A novel species isolated from Queen Maud Land, Antarctica

Scanning electron micrograph of Marisediminicola senii

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. 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.

Cells of the isolated strain are Gram-stain-variable, aerobic, cocci shaped with sizes of 0.2–0.3µm in diameter. Strain is catalase positive and oxidase-negative. Colonies formed on Zobell marine agar are orange, raised, circular, translucent and ~3mm in diameter after incubation for 7 days at 20°C. Nitrate and nitrite are not reduced by the strain. Strain was negative for indole production, H2S production and could not hydrolyze urea and gelatin. However, strain hydrolyses aesculin. Strain shows positive result for 4-nitrophenyl-β-d-galactopyranoside while negative for l-tryptophan, d-glucose, l-arginine, d-glucose, l-arabinose, d-mannose, d-mannitol, N-acetyl-glucosamine, maltose, potassium gluconate, capric acid, adipic acid, malic acid, trisodium citrate, phenylacetic acid. Only d-glucose, methyl-α-d-mannopyranoside were utilized as carbon sources. Strain is positive for esterase, esterase lipase, leucine arylamidase and valine arylamidase and weakly positive for cysteine arylamidase. Strain consists of diphosphatidylglycerol and phosphatidylglycerol as major polar lipids.

Phylogenetic analysis based on 16S rRNA gene sequences revealed highest sequence similarity of the strain with Marisediminicola antarctica ,demonstrated distinct phylogenetic positioning of strain within the genus Marisediminicola. 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.

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/

Understanding microbial salt-stress biology through “omic” approaches

Halotolerant microorganisms are capable of growing in the absence as well as in the presence of relatively high salt concentrations. The biology of the salt affected habitats is studied using high throughput “omic” approaches consisting of metagenomics, transcriptomics, metatranscriptomics, metabolomics, and proteomics. The study of Metagenome-assembled genomes of uncultured halophilic microbes has uncovered the genomic basis of salt stress tolerance in “yet to culture” microorganisms. Also, functional metagenomic approaches have been used to decipher the novel genes from uncultured microbes and their possible role in microbial salt-stress tolerance. A recently published collaborative review helped in understanding microbial salt-stress biology and it also summarized the key molecular processes contributing to microbial salt-stress response.

Microorganisms employ two different strategies to adjust to hypersaline conditions: ‘salt-out’ strategy and ‘salt-in’ strategy. ‘salt-out’ strategy is adopted by halotolerant microbes while ‘salt-in’ strategy is common in halophiles. The review article described the important genes governing microbial halotolerance. The description of many genes, gene clusters or operons that are reported to play an important role in microbial salt-stress response are mostly related to compatible osmolyte biosynthesis. Ectoine biosynthesis gene cluster is considered as a potential marker gene for halotolerance in bacteria. A brief and comprehensive description of genes related to compatible osmolyte biosynthesis, along with their encoded enzymes is presented in the review.

Ectoine biosynthesis: an osmoadaptive response to salt stress is reported in bacteria and is conventionally believed to be absent in Archaea, and Eukarya. The annotation of the genome sequences of ammonia oxidizing archaea has first time lead to the observation about the presence of genes for ectoine biosynthesis even in ammonia-oxidizing archaea. Later, ectoine biosynthetic genes were observed in methanogen genome as well. But the mere presence of the ectoine biosynthesis genes in the genomes of archaea and methanogen does not imply that these genes are functional and ectoine synthesis do exist in Archaea. Further genomic and molecular studies uncovered the uncommon instance of ectoine biosynthesis in Archaea.

Microbes adopting ‘high salt-in’ strategy, display different genomic features. The ‘salt-in’ strategy is well documented in haloarchaea and extremely halophilic bacteria like Salinibacter ruber. The genome of obligate halophiles adopting ‘salt-in’ strategy possess distinct genomic and molecular features supporting a halophilic lifestyle. Most of the halophiles have highly acidic proteome. The halophiles relying on ‘salt-in’ strategy have evolved unique molecular features that differentiate them from microbes adopting ‘salt-out’ strategy for halotolerance.

Genome-resolved metagenomics offer a great opportunity to explore the niche adaptation and metabolic potential of uncultivated microbes. The MAGs obtained can serve as the blueprint for understanding the physiology and salt-stress adaptation strategies of uncultured microbes. The metagenomic genome reconstruction has been applied to recover the genomes of uncultured halophiles.

Using functional metagenomic approach, molecular basis of halotolerance in uncultured microbes is studied. The halotolerant metagenomic clones are studied for the identification and characterization of genes present in metagenomic DNA insert which actually renders the salt tolerance to such metagenomic clones. The techniques like transposon mutagenesis are also used to confirm the role of identified genes in halotolerance. A number of salt-tolerant genes are identified using functional metagenomics. But there are few limitations to metagenomics approach. The major limitation is because many genes/ORFs imparting salt stress tolerance to metagenomic clones, tend to annotate as the hypothetical protein and some even do not show similarity to any other known protein in the database.

The review also covered the detailed transcriptomic studies in microbial halotolerance research like microarray-based gene expression studies for salt-stress response and next-generation sequencing-based transcriptomic studies. The review also provide proteomic insights into microbial halotolerance, metabolic basis of microbial salt-tolerance.

“Omic'”-based microbial halotolerance research suffer few shortcomings like scarce information about halophiles confronting low salt conditions, halophiles warranting reassessment of ‘salt-in’ and ‘salt-out’ delimitations etc. The review concludes that the “Omic” landscape of microbial salt stress tolerance is as vast as the salt afflicted habitats on the earth landscape. It is important to undertake detailed and comprehensive studies that can generate in-depth data at different “Omic” levels on a single biological sample, in order to generate the systems biology view of microbial salt-stress tolerance

Reference: https://www.tandfonline.com/doi/full/10.1080/1040841X.2020.1819770

A novel species isolated from a bacterial consortia of contaminated soil enriched for the remediation of e-waste

The genus Pseudomonas is widespread and has been reported to occur in diverse ecological niches. Members of the genus Pseudomonas are metabolically versatile and harbor various biotechnologically important properties. Pseudomonas sesami is reported to have plant growth-promoting activity. Strains of Pseudomonas produce thermotolerant proteolytic and lipolytic enzymes which result in food spoilage. Pseudomonas putida, Pseudomonas furukawaii, Pseudomonas knackmussii and many other pseudomonads have been reported for the remediation of xenobiotic compounds. In the present study, researchers at NCMR-NCCS Pune report the detailed characterization of a Pseudomonas strain, which was isolated from soil samples from Lalkuan, Nainital, Uttarakhand, India. The strain was found to be part of the bacterial consortia obtained for developing remediation of e-waste.

The strain was Gram-stain-negative, rod-shaped, aerobic, oxidase-positive and catalase-positive. Colonies are L-form with entire margins, creamy color, umbonate elevation and non-mucoid. Cell can tolerate up to 3% salinity. Based on 16S rRNA gene sequence the strain belongs to the genus Pseudomonas and showed highest sequence similarity to Pseudomonas furukawaii followed by Pseudomonas aeruginosa and Pseudomonas resinovorans. The G+C content in the genome was 64.24mol%. The phylogenetic analysis revealed that the strain forms a distinct clade in the family Pseudomonadaceae. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The phenotypic, chemotaxonomic and genetic analysis, including overall genome relatedness index values, indicated that the strain represents a novel species of the genus Pseudomonas, for which the name Pseudomonas lalkuanensis sp. nov. is proposed.

The cells of the strain were motile as observed by using the hanging drop method. The oxidase and catalase activities were investigated using an oxidase disc and observing bubble production. The phylogenetic analysis showed that strain formed a separate clade with P. resinovorans keeping P. furukawaii and P. aeruginosa in an outer clade with strong bootstrap support. This phylogenetic analysis reveals that the strain is phylogenetically distinct from P. furukawaii and P. resinovorans. The orthoANI and dDDH values of the strain were clearly below the thresholds for the proposal of novel prokaryotic species indicating that the strain belongs to a novel species of the genus Pseudomonas.

Reference: https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.004559

Bacterial communities associated with the biofilm formation in Pangong Tso Lake

Pangong Tso Lake is situated in the Himalayan Plateau on both sides of India/China border. This high-altitude lake has an oligotrophic environment with extremes of temperature and exposure to UV radiation. The water of the Pangong Tso is generally very clear. The sediments, including the pebbles and small rocks, did not show any biofilm or microbial mats formation in the past.  However, human activities have increased tremendously near this lake, which might lead to disturbance of this lake ecosystem.  The presence of biofilms in a small area near the shore of the Pangong Tso next to the Maan village was observed by researchers.

Pangong Tso lake

Researchers at NCMR-NCCS Pune were curious to understand the bacterial communities associated with the Pangong Tso lake sediment, water and biofilms. Researchers also studied the metabolic potential of the bacterial community. They used amplicon sequencing of the particular region of 16S rRNA gene and other different tools for this study.  Based on the previous findings on biofilm bacterial communities, researchers hypothesized that the biofilm bacterial communities at Pangong Tso Lake consist of phototrophs and chemotrophs. They also hypothesized that the diversity of the biofilms community is different from suspended water and sediments, where biofilm formation was not observed.

Researchers collected sediment and microbial biofilms sample from the Pangong Tso Lake. Analysis of physio-chemical parameters of water was done. The Calcium and Magnesium chloride contents of water were analyzed .The dissolved Chloride content of water, Sulphate concentration, Nitrate nitrogen and Ammonium nitrogen estimation was done using different techniques. DNA extraction was done from water, sediment and microbial biofilm samples. Different bioinformatics and statistic tools were used in the study. The metabolic potential of the microbial community was predicted using functional prediction tool Tax4Fun and the relative abundance of highly abundant genes involved in different functions were compared across the biofilm, sediment and the water sample.

Overall a total of 6,682,012 raw sequences were generated in the study. Proteobacteria was the most dominant and diverse phylum followed by Bacteroidetes, Acidobacteria, Planctomycetes, Actinobacteria, Firmicutes, Verrucomicrobia, Chlorofexi and Gemmatimonadetes. Significant differences were observed in the microbial diversity of water with sediment and microbial biofilm samples. The water sample was least diverse in comparison to the microbial biofilm and sediment samples. Among the top 50 bacterial genera, which constitutes about 50% of the entire microbiome, Loktanella was highly abundant in the water sample, Rhizobium in sediment samples, and Planktosalinus and Aliidomarina were in biofilm samples. The relative abundance of Proteobacteria was the highest in the water. A sharp decline was observed in the relative abundance of Proteobacteria in sediment and biofilm samples.

Loktanella constitutes nearly half of the total bacterial communities in the water sample, while Loktanella represented less than 1% in the biofilm and sediment samples. Differences were observed in the relative abundance of bacterial taxa across the biofilm and the sediment samples at the phylum and genus based on the Welch t test. Bacterial phyla Verrucomicrobia, Deinococcus-Thermus and Cyanobacteria were explicitly enriched in the biofilm samples. The abundance of Planktosalinus, Aliidiomarina, Halomonas, Predibacter, Paracoccus, and Hyphomonas was significantly high in the microbial mat, whereas Enterobacter and Mesorhizobium were highly abundant in the sediment samples. In addition to this higher abundance of Flavobacterium, Pseudomonas, Luteolibacter, Dyadobacter, Chryseobacterium, Halomonas, Stenotrophomonas, Hyphomonas, Enterobacter, Peredibacter, Acinetobacter, Arenibacter and Exiguobacterium was also recorded across the samples.

A total of 49 pathways were highly abundant, with more than 0.5% mean relative abundance. The pathways related to different functions like peptidases, porphyrin and chlorophyll metabolism, glycoxylate and dicarboxylate metabolism, chaperones and folding catalysts, DNA repair and recombination proteins, pyruvate metabolism, nitrogen metabolism, propanoate metabolism, cysteine and methionine metabolism, butanoate metabolism, transcription machinery, prokaryotic defense system, alanine, aspartate and glutamate metabolism, and homologous recombination were highly abundant in the biofilm samples.

The less diverse bacterial communities in microbial biofilm in comparison to sediments indicated the enrichment of a specific group of bacteria. Stratification of Cyanobacteria (primary producer), sulfate-reducing/ oxidizing bacteria and anoxygenic phototrophic bacteria in the hypersaline microbial mat, took place according to the micro-gradient of oxygen, sulfide, and light which selectively allows the specific bacteria to colonize. The higher abundance of Cyanobacteria in the biofilm samples in comparison to sediment and water sample supported the hypothesis on the establishment of primary producers in the biofilm samples. Sediment samples were the most diverse in comparison to water and microbial biofilm samples, which represents both rare and abundant taxa in the sample. The less diverse bacterial communities in microbial biofilm in comparison to sediments indicated the enrichment of a specific group of bacteria.

To conclude, significant differences were observed in the bacterial diversity in the lake water, sediment, and microbial biofilm samples. Enrichment of specific phyla like Verrucomicrobia, Deinococcus-Thermus, and Cyanobacteria in the microbial biofilm samples indicated the development of saprophytic and photosynthetic communities, which is an important succession event in this high-altitude lake. The predictive analysis of potential functions of these communities also supported the observation as the genes involved in porphyrin and chlorophyll metabolism, glyoxylate and dicarboxylate metabolism, DNA repair and recombination proteins were enriched in the microbial biofilm samples.

Reference: https://link.springer.com/article/10.1007/s00284-020-02244-4

Characterization of hyper tolerant bacteria for arsenic oxidation

Groundwater arsenic pollution causes many deaths worldwide. Arsenic levels in ground water are increasing day by day due to human activities, leading to higher threats of arsenic exposure. Arsenic release in drinking water resources causes major health problems.

Researchers at SPPU Pune, NCMR-NCCS Pune and NCL Pune collaboratively attempted to bio-prospect the microorganisms causing arsenic transformation. They used culture-dependent and independent approaches to study the microorganisms from Lonar Lake. Growth and Arsenic oxidation potential of microorganisms at increasing concentration was studied. The study also tried to understand possible pathway of Arsenic oxidation by studying the genes, transcripts and proteins involved.

Soil samples were collected from alkaline Lonar Crater Lake in Maharashtra. DNA was extracted from soil sample using soil DNA extraction kit. Unculturable and culturable diversity of soil sample was studied. Hyper-tolerance towards arsenic was studied. Growth and As(III) oxidation profile, ArsB amplification, enzyme inhibitor assay, As (III) oxidase assay, resting cells assay, Liquid chromatography mass spectrometry analysis , relative quantification of transcripts, microcosm studies and statistical analysis was done.

Bacterial community in the sample set comprised of total 21 phyla. Proteobacteria was predominantly found in the samples followed by Bacteroidetes. The bacterial member Pelagibacteraceae was detected predominantly in the sample followed by Microbacteriaceae, Flavobacteriaceae, Flammeovirgaceae, Vibrionaceae and Rhodobacteraceae with more than 5% abundance in all the samples. The bacterial diversity from Lonar Lake soil exhibited the presence of 10 As(III) oxidizing, 2 As(V) reducing, and 5 arsenic tolerant bacteria. Total 10 different genera were obtained viz. Bacillus, Lysinibacillus, Halomonas, Noviherbaspirillum, Roseomonas, Zobellela, Allidiomarina, Indibacter, Nocardioides, and Oceanimonas.

Arsenic hyper-tolerant Firmicute Bacillus firmus L-148 was isolated from arsenic limiting Lonar lake soil, which tolerated more than 3 M arsenic and could oxidize 75 mM arsenite [As (III)] in 14 days. It oxidized As (III) in presence of heavy metals. B. firmus L-148 was studied at the biochemical, protein, genomic and transcript level for understanding its arsenic oxidizing machinery. This study can be explored for bioremediation of arsenic contaminated water.

The tolerance towards arsenic in bacteria may be due to many reasons like expression of certain genes to combat the deleterious toxic effect. Expression of ArsA can contribute to high tolerance apart from the presence of more than one arsenic transforming operons.  Once it gets delivered, arsenic shows actual level of oxidation . The means of transport of Arsenic was through water pipes and oxidation of samples in the waste water.

Though the potential cultures in this study were isolated from trivial arsenic content environment, they tolerated moderate to high concentration of As(III) and As(V). These findings clearly demonstrated that arsenic tolerance level of bacteria is not correlated to the arsenic content of the environment in which they thrive.

Reference: https://www.sciencedirect.com/science/article/pii/S0269749119360701#:~:text=Arsenic%20hyper%2Dtolerant%20Firmicute%20Bacillus,unusual%20pH%20optima%20at%209.2.

Stress tolerance in bacterial strains of the genus Rhodanobacter isolated from a mixed waste contaminated subsurface

Oak Ridge Integrated Field Research Challenge (ORIFRC) site is characterized by low pH and consists of high nitrate, organics and heavy metals. ORIFRC field laboratory comprises variety of contaminants (uranium, technetium, nitrate, volatile organic carbon species etc.) which are of interest to US Department of Energy. Rhodanobacter is a dominant bacterial species found at this site and ideal for remediation of such mixed contaminated sites.

A collaborative study was conducted by researchers at Florida State University, NCMR-NCCS Pune, University of Illinois, Georgia Institute of Technology and Symbiosis School of Biological Sciences to understand the physiologic basis of stress tolerance in members of the genus Rhodanobacter. The study was conducted in order to understand how bacterial strains of the genus Rhodanobacter survive and dominate in the mixed waste contaminated habitats of the ORIFRC site. To address this, a systematic analysis of relevant phenotypic properties of strains of the genus Rhodanobacter was studied.

Eight strains of Rhodanobacter were isolated from high and low contaminated zones and used for pH and nitrate utilization studies. NaCl, nitrate, nitrite and heavy metal tolerance capacity was studied for the two selected strains of R. denitrificans. Based on metals known to be present at the ORIFRC site, Rhodanobacter strains were tested for tolerance to zinc, cadmium, cobalt, nickel, copper and uranium. To determine the effect of incubation time on growth of R. denitrificans at high metal concentrations, studies were carried out with nickel and uranium since these two metals were found to be present at very high concentrations at the test site.

The results supported the growth potential of Rhodanobacter in acidic subsurface groundwater conditions and confirmed that under suitable cultivation conditions, isolated R. denitrificans strains can tolerate acidic pH consistent with ORIFRC site pH values. It was also observed that organisms adapted to stress better under conditions of high organic content. The ability of Rhodanobacter strains to grow at extremely low pH and under high nitrate and heavy metals concentrations is responsible for their dominance at the contaminated subsurface of the ORIFRC site. The data indicated that both the strains are well adapted to the eco physiological conditions of the contaminated ORIFRC site.

As bacteria from the genus Rhodanobacter are denitrifiers, their activity in the ORIFRC site subsurface is also linked to carbon and nitrogen cycling and may play a critical role in the bioremediation of uranium. Based on prior findings and the results of the current study, researchers postulated that low pH tolerance and high level of stress tolerance for a range of metals along with denitrification potential gives a selective advantage to members of the genus Rhodanobacter. Bacteria from the genus Rhodanobacter are facultative anaerobes, and this physiologic capability makes them ideal candidates for robust growth in the contaminated subsurface of the ORIFRC site. Due to their enhanced stress tolerance abilities, Rhodanobacter spp. survives at low pH and in the presence of elevated concentrations of heavy metals, nitrate and nitrite.

Reference: https://link.springer.com/article/10.1007/s11783-020-1315-0

PAN-India SARS-CoV-2 genome sequencing reveals important insights into the outbreak

The ongoing pandemic of Severe Acute Respiratory Syndrome (SARS-CoV-2) has emerged as a global health problem and has adversely affected the world. The novel corona virus is spreading rapidly creating a threat for humankind. It is estimated that it can spread twice as fast as the 1918 Spanish flu virus. Whole-genome sequencing of pathogens, especially viruses, is a powerful tool to generate rapid information on outbreaks. The results from this technique help in effective understanding of the introduction of the infection ,dynamics of transmission, contact tracing networks and impact of informed outbreak control decisions. This technique has been effective in earlier outbreaks like the Ebola virus.

A collaborative study was conducted by researchers from NIBMG Kalyani, ILS Bhubaneswar, CDFD Hyderabad, NCBS Bengaluru, InStem Bengaluru, NCCS Pune and ICMR-Regional Centre for Medical Research, Bhubaneswar in order to achieve initial goal of completing the sequencing of 1000 SARS-CoV-2 genomes. The nasal and oral swabs were collected from individuals testing positive for COVID-19. The samples were collected from 10 states covering different zones within India. Phylodynamic analysis, mutation analysis and haplotype network analysis was performed. One thousand and fifty two sequences were used for phylodynamic, temporal and geographic mutation patterns and haplotype network analyses. This study will contribute in understanding how the virus is spreading, ultimately helping to restrict transmission, prevent new cases of infection, and provide information for research on how to interevent the spread of infection.

Preliminary results indicated that multiple lineages of SARS-CoV-2 are circulating in India, might have introduced by travel from Europe, USA and East Asia. In particular, there is a predominance of the D614G mutation, which is found to be emerging in almost all regions of the country. Scientists were able to estimate the possible source of country of different varieties of the virus introduced in India because of travel. The virus has also mutated and one of the mutations has attained highest frequencies across most of the states. There are two lineages of the virus named as 20A and 20B which are predominant across the country. The haplotype 20A is most abundant in northern and eastern India, 20B haplotype was abundant in southern and western India. The ancestral haplotypes of 19A and 19B were mostly found in Northern and Eastern India, with 19B being the most abundant in the latter region.

Analysis indicated that the haplotype diversities across India and in each region continued to increase until May 2020, after that it reduced drastically with the emergence of the A2a haplotypes which has overtaken other lineages by June 2020. Such interpretations might enable improved understanding of the virus and hence the health decisions. From the haplotype network, researchers observed that Maharashtra, Karnataka created three distinct haplotype nodes and sequences from Odisha, West Bengal and Uttarakhand sparse in different haplotype nodes. They also observed a haplotype node with the majority of the genomes from West Bengal, Odisha and a small percentage of the samples belonging to Uttarakhand.

Analysis of probable country of origin of these SARS-CoV-2 sequences in India revealed that they had been probably introduced by travel from multiple countries across the globe. 20A, B and C haplotypes were introduced from multiple countries in Europe and also American continents. Interestingly, 20A alone is predicted to have been introduced by travel from Italy, Saudi Arabia, United Kingdom and Switzerland. Similarly, 20B was introduced from the United Kingdom, Brazil, Italy and Greece. In contrast, 19A was introduced from China alone while 19B was introduced by travel from China, Oman and Saudi Arabia.

The number of COVID-19 occurrences in India has increased drastically over the time. Although most of the states have their own strategic lockdown devised to control the outbreak, it will be more efficient if we can include the geographical transmission pattern information in the planning of such strategies. In the current study, scientists have tried to explore the transmission of the infection among different states of India. It is necessary to add more genomic datasets to understand clear picture.

Reference: https://www.biorxiv.org/content/10.1101/2020.08.03.233718v1.full.pdf

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.