. The bacterial communities showed divergence in the gene abundance of ammonia and sulfur cycling along the different depths. Members of Thaumarchaeota from the domain archaea have the ability to oxidize ammonia and are present ubiquitously in soil, ocean and extreme environments. Members
of Desulfobulbus that reduce both iron and sulfur were observed in this study known for the potential to reduce iron oxide. Sulfurovum and Sulfurimonas belong to the Epsilonproteobacteria and are known for their important role in sulfur cycling in marine and other aquatic environments . The predominance of Sulfurovum with a significant proportion of Sulfurimonas at this site may play the crucial role in the sulfur cycle as Sulfurovum is known to grow chemolithoautotrophically using hydrogen, sulfur, and thiosulfate as an electron donor while oxygen, nitrate, thiosulfate, and sulfur as an electron acceptor.

The study provided a detailed insight into the microbial community composition at Krossfjorden and understanding their metabolic fate. The study also tried to understand the potential of the microbial community to oxidize ammonia and Sulfur at different sites of Arctic fjord by targeted metagenomics.

Reference: https://www.sciencedirect.com/science/article/abs/pii/S0888754320320024

Description of a novel taxon associated with Sugarcane Grassy Shoot (SCGS) disease

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. Sugarcane is the world’s fourth largest and commercially important crop. Sugarcane Grassy Shoot disease is related to Rice Yellow Dwarf (RYD) phytoplasma which occurs in sugarcane growing countries throughout the world.

The major characteristic of SCGS disease are stunting, profuse tillering, side shoots, chlorotic stripes and bleached white leaf blades. The common symptoms of SCGS in sugarcane plant are narrowing and partially or almost chlorotic leaf lamina, excessive tillering and witches’ broom symptoms. Severely infected younger plants appear yellowish. The phytoplasma infection often leads to stunted growth, reduction in leaf size, and excessive proliferation of shoots.

Complete leaf chlorosis in SCGS disease &
Grassy appearance of phytoplasma-infected sugarcane plant

It’s important to study the genome of phytoplasma 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. Recently, the researchers at NCMR Pune successfully isolated and sequenced sugarcane phytoplasma. In this study, researchers demonstrated the phylogenetic position of 16SrXI-B group phytoplasmas by characterizing the phytoplasma strain associated with Sugarcane Grassy Shoot (SCGS) disease based on comparative genome features and phylogenetic analyses with its closely related phytoplasma taxa and proposed a novel ‘Ca. Phytoplasma’ taxon. This study is the first description of phytoplasma from India and the first description of phytoplasma species based on genome sequences.

Reference: https://pubmed.ncbi.nlm.nih.gov/33289626/