Search

Trans-Himalayan hot spring waters rich in boron, chlorine, sodium and sulfur (but poor in calcium and silicon) are known based on PCR-amplified 16S rRNA gene sequence data to harbor high diversities of infiltrating bacterial mesophiles. Yet, little is known about the community structure and functions, primary productivity, mutual interactions, and thermal adaptations of the microorganisms present in the steaming waters discharged by these geochemically peculiar spring systems. We revealed these aspects of a bacteria-dominated microbiome (microbial cell density ~8.5 × 104 mL-1; live:dead cell ratio 1.7) thriving in the boiling (85°C) fluid vented by a sulfur-borax spring called Lotus Pond, situated at 4436 m above the mean sea-level, in the Puga valley of eastern Ladakh, on the Changthang plateau. Assembly, annotation, and population-binning of >15-GB metagenomic sequence illuminated the numeral predominance of Aquificae. While members of this phylum accounted for 80% of all 16S rRNA-encoding reads within the metagenomic dataset, 14% of such reads were attributed to Proteobacteria. Post assembly, only 25% of all protein-coding genes identified were attributable to Aquificae, whereas 41% was ascribed to Proteobacteria. Annotation of metagenomic reads encoding 16S rRNAs, and/or PCR-amplified 16S rRNA genes, identified 163 bacterial genera, out of which 66 had been detected in past investigations of Lotus Pond's vent-water via 16S amplicon sequencing. Among these 66, Fervidobacterium, Halomonas, Hydrogenobacter, Paracoccus, Sulfurihydrogenibium, Tepidimonas, Thermus and Thiofaba (or their close phylogenomic relatives) were presently detected as metagenome-assembled genomes (MAGs). Remarkably, the Hydrogenobacter related MAG alone accounted for ~56% of the entire metagenome, even though only 15 out of the 66 genera consistently present in Lotus Pond's vent-water have strains growing in the laboratory at >45°C, reflecting the continued existence of the mesophiles in the ecosystem. Furthermore, the metagenome was replete with genes crucial for thermal adaptation in the context of Lotus Pond's geochemistry and topography. In terms of sequence similarity, a majority of those genes were attributable to phylogenetic relatives of mesophilic bacteria, while functionally they rendered functions such as encoding heat shock proteins, molecular chaperones, and chaperonin complexes; proteins controlling/modulating/inhibiting DNA gyrase; universal stress proteins; methionine sulfoxide reductases; fatty acid desaturases; different toxin-antitoxin systems; enzymes protecting against oxidative damage; proteins conferring flagellar structure/function, chemotaxis, cell adhesion/aggregation, biofilm formation, and quorum sensing. The Lotus Pond Aquificae not only dominated the microbiome numerically but also acted potentially as the main primary producers of the ecosystem, with chemolithotrophic sulfur oxidation (Sox) being the fundamental bioenergetic mechanism, and reductive tricarboxylic acid (rTCA) cycle the predominant carbon fixation pathway. The Lotus Pond metagenome contained several genes directly or indirectly related to virulence functions, biosynthesis of secondary metabolites including antibiotics, antibiotic resistance, and multi-drug efflux pumping. A large proportion of these genes being attributable to Aquificae, and Proteobacteria (very few were ascribed to Archaea), it could be worth exploring in the future whether antibiosis helped the Aquificae overcome niche overlap with other thermophiles (especially those belonging to Archaea), besides exacerbating the bioenergetic costs of thermal endurance for the mesophilic intruders of the ecosystem. [ABSTRACT FROM AUTHOR]

Abstract Background In 2006, a cluster of malaria deaths in the highly endemic Jalpaiguri district, West Bengal, India, led to assignment of additional resources. Malaria deaths decreased, but continued to occur. A study was conducted to identify the risk factors for residual malaria deaths. Methods Malaria death was defined as a death from fever with microscopically confirmed Plasmodium falciparum among residents of Jalpaiguri during 2007–2008. For each case, three age-, sex- and locality-matched controls were recruited among microscopically confirmed falciparum malaria patients cured during the same period. Clinical and treatment information was abstracted from records. Information about knowledge about malaria, presence of bed nets and DDT spraying was collected through interviews of the close relatives of study subjects. Odds ratio (OR) were calculated using multivariate methods. Results 51 malaria deaths were matched with 153 controls, which did not differ by age (median: 35 versus 36 years) and proportion of males (63% versus 63%). On multiple logistic regression analysis, compared with survivors, malaria deaths were more likely to have been admitted with already existing complications [OR = 4.1, 95% confidence interval (CI) = 1.6–10)], treated at a private facility (OR = 3.7, 95% CI = 1.2–12), received treatment after 48 hours of fever onset (OR = 14, 95% CI = 2.9–64), received chloroquine (OR = 13.3, 95% CI = 3.7–47). Households of the deceased were also more likely to miss bed nets (OR = 6.3, 95% CI = 1.9–24) and DDT spraying (OR = 9.2, 95% CI = 2.8–31). Conclusion Elimination of malaria deaths will require education of providers for prompt referral before complications, engagement of the private sector, community awareness for early treatment as well as scaled-up use of bed nets use and DDT. Use of newer generation anti-malarials must to be generalized.

To explore the potential role of tetrathionate in the sulfur cycle of marine sediments, population ecology of microorganisms capable of metabolizing this polythionate was revealed at 15-30 cm resolution along two, ~ 3-m-long, cores collected from 530 and 580 meters below the sea level, off India's west coast, within the oxygen minimum zone (OMZ) of the Arabian Sea. Metagenome analysis along the two sediment-cores revealed widespread occurrence of genes involved in microbial formation, oxidation, and reduction of tetrathionate; high diversity and relative-abundance was also detected for bacteria that are known to render these metabolisms in vitro. Results of slurry-incubation of the sediment-samples in thiosulfate- or tetrathionate-containing microbial growth media, data obtained via pure-culture isolation, and finally metatranscriptome analyses, corroborated the in situ functionality of tetrathionate-forming, oxidizing, and reducing microorganisms. Geochemical analyses revealed the presence of up to 11.1 μM thiosulfate along the two cores, except a few sample-sites near the sediment-surface. Thiosulfate oxidation by chemolithotrophic bacteria prevalent in situ is the apparent source of tetrathionate in this ecosystem. However, potential abiotic origin of the polythionate can neither be ruled out nor confirmed from the geochemical information currently available for this territory. Tetrathionate, in turn, can be either oxidized to sulfate (via oxidation by the chemolithotrophs present) or reduced back to thiosulfate (via respiration by native bacteria). Up to 2.01 mM sulfide present in the sediment-cores may also reduce tetrathionate abiotically to thiosulfate and elemental sulfur. As tetrathionate was not detected in situ, high microbiological and geochemical reactivity of this polythionate was hypothesized to be instrumental in its cryptic status as a central sulfur cycle intermediate. [ABSTRACT FROM AUTHOR]

To explore the potential role of tetrathionate in the sulfur cycle of marine sediments, the population ecology of tetrathionate-forming, oxidizing, and respiring microorganisms was revealed at 15-30 cm resolution along two, ~ 3-m-long, cores collected from 530- and 580-mbsl water-depths of Arabian Sea, off India's west coast, within the oxygen minimum zone (OMZ). Metagenome analysis along the two sediment-cores revealed widespread occurrence of the structural genes that govern these metabolisms; high diversity and relative-abundance was also detected for the bacteria known to render these processes. Slurry-incubation of the sediment-samples, pure-culture isolation, and metatranscriptome analysis, corroborated the in situ functionality of all the three metabolic-types. Geochemical analyses revealed thiosulfate (0-11.1 µM), pyrite (0.05-1.09 wt %), iron (9232-17234 ppm) and manganese (71-172 ppm) along the two sediment-cores. Pyrites (via abiotic reaction with MnO2) and thiosulfate (via oxidation by chemolithotrophic bacteria prevalent in situ) are apparently the main sources of tetrathionate in this ecosystem. Tetrathionate, in turn, can be either converted to sulfate (via oxidation by the chemolithotrophs present) or reduced back to thiosulfate (via respiration by native bacteria); 0-2.01 mM sulfide present in the sediment-cores may also reduce tetrathionate abiotically to thiosulfate and elemental sulfur. Notably tetrathionate was not detected in situ - high microbiological and geochemical reactivity of this polythionate is apparently instrumental in the cryptic nature of its potential role as a central sulfur cycle intermediate. Biogeochemical roles of this polythionate, albeit revealed here in the context of OMZ sediments, may well extend to the sulfur cycles of other geomicrobiologically-distinct marine sediment horizons. [ABSTRACT FROM AUTHOR]

Detailed phenotypic and genotypic characterization was done to establish the taxonomic position of a novel bacterial strain GG226T, frequently been isolated from the gut of Lepidocephalichthys guntea. Strain GG226T a Gram-negative, facultatively anaerobic, rod-shaped, motile, alkaliphilic bacterium. The 16S rRNA gene sequences analysis disclosed that GG226T belongs to genus Verticiella due to its maximum sequence identity with Verticiella sediminum XH089T (98.4%), the sole representative of this genus. A genome BLAST distance phylogeny (GBDP) tree, single nucleotide polymorphism (SNP) tree, and multi locus species tree (MLST) reconfirmed that GG226T shares its closest taxonomic identity with Verticiella sediminum XH089T. The DNA G + C content was estimated to be 67 mol%. When compared with Verticiella sediminum XH089T the DNA-DNA hybridization (dDDH) value was 21.90% and the average nucleotide identity (ANI) value was 80.13%; both of which were sufficiently below the threshold value (≤ 70% and ≤ 95–96%) for new prokaryotic species validation. The dominant fatty acids (> 5% of total fatty acids) were C16:0, summed feature 3 (C16:1ω7c/C16:1ω6c), C17:0 cyclo, and C12:0 3-OH. The strain GG226T has shown significant growth in pH 9 and 10, and noticeable high resistance to sodium arsenate (MIC: > 500 mM). The results of biochemical tests, phenotypic characteristics, genotypic data, and physiological properties could differentiate strain GG226T from its closest taxonomic relative. Hence, characterization based on chemotaxonomic, phenotypic, genomic, and phylogenetic evidence demonstrated that the strain GG226T represents a novel species of the genus Verticiella, for which the name Verticiella alkaliphila sp. nov. (type strain GG226T = MCC 5181T = JCM 36073T) is proposed. [ABSTRACT FROM AUTHOR]

New sputum negative (NSN) tuberculosis case detection in Jalpaiguri district has been consistently low. Availability and accessibility of health facilities with chet x-rays is key for the diagnosis of NSN cases. To identify factors associated with utilisation of x-ray facilities in the district, we interviewed 4,875 chest symptomatics who were sputum negative on two occasions with an antibiotics course in between. Chest radiography was available in only three public health facilities in the district. Low income, long distance from the public health facilities with chest radiography and high cost of x-rays at private hospitals were key factors associated with symptomatics not undergoing X-ray. It is necessary to increase facilities for radiological diagnosis and provide mobility support for the symptomatics in Jalpaiguri.