Temperature - A critical abiotic paradigm that governs bacterial heterogeneity in natural ecological system

A baseline data has been presented here to prove that among the abiotic factors, temperature is the most critical factor that regulates and governs the bacterial diversity in a natural ecosystem. Present study in Yumesamdong hot springs riverine vicinity (Sikkim), parades a gamut of bacterial communities in it and hosts them from semi-frigid region (- 4-10 °C) to fervid region (50-60 °C) via an intermediate region (25-37 °C) within the same ecosystem. This is an extremely rare intriguing natural ecosystem that has no anthropogenic disturbances nor any artificial regulation of temperature. We scanned the bacterial flora through both the culture-dependent and culture-independent techniques in this naturally complex thermally graded habitat. High-throughput sequencing gave bacterial and archaeal phyla representatives of over 2000 species showcasing their biodiversity. Proteobacteria, Firmicutes, Bacteroidetes and Chloroflexi were the predominant phyla. A concave down-curve significance was found in temperature-abundance correlation as the number of microbial taxa decreased when the temperature increased from warm (35 °C) to hot (60 °C). Firmicutes showed significant linear increase from cold to hot environment whereas Proteobacteria followed the opposite trend. No significant correlation was observed for physicochemical parameters against the bacterial diversity. However, only temperature has shown significant positive correlation to the predominant phyla at their respective thermal gradients. The antibiotic resistance patterns correlated with temperature gradient where the prevalence of antibiotic resistance was higher in case of mesophiles than that of psychrophiles and there was no resistance in thermophiles. The antibiotic resistant genes obtained were solely from mesophiles as it conferred high resistance at mesophilic conditions enabling them to adapt and metabolically compete for survival. Our study concludes that the temperature is a major factor that plays a significant contribution in shaping the bacterial community structure in any thermal gradient edifice.

Baseline metagenome-assembled genome (MAG) data of Sikkim hot springs from Indian Himalayan geothermal belt (IHGB) showcasing its potential CAZymes, and sulfur-nitrogen metabolic activity

Here we present the construction and characterization of metagenome assembled genomes (MAGs) from two hot springs residing in the vicinity of Indian Himalayan Geothermal Belt (IHGB). A total of 78 and 7 taxonomic bins were obtained for Old Yume Samdong (OYS) and New Yume Samdong (NYS) hot springs respectively. After passing all the criteria only 21 and 4 MAGs were further studied based on the successful prediction of their 16 S rRNA. Various databases were used such as GTDB, Kaiju, EzTaxon, BLAST XY Plot and NCBI BLAST to get the taxonomic classification of various 16 S rRNA predicted MAGs. The bacterial genomes found were from both thermophilic and mesophilic bacteria among which Proteobacteria, Chloroflexi, Bacteroidetes and Firmicutes were the abundant phyla. However, in case of OYS, two genomes belonged to archaeal Methanobacterium and Methanocaldococcus. Functional characterization revealed the richness of CAZymes such as Glycosyl Transferase (GT) (56.7%), Glycoside Hydrolase (GH) (37.4%), Carbohydrate Esterase family (CE) (8.2%), and Polysaccharide Lyase (PL) (1.9%). There were negligible antibiotic resistance genes in the MAGs however, a significant heavy metal tolerance gene was found in the MAGs. Thus, it may be assumed that there is no coexistence of antibiotic and heavy metal resistance genes in these hot spring microbiomes. Since the selected hot springs possess good sulfur content thus, we also checked the presence of genes for sulfur and nitrogen metabolism. It was found that MAGs from both the hot springs possess significant number of genes related to sulfur and nitrogen metabolism.

First report on metagenomics and their predictive functional analysis of fermented bamboo shoot food of Tripura, North East India

Moiya pansung, mileye amileye, moiya koshak, and midukeye are naturally fermented bamboo shoot foods of Tripura. The present study aimed to reveal the whole microbial community structure of naturally fermented moiya pangsung, mileye amileye, moiya koshak, and midukeye along with the prediction of microbial functional profiles by shotgun metagenomic sequence analysis. The metataxonomic profile of moiya pangsung, mileye amileye, moiya koshak, and midukeye samples showed different domains, viz., bacteria (97.70%) followed by the virus (0.76%), unclassified (0.09%), eukaryotes (1.46%) and archaea (0.05%). Overall, 49 phyla, 409 families, 841 genera, and 1,799 species were found in all the fermented bamboo shoot samples collected from different places of Tripura. Firmicutes was the most abundant phylum (89.28%) followed by Proteobacteria (5.13%), Bacteroidetes (4.38%), Actinobacteria (1.02%), and Fusobacteria (0.17%). Lactiplantibacillus plantarum was the most abundant species in moiya pangsung, mileye amileye, moiya koshak, and midukeye followed by Lactococcus lactis, Levilactobacillus brevis, Leuconostoc mesenteroides, Weissella paramesenteroides, Leuconostoc kimchii, Pediococcus pentosaceus, Leuconostoc gasicomitatum, and Lacticaseibacillus casei. A few phyla of fungus were found, viz., Ascomycota, Basidiomycota, and Glomeromycota, where Ascomycota was present in high abundance. Functional analysis of moiya pangsung, mileye amileye, moiya koshak, and midukeye metagenome revealed the genes for the synthesis and metabolism of a wide range of bioactive compounds including, various essential amino acids, and conjugated amino acids. The abundance profile and predictive analysis of fermented bamboo shoots revealed a huge plethora of essential microorganisms and KEGG analysis revealed genes for amino acid metabolism, pectin degradation, lipid metabolism, and many other essential pathways that can be essential for the improvement of nutritional and sensory qualities of the fermented bamboo shoot products.

Post-monsoon seasonal variation of prokaryotic diversity in solfataric soil from the North Sikkim hot spring

The solfataric soil sediments of the hot springs of Sikkim located at Yume Samdung and Lachen valley were studied for deciphering the bacterial diversity. The main aim here is to present a comparative study and generate a baseline data on the post-monsoon seasonal variation for the months of October and December, analyzed through 16S rRNA V3-V4 amplicon sequencing. The results have shown that there is not much variation at phylum level in the month of October in all the three hot springs such as New Yume Samdung (NYS), Old Yume Samdung (OYS), and Tarum (TAR) hot spring. The abundant phyla mainly present were Firmicutes, followed by Proteobacteria, Actinobacteria, and Bacteroidetes. Similarly, in the month of December, Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes were prevalent; however, the percent relative abundance of these phyla in the month of December is relatively less. Besides this decrease in percent abundance, it was interestingly seen that relatively more phyla were found contributing towards the bacterial diversity in the month of December. Similar to phylum level, at genus level, there was not much variation seen among various prevalent genera of the three studied hot springs in both months. The major genera prevalent in both months among all the three hot springs were followed by Bacillus, Desulfotomaculum, Lactobacillus, and Paenibacillus. A similar trend was also seen at gene level that relative abundance of various genera was higher in the month of October but more genera were found to be contributing towards bacterial diversity in the month of December. Few distinct genera were found to be more abundant in the month of December such as Rhodopirellula and Blastopirellula. The results may conclude that there is not much variation in the abundance and type of bacterial communities during the post-monsoon season in the month of October and December. However, this may be assumed that there is the accumulation or increase in the bacterial communities during the winter (relatively higher temperature among hot springs) and may favor few mesophilic and more thermophilic communities as well.

Coexistence of Heavy Metal Tolerance and Antibiotic Resistance in Thermophilic Bacteria Belonging to Genus Geobacillus

Hot springs are thought to be potential repositories for opportunistic infections, such as antibiotic-resistant strains. However, there is a scarcity of information on the mechanisms of antibiotic resistance gene (ARG) uptake, occurrence, and expression in thermophilic bacteria. Furthermore, because the genesis and proliferation of ARGs in environmental microorganisms are unknown, the research on antibiotic resistance profiles and probable mechanisms in thermophilic bacteria will become increasingly important. The goals of this study are to explore bacterial diversity, antibiotic and heavy metal resistance, and the prevalence and presence of ARG and metal resistance gene (MRG) in Geobacillus species. The 16S rRNA sequencing was used to determine the culturable bacterium diversity of 124 isolates. Standard Kirby Bauer Disc Diffusion and tube dilution procedures were used to determine antibiotic sensitivity and minimum inhibitory concentration (MIC). The tube dilution method was also used to check metal tolerance. To detect ARG and heavy MRG (HMRG), whole genome sequencing studies of the type species of the genus Geobacillus and five randomly selected Geobacillus species were performed. Graph Pad Prism and XLSTAT were used to perform statistical analyses such as ANOVA, EC50 analysis, and principal component analysis (PCA). The phylum Firmicutes and the genus Geobacillus dominated the culture-dependent bacterial diversity. Surprisingly, all thermophilic isolates, i.e., Geobacillus species, were sensitive to at least 10 different antibiotics, as evidenced by the lack of ARGs in whole genome sequencing analysis of numerous Geobacillus species. However, some of these isolates were resistant to at least five different heavy metals, and whole genome sequencing revealed the presence of MRGs in these thermophilic bacteria. The thermophilic genus Geobacillus is generally antibiotic sensitive, according to this study. In contrast, heavy metal is tolerated by them. As a result, it is possible that ARGs and MRGs do not coexist in these bacteria living in hot springs.

Bacterial diversity, physicochemical and geothermometry of South Asian hot springs

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Statistical analysis using physicochemical parameters reveals that the processes involved in the hot springs of HGB may include water mixing or exhibiting simple dissolution, ion exchange and reverse ion exchange.

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Study shows the water in the hot springs of HGB is mainly Na-Cl, Na-HCO₃, Ca⁺²-Na⁺-HCO₃⁻, Ca⁺²- HCO3⁻ and mixed type.

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Geothermometry reveals the temperature of these geothermal features ranges approximately between 100-250°C.

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Microbial study reveals that the Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria as predominant phyla showing significant positive correlation with physicochemical parameters like temperature, pH, Na, HCO₃, etc.

Extreme ecosystems with enormous arrays of physicochemical or biological physiognomies serve as an important indicator of various processes occurred and/or occurring in and on the Earth. Among extreme habitats, hot springs represent geothermal features which are complex systems with a well-defined plumbing system. Besides geological tectonic based hypsography and orology annotations, the hot springs have served as hot spots for ages where there is an amalgamation of nature, religion, faith, health, and science. Thus, there remains an escalating scope to study these hot springs all over the world. The Himalayan Geothermal Belt (HGB) banquets three densely demographic countries i.e. Pakistan, India and China, that hosts numerous hot springs. Studies on the hot springs distributed over these countries reveal Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria as the predominant bacterial phyla. The bacterial diversity shows a significant positive correlation with physicochemical parameters like temperature, pH, Na⁺, HCO₃⁻, etc. Physicochemical analyses of these hot springs indicate the water mainly as Na-Cl, Na-HCO₃, SO₄-Cl, and mixed type, with temperature ranging approximately between 100-250°C as predicted by various geothermometers. Numerous studies although done, not much of a comprehensive database of the analysis are provided on the hot springs harboured by the HGB. This review aims to give a cumulative illustration on comparative facets of various characteristic features of hot springs distributed over the HGB. These are found to be of great importance with respect to the exploitation of geothermal energy and microflora in various sectors of industries and biotechnology. They are also important sources in terms of socio-economic perspective, and routes to eco-medical tourism.

Draft genome sequence of Stenotrophomonas maltophilia strain P13 gives insight into its protease production and assessment of sulfur and nitrogen metabolism

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In this study draft genome sequence of Stenotrophomonas maltophilia strain P13 which was isolated from Kanchengayao glacier, North Sikkim, India.

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The genome of P13 strain possesses 2689,565 total reads, with an average G + C content of 69.9%.

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The major enzymes present are beta-galactosidase, thiol peroxidase, thiolredoxin reductase, glutamate synthase, and glutamate-ammonia-ligase adenyltransferase.

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FAME, morphological and biochemical characterization, and scanning electron microscopy (SEM) of Stenotrophomonas maltophilia strain P13 are provided.

Stenotrophomonas maltophilia strain P13 was isolated from the Kanchengayao glacier's accumulation zone. A comprehensive study was done on this strain as it produced protease enzyme and thus having industrial potential. The whole genome sequence, FAME, morphological and biochemical characteristics of the S. maltophilia strain P13 is being presented. The genome of P13 strain possesses 2,689,565 total reads, with an average G + C content of 69.9%. The whole-genome assembly is having 548 contigs (with PEGs). The genome contains 2,985 coding sequences with 55 rRNA predicted genes. More than 88% of the total pre-processed reads from samples were mapped. The identified coding proteins were classified into 27 functional categories based on COG classification. The genome was found to possess genes for ammonium assimilation, galactosylceramide and sulfatide metabolism. The major enzymes present are beta-galactosidase, thiol peroxidase, thiolredoxin reductase, glutamate synthase, and glutamate-ammonia-ligase adenyltransferase. The genome information of Stenotrophomonas maltophilia P13 provides the basis for understanding the functional properties and abilities to act as a potential cold-active enzyme producer and nitrogen-fixing bacteria.

Reclassification of Geobacillus galactosidasius and Geobacillus yumthangensis as Parageobacillus galactosidasius comb. nov. and Parageobacillus yumthangensis comb. nov., respectively

Members of the genus Geobacillus within the phylum Firmicutes are Gram-stain-positive, aerobic, endospore-forming, obligate thermophiles. In 2016, the genus Geobacillus was subdivided into two genera based on whole-genome approaches. The new genus, Parageobacillus, comprises five genomospecies. In this study, we recommend the reclassification of two Geobacillus species, Geobacillus galactosidasius and Geobacillus yumthangensis, into the genus Parageobacillus. We have applied whole genome approaches to estimate the phylogenetic relatedness among the 18 Geobacillus and Parageobacillus type strains for which genome sequences are currently publicly available. The phylogenomic metrics AAI (average amino acid identity), ANI (average nucleotide identity) and dDDH (digital DNA-DNA hybridization) denoted that the type strains of G. galactosidasius and G. yumthangensis belong to the genus Parageobacillus. Furthermore, a phylogeny based on comparison of the 16S rRNA gene sequences, recN gene sequences and core genes identified from the whole-genome analyses designated that the type strains of G. galactosidasius and G. yumthangensis belong in the genus Parageobacillus. With these findings, we consequently propose that G. galactosidasius and G. yumthangensis should be reclassified as Parageobacillus galactosidasius comb. nov. and Parageobacillus yumthangensis comb. nov.

Distribution of Antibiotic-Resistant Enterobacteriaceae Pathogens in Potable Spring Water of Eastern Indian Himalayas: Emphasis on Virulence Gene and Antibiotic Resistance Genes in Escherichia coli

Every year millions of people die due to fatal waterborne diseases around the world especially in developing countries like India. Sikkim, a northeastern state of India, greatly depends on natural water sources. About 80% of the population of Sikkim depends on natural spring water for domestic as well as agricultural use. Recent waterborne disease outbreaks in the state raises a concerning question on water quality. In this study, we analyzed water quality especially for the detection of Enterobacteriaceae members from four districts of the state. Isolation with selective culture media techniques and taxonomic characterization of Enterobacteriaceae bacteria with 16S rRNA gene showed the prevalence of Escherichia coli (37.50%), Escherichia fergusonii (29.41%), Klebsiella oxytoca (36.93%), Citrobacter freundii (37.92%), Citrobacter amalonaticus (43.82%), Enterobacter sp. (43.82%), Morganella morganii (43.82%), Hafnia alvei (32.42%), Hafnia paralvei (38.74%), and Shigella flexneri (30.47%) in the spring water of Sikkim. Antibiotic susceptibility test (AST) showed resistance of the isolates to common antibiotics like ampicillin, amoxicillin as well as to third generation antibiotics like ceftazidime and carbapenem. None of the isolates showed resistance to chloramphenicol. E. coli isolated from spring water of Sikkim showed presence of different virulence genes such as stx1 (81.81%), elt (86.66%), and eae (66.66%) along with resistance gene for ampicillin (CITM) (80%), quinolones (qnrB) (44.44%), tetracycline (tetO) (66.66%), and streptomycin (aadA1) (66.66%). The data indicates a high incidence rate of multiple antibiotic resistant enteric bacteria in the spring water of Sikkim. Additionally, the presence of enteric bacteria in the water samples indicates widespread fecal contamination of the spring water.

Distribution of antibiotic and metal resistance genes in two glaciers of North Sikkim, India

Glacier studies as of late have ruffled many eyeballs, exploring this frigid ecology to understand the impact of climate change. Mapquesting the glaciers led to the discovery of concealed world of "psychrophiles" harboring in it. In the present study, the antibiotic resistance genes (ARGs) and heavy metal resistance genes (MRGs) were evaluated through both the culture-dependent and culture-independent methods. Samples were collected from two different glaciers, i.e., debris-covered glacier (Changme Khangpu) and debris-free glacier (Changme Khang). Functional metagenomics of both the glacier samples, provided evidence of presence of resistant genes against various antibiotic groups. Bacitracin resistant gene (bacA) was the predominant ARG in both the glaciers. MRGs in both the glacier samples were diversified as the genes detected were resistant against various heavy metals such as arsenic, tungsten, mercury, zinc, chromium, copper, cobalt, and iron. Unique MRGs identified from Changme Khangpu glacier were resistant to copper (cutA, cutE, cutC, cutF, cueR, copC, and copB) and chromium (yelf, ruvB, nfsA, chrR, and chrA) whereas, from Changme Khang glacier they showed resistance against cobalt (mgtA, dmef, corD, corC, corB, and cnrA), and iron (yefD, yefC, yefB, and yefA) heavy metals. ARGs aligned maximum identity with Gram-negative psychrotolerant bacteria. The cultured bacterial isolates showed tolerance to high concentrations of tested heavy metal solutions. Interestingly, some of the antibiotic resistant bacterial isolates also showed tolerance towards the higher concentrations of heavy metals. Thus, an introspection of the hypothesis of co-occurrence and/co-selection of ARGs and MRGs in such environments has been highlighted here.

Draft genome sequence of Lactobacillus plantarum strain DMR17 isolated from homemade cow dahi of Sikkim Himalayan region: an evaluation of lactate fermentation and secondary metabolism

Lactobacillus plantarum DMR17 was isolated from homemade cow dahi of Sikkim Himalayan region of India. Here, we report the draft genome sequence of this strain. A total of 21,176,638 paired-end reads were obtained which were assembled into 65 contigs. The reference genome used was L. plantarum WCFS1. The genome size of DMR17 was 3,228,341 bp with G + C content of 46.25%. 3302 coding sequences were predicted including 68 tRNA and 67 rRNA genes. More than 88% of the total pre-processed reads from the sample were mapped to the reference genome. The identified coding proteins were classified into 27 functional categories based on COG classification. The genome was found to possess genes for lactate and mixed acid fermentation. The genome also showed the presence of genes for catabolism of aromatic compounds, phosphorous, and other metabolism. The genome information of L. plantarum DMR17 provides the basis for understanding the functional properties and to consider its use as a potential component of functional foods especially dahi.

A systematic review of the genera Geobacillus and Parageobacillus: their evolution, current taxonomic status and major applications

The genus Geobacillus, belonging to the phylum Firmicutes, is one of the most important genera and comprises thermophilic bacteria. The genus Geobacillus was erected with the taxonomic reclassification of various Bacillus species. Taxonomic studies of Geobacillus remain in progress. However, there is no comprehensive review of the characteristic features, taxonomic status and study of various applications of this interesting genus. The main aim of this review is to give a comprehensive account of the genus Geobacillus. At present the genus acomprises 25 taxa, 14 validly published (with correct name), nine validly published (with synonyms) and two not validly published species. We describe only validly published species of the genera Geobacillus and Parageobacillus. Vegetative cells of Geobacillus species are Gram-strain-positive or -variable, rod-shaped, motile, endospore-forming, aerobic or facultatively anaerobic, obligately thermophilic and chemo-organotrophic. Growth occurs in the pH range 6.08.5 and a temperature of 37-75 °C. The major cellular fatty acids are iso-C15:o, iso-C16:0 and iso-C17:o. The main menaquinone type is MK-7. The G-+C content of the DNA ranges between 48.2 and 58 mol%. The genus Geobacillus is widely distributed in nature, being mostly found in many extreme locations such as hot springs, hydrothermal vents, marine trenches, hay composts, etc. Geobacillus species have been widely exploited in various industrial and biotechnological applications, and thus are promising candidates for further studies in the future.

Metavirome and its functional diversity analysis through microbiome study of the Sikkim Himalayan hot spring solfataric mud sediments

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This study is the first ever report on the virus diversity among the hot springs of Sikkim, India.

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The study revealed the dominance of Siphoviridae, Myoviridae and Phycodnaviridae in the two hot spring solfataric mud sediments.

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The metavirome ecology of the two hot springs have dsDNA viromes in abundance.

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Giant DNA viruses such as Pandoravirus and Pithovirus were found through metagenomic approach.

Viruses are the most prodigious repertory of the genetic material on the earth. They are elusive, breakneck, evolutionary life particles that constitute a riveting concealed world. Environmental viruses have been obscurely explored, and hence, such an intriguing world of viruses was studied in the Himalayan Geothermal Belt of Indian peninsula at Sikkim corridor through hot springs. The hot springs located at the North Sikkim district were selected for the current study. The solfataric mud sediment samples were pooled from both the hot springs. The virus community showed significant diversity among the two hot springs of Yume Samdung. Reads for viruses among the mud sediments at Old Yume Samdung hot springs (OYS) was observed to be 11% and in the case of New Yume Samdung hot springs (NYS) it was 6%. Both the hot springs were abundant in dsDNA viromes. The metavirome reads in both the OYS and NYS hot spring mud sediments showed the predominance of Caudovirales; Herpesvirales; Ortervirales among which viral reads from Siphoviridae, Myoviridae, Phycodnaviridae and Podoviridae were abundantly present. Other viral communities belonged to families like Baculoviridae, Mimiviridae, Parvoviridae, Marseilleviridae etc. Interestingly, in the case of NYS, the unassigned group reads belonged to some unclassified giant DNA viruses like genera Pandoravirus and Pithovirus. Other interesting findings were – reads for Badnavirus having ds (RT-DNA) was exclusively found in NYS whereas Rubulavirus having ss(-)RNA was exclusively found in OYS sample. This is the first ever report on viruses from any hot springs of Sikkim till date.

Diversity analysis and metagenomic insights into antibiotic and metal resistance among Himalayan hot spring bacteriobiome insinuating inherent environmental baseline levels of antibiotic and metal tolerance

OBJECTIVES

Mechanisms of occurrence and expression of antibiotic resistance genes (ARGs) in thermophilic bacteria are still unknown owing to limited research and data. In this research, comparative profiling of ARGs and metal tolerance genes among thermophilic bacteria has been done by functional metagenomic methods.

METHODS

Shotgun metagenomic sequence data were generated using Illumina HiSeq 4000. Putative ARGs from the PROKKA predicted genes were identified with the ardbAnno V.1.0 script available from the ARDB (Antibiotic Resistance Genes Database) consortium using the non-redundant resistance genes as a reference. Putative metal resistance genes (MRGs) were identified by using BacMetScan V.1.0. The whole-genome sequencing for bacterial isolates was performed using Illumina HiSeq 4000 sequencing technology with a paired-end sequencing module.

RESULTS

Metagenomic analysis showed the dominance of Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes in two hot springs of Sikkim. ARG analysis through shotgun gene sequencing was found to be negative in the case of thermophilic bacteria. However, few genes were detected but they showed maximum similarity with mesophilic bacteria. Concurrently, MRGs were also detected in the metagenome sequence of isolates from hot springs. Detection of MRGs and absence of ARGs investigated by whole-genome sequencing in the reference genome sequence of thermophilic Geobacillus also conveyed the same message.

CONCLUSION

The study of ARGs and MRGs (Heavy metal resistance gene) among culturable and non-culturable bacteria from the hot springs of Sikkim via metagenomics showed a preferential selection of MRGs over ARGs. The absence of ARGs also does not support the co-selection of ARGs and MRGs in these environments. This evolutionary selection of metal resistance over antibiotic genes may have been necessary to survive in the geological craters which have an abundance of different metals from earth sediments rather than antibiotics. Furthermore, the selection could be environment driven depending on the susceptibility of ARGs in a thermophilic environments as it reduces the chances of horizontal gene transfer.

Bacterial diversity and functional metagenomics expounding the diversity of xenobiotics, stress, defense and CRISPR gene ontology providing eco-efficiency to Himalayan Hot Springs

Sikkim is one of the bio-diverse states of India, which harbors diverse alkaline and sulfur rich hot springs in its vicinity. However, there is a dearth of data present in terms of microbial and its functional diversity as only a few hot springs have been studied in this area. Thus, in this regard, microbial and functional diversity of two hot springs by NGS, PLFA, and culture-independent approaches were carried out. PLFA and culture-dependent analysis was complementary as the Gram-positive bacteria were abundant in both the hot springs with the dominance of phylum Firmicutes with Geobacillus. Metagenomic analysis revealed the abundance of Proteobacteria, Actinobacteria, and Firmicutes in both hot springs. Functional metagenomics suggested that both Yumthang and Reshi hot spring possess a diverse set of genes analogous to stress such as genes allied to osmotic, heat shock, and acid stresses; defense analogies such as multidrug resistance efflux pump, multidrug transport system, and β-lactamase; and CRISPR analogues such as related to Cas1, Cas2, Cas3, cmr1-5 proteins, CT1972, and CT1133 gene families. The xenobiotic analogues were found against benzoate, nitrotolune, xylene, DDT, and chlorocyclohexane/chlorobenzene degradation. Thus, these defensive mechanisms against environmental and anthropogenic hiccups and hindrances provide the eco-efficiency to such thermal habitats. The higher enzymatic, degradation, defense, stress potential and the lower percentage identity (< 95%) of isolates encourage the further exploration and exploitation of these habitats for industrial and biotechnological purposes.

Microbial ecology of two hot springs of Sikkim: Predominate population and geochemistry

Northeastern regions of India are known for their floral and faunal biodiversity. Especially the state of Sikkim lies in the eastern Himalayan ecological hotspot region. The state harbors many sulfur rich hot springs which have therapeutic and spiritual values. However, these hot springs are yet to be explored for their microbial ecology. The development of neo generation techniques such as metagenomics has provided an opportunity for inclusive study of microbial community of different environment. The present study describes the microbial diversity in two hot springs of Sikkim that is Polok and Borong with the assist of culture dependent and culture independent approaches. The culture independent techniques used in this study were next generation sequencing (NGS) and Phospholipid Fatty Acid Analysis (PLFA). Having relatively distinct geochemistry both the hot springs are thermophilic environments with the temperature range of 50-77 °C and pH range of 5-8. Metagenomic data revealed the dominance of bacteria over archaea. The most abundant phyla were Proteobacteria and Bacteroidetes although other phyla were also present such as Acidobacteria, Nitrospirae, Firmicutes, Proteobacteria, Parcubacteria and Spirochaetes. The PLFA studies have shown the abundance of Gram Positive bacteria followed by Gram negative bacteria. The culture dependent technique was correlative with PLFA studies. Most abundant bacteria as isolated and identified were Gram-positive genus Geobacillus and Anoxybacillus. The genus Geobacillus has been reported for the first time in North-Eastern states of India. The Geobacillus species obtained from the concerned hot springs were Geobacillus toebii, Geobacillus lituanicus, Geobacillus Kaustophillus and the Anoxybacillus species includes Anoxybacillus gonensis and Anoxybacillus Caldiproteolyticus. The distribution of major genera and their statistical correlation analyses with the geochemistry of the springs predicted that the temperature, pH, alkalinity, Ca²⁺, Mg²⁺, Cl²⁺, and sulfur were main environmental variables influencing the microbial community composition and diversity. Also the piper diagram suggested that the water of both the hot springs are Ca-HCO^3- type and can be predicted as shallow fresh ground waters. This study has provided an insight into the ecological interaction of the diverse microbial communities and associated physicochemical parameters, which will help in determining the future studies on different biogeochemical pathways in these hot springs.

Geobacillus yumthangensis sp. nov., a thermophilic bacterium isolated from a north-east Indian hot spring

A thermophilic, spore-forming, rod-shaped bacterium isolated from the Yumthang hot spring in North Sikkim, India was subjected to taxonomic studies. The thermophilic bacterial isolate was designated as strain AYN2^T. Cells were Gram-stain-positive, aerobic, motile, rod-shaped, catalase-positive and methyl red-negative. Strain AYN2^T was able to grow in the pH range from 6 to 10 (optimum, pH 7.5-8.0), at 40-70 °C (60 °C) and in NaCl concentrations of 0-4 % (1 %). The major cellular fatty acids were iso-C15 : 0 (12.8 %), iso-C16 : 0 (13.9 %) and iso-C17 : 0 (13.8 %). No matches were found in the rtsba6 Sherlock libraries. The G+C content of the genomic DNA was 42.11 mol%. Based on phylogenetic analysis of the 16S rRNA gene sequences, strain AYN^T showed highest sequence similarity to the type strain of Geobacillus toebii (96 %). However, the phenotypic properties of strain AYN2^T were clearly distinct from those of G. toebii and related species. On the basis of polyphasic analysis, strain AYN2^T represents a novel species in the genus Geobacillus, for which the name Geobacillus yumthangensis sp. nov. is proposed. The type strain is AYN2^T(MTCC=12749=KCTC=33950= JCM 32596).

Knowledge, Attitude of Sikkim Primary School Teachers About Paediatric Hearing Loss

Our purpose of the study was to assess the knowledge and any gaps of early educators regarding hearing impairment, and to attempt to delineate the attitudes and perceptions of the educators regarding the outcomes of their students with hearing disabilities and their views on inclusive teaching, using a questionnaire based study. Only 71 respondents completed the questionnaire. The present questionnaire based study was conducted on 100 primary school teachers, undertaken on randomly selected schools from Gangtok, East Sikkim. Their knowledge and attitudes regarding hearing impairment in children in the areas of cause, diagnosis, investigations, treatment, prevention, special care and inclusion into mainstream schools were assessed. Our study showed that the knowledge of causes, investigation and treatment of hearing impairement [HI] among respondents/teachers was poor. The data was shown statistically significant with P < 0.001. However, responses testing behavior and attitudes towards HI was encouraging. 52.9% respondents disagreed that HI was a social handicap and 88.2% felt that teachers need special training before a HI child is admitted to the school. The results were statistically significant with P < 0.001. The biggest obstacle found for inclusive education of HI children was a lack of proper training to teachers (40.8%) and attitude of other students (29.5%).

Bacterial Diversity in an Alpine Debris-Free and Debris-Cover Accumulation Zone Glacier Ice, North Sikkim, India

The Himalayas are water tower for billions of people; however in recent years due to climate change several glaciers of Himalaya are receding or getting extinct which can lead to water scarcity and political tensions. Thus, it requires immediate attention and necessary evaluation of all the environmental parameters which can lead to conservation of Himalayan glaciers. This study is the first attempt to investigate the bacterial diversity from debris-free Changme Khang (CKG) and debris-cover Changme Khangpu (CK) glacier, North Sikkim, India. The abundance of culturable bacteria in CKG glaciers was 1.5 × 10⁴ cells/mL and CK glacier 1.5 × 10⁵ cells/mL. A total of 50 isolates were isolated from both the glacier under aerobic growth condition. The majority of the isolates from both the glaciers were psychrotolerant according to their growth temperature. Optimum growth temperatures of the isolates were between 15 and 20 °C, pH 6-8 and NaCl 0-2%. The phylogenetic studies of 16S RNA gene sequence suggest that, these 21 isolates can be assigned within four phyla/class, i.e., Firmicutes, Beta-proteobacteria, Gamma-proteobacteria and Actinobacteria. The dominant phyla were Firmicutes 71.42% followed by Actinobacteria 14.28%, Alpha-proteobacteria 9.52% and Beta-proteobacteria 4.76%. The isolate Bacillus thuringiensis strain CKG2 showed the highest protease activity (2.24 unit/mL/min). Considering the fast rate at which Himalayan glaciers are melting and availability of limited number of research, there is urgent need to study the microbial communities confined in such environments.