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وضعیت برونداد علمی دانشگاه علوم پزشکی کردستان براساس شاخصهای علم سنجی تا پایان سال 2011 میلادی

Bacteria present in cave often survive by modifying their metabolic pathway or other mechanism. Understanding these adopted bacteria and their survival strategy inside the cave is an important aspect of microbial ecology. Present study focuses on the bacterial community and geochemistry in five caves of Mizoram, Northeast India. The objective of this study was to explore the taxonomic composition and presumed functional diversity of cave sediment metagenomes using paired end Illumina sequencing using V3 region of 16S rRNA gene and bioinformatics pipeline. Actinobacteria, Proteobacteria, Verrucomicrobia and Acidobacteria were the major phyla in all the five cave sediment samples. Among the five caves the highest diversity is found in Lamsialpuk with a Shannon index 12.5 and the lowest in Bukpuk (Shannon index 8.22). In addition, imputed metagenomic approach was used to predict the functional role of microbial community in biogeochemical cycling in the cave environments. Functional module showed high representation of genes involved in Amino Acid Metabolism in (20.9%) and Carbohydrate Metabolism (20.4%) in the KEGG pathways. Genes responsible for carbon degradation, carbon fixation, methane metabolism, nitrification, nitrate reduction and ammonia assimilation were also predicted in the present study. The cave sediments of the biodiversity hotspot region possessing a oligotrophic environment harbours high phylogenetic diversity dominated by Actinobacteria and Proteobacteria. Among the geochemical factors, ferric oxide was correlated with increased microbial diversity. In-silico analysis detected genes involved in carbon, nitrogen, methane metabolism and complex metabolic pathways responsible for the survival of the bacterial community in nutrient limited cave environments. Present study with Paired end Illumina sequencing along with bioinformatics analysis revealed the essential ecological role of the cave bacterial communities. These results will be useful in documenting the biospeleology of this region and systematic understanding of bacterial communities in natural sediment environments as well.

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Dominant bacterial phyla in caves and their predicted functional roles in C and N cycle.

Metagenomic analysis for profiling of microbial communities and tolerance in metal-polluted pulp and paper industry wastewater.

Persister cells are phenotypic variants within a microbial population, which are dormant and transiently tolerant to stress. Persistence has been studied extensively in bacteria, and in eukaryotes to a limited extent, however, it has never been observed in archaea. Using the model haloarchaeon, Haloferax volcanii DS2, we demonstrated persister cell formation in this domain, with time-kill curves exhibiting a characteristic biphasic pattern following starvation or exposure to lethal concentrations of various biocidal compounds. Repeated challenges of surviving cells showed that, as with bacteria, persister formation in H. volcanii was not heritable. Additionally, as previously shown with bacteria, persister formation in H. volcanii was suppressed by exogenous indole. The addition of spent culture media to assays conducted on planktonic cells showed that H. volcanii-conditioned media stimulated persistence, whereas conditioned media of other haloarchaea or halophilic bacteria did not, suggesting the involvement of a species-specific signal. Using a TLC overlay assay, the quorum sensing bioreporter Agrobacterium tumefaciens ATCC BAA-2240 detected the presence of C4 and C6 acyl homoserine lactone-like signal molecules in a H. volcanii culture extract. While synthetic bacterial AHLs did not induce persistence, this is potentially due to structural differences between bacterial and archaeal signals, and does not discount a quorum sensing component in haloarchaeal persister formation. The observation of persister cell formation by this haloarchaeon may provide some insights into the survival of these organisms in stressful or dynamic environments.

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Archaeal Persisters: Persister Cell Formation as a Stress Response in Haloferax volcanii.

Understanding the mechanisms underlying microbial resistance and resilience to perturbations is essential to predict the impact of climate change on Earth’s ecosystems. However, the resilience and adaptation mechanisms of microbial communities to natural perturbations remain relatively unexplored, particularly in extreme environments. The response of an extremophile community inhabiting halite (salt rocks) in the Atacama Desert to a catastrophic rainfall provided the opportunity to characterize and de-convolute the temporal response of a highly specialized community to a major disturbance. With shotgun metagenomic sequencing, we investigated the halite microbiome taxonomic composition and functional potential over a 4-year longitudinal study, uncovering the dynamics of the initial response and of the recovery of the community after a rainfall event. The observed changes can be recapitulated by two general modes of community shifts—a rapid Type 1 shift and a more gradual Type 2 adjustment. In the initial response, the community entered an unstable intermediate state after stochastic niche re-colonization, resulting in broad predicted protein adaptations to increased water availability. In contrast, during recovery, the community returned to its former functional potential by a gradual shift in abundances of the newly acquired taxa. The general characterization and proposed quantitation of these two modes of community response could potentially be applied to other ecosystems, providing a theoretical framework for prediction of taxonomic and functional flux following environmental changes.

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Halophilic microbial community compositional shift after a rare rainfall in the Atacama Desert

Haloarchaea are unique microorganism's resistant to environmental and osmotic stresses and thrive in their habitats despite extreme fluctuating salinities In the present study, haloarchaea were isolated from hypersaline thalossohaline salterns of Bhandup, Mumbai, India and were identified as Haloferax prahovense, Haloferax alexandrines, Haloferax lucentense, Haloarcula tradensis, Haloarcula marismortui and Haloarcula argentinensis The mechanism of adaptation to contrasting salinities (15 M and 45 M) was investigated in the extreme haloarchaeon, Hal marismortui RR12 Hal marismortui RR12 increased the intracellular sequestration of K(+) and Cl(-) ions in hypo salinity and hyper salinity respectively as detected by Energy-dispersive X-ray spectroscopy microanalysis (EDAX) and Inductively Coupled Plasma- atomic Emission Spectroscopy (ICP-AES) indicating the presence of 'salt-in' strategy of osmoadaptation As a cellular response to salinity stress, it produced small heat shock like proteins (sHSP) identified using MALDI-TOF MS and increased the production of protective red carotenoid pigment This is the first report on the study of the concomitant cellular, molecular and physiological mechanism adapted by Hal marismortui RR12 when exposed to contrasting salinities in external environment

Biology and survival of extremely halophilic archaeon Haloarcula marismortui RR12 isolated from Mumbai salterns, India in response to salinity stress.

Marine microbes play a key role and contribute largely to the global biogeochemical cycles. This study aims to explore microbial diversity from one such ecological hotspot, the continental shelf of Agatti Island. Sediment samples from various depths of the continental shelf were analyzed for bacterial diversity using deep sequencing technology along with the culturable approach. Additionally, imputed metagenomic approach was carried out to understand the functional aspects of microbial community especially for microbial genes important in nutrient uptake, survival and biogeochemical cycling in the marine environment. Using culturable approach, 28 bacterial strains representing 9 genera were isolated from various depths of continental shelf. The microbial community structure throughout the samples was dominated by phylum Proteobacteria and harbored various bacterioplanktons as well. Significant differences were observed in bacterial diversity within a short region of the continental shelf (1–40 meters) i.e. between upper continental shelf samples (UCS) with lesser depths (i.e. 1–20 meters) and lower continental shelf samples (LCS) with greater depths (i.e. 25–40 meters). By using imputed metagenomic approach, this study also discusses several adaptive mechanisms which enable microbes to survive in nutritionally deprived conditions, and also help to understand the influence of nutrition availability on bacterial diversity.

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Insights into Diversity and Imputed Metabolic Potential of Bacterial Communities in the Continental Shelf of Agatti Island.

A novel Gram-stain-positive, spore-forming, aerobic, non-motile, rod-shaped bacterium designated strain SD111(T) that forms red-pigmented colonies was isolated from a marine sediment sample (collected from 5 m depth) from Lakshadweep, India. Strain SD111(T) grew well on seawater agar at pH 6-10 (optimum pH 7.5±0.2). It showed maximum (97.6 %) 16S rRNA gene sequence similarity and formed a monophyletic clade with Domibacillus robiginosus WS 4628(T) ( = DSM 25058(T)). The genomic DNA G+C content was 37.4 mol% and the strain showed 37.7 % DNA-DNA relatedness to D. robiginosus DSM 25058(T). The major fatty acids were anteiso-C15 : 0, C16 : 0, iso-C15 : 0 and iso-C16 : 0 and MK-6 was the predominant quinone. The polar lipid profile of strain SD111(T) consisted of unidentified phospholipids (PL1 and PL2), phosphatidylglycerol (PG) and diphosphatidylglycerol (DPG). The cell wall contained meso-diaminopimelic acid and the peptidoglycan was of A1γ type. Glucose and ribose were detected as major cell-wall sugars. Results from polyphasic studies indicated that SD111(T) represents a novel species of the genus Domibacillus for which the name Domibacillus indicus sp. nov. is proposed. The type strain is SD111(T) ( = MCC 2255(T) = DSM 28032(T)).

Description of Domibacillus indicus sp. nov., isolated from ocean sediments and emended description of the genus Domibacillus.

Culture-dependent and independent approaches were used to understand the microbiota thriving in tertiary coalbed, located in Jammu and Kashmir, India. We observed changes in physicochemical properties of the surface sediment (CM1) and coalbed (CM2) which detailed the influence of environmental factors on the structure and capabilities of bacterial communities. A total of 316 bacterial isolates representing 35 genera were isolated. We noted comparable difference in uncultivable bacterial communities which revealed the predominance of Proteobacteria in both the study sites. Moreover, we observed differential abundance of phyla Actinobacteria (49.6%), Firmicutes (4.2%), and Bacteroidetes (0.8%) in CM1, whereas Actinobacteria (11%), Firmicutes (37.8%), and Bacteroidetes (2.3%) in CM2. Additionally, functional imputations using PICRUSt depicted ∼30% higher assemblage of major gene families in CM1 in comparison to CM2. Bacterial communities residing at CM1 were predominantly involved in methane oxidation, whereas CM2 communities found to play a vital process of conversion of coal to biogenic-methane enabling microbes to survive under constraints of high sulfur content, salt precipitation, and low nutrients and also provide clues to understand the potential of methanogenesis.

Geochemistry Shapes Bacterial Communities and their Metabolic Potentials in Tertiary Coalbed

The survival of archaeabacteria in extreme inhabitable environments on earth that challenge organismic survival is ubiquitously known. However, the studies related to the effect of hypergravity on the growth and proliferation of archaea are unprecedented. The survival of organisms in hypergravity and rocks in addition to resistance to cosmic radiations, pressure and other extremities is imperative to study the possibilities of microbial travel between planets and endurance in hyperaccelerative forces faced during ejection of rocks from planets. The current investigation highlights the growth of an extremophilic archaeon isolated from a rocky substrate in hypergravity environment. The haloalkaliphilic archaeon, Natronococcus jeotgali RR17 was isolated from an Indian laterite rock, submerged in the Arabian sea lining Coastal Maharashtra, India. The endolithic haloarchaeon was subjected to hypergravity from 56 – 893 X gusing acceleration generated by centrifugal rotation. The cells of N. jeotgali RR17 proliferated and demonstrated good growth in hypergravity (223 X g). This is the first report on isolation of endolithic haloarchaeon N. jeotgali RR17 from an Indian laterite rock and its ability to proliferate in hypergravity. The present study demonstrates the ability of microbial life to survive and proliferate in hypergravity. Thus the inability of organismic growth in hypergravity may no longer be a limitation for astrobiology studies related to habitability of substellar objects, brown dwarfs and other planetary bodies in the universe besides planet earth.

Sunil Kumar Dhar

Papers

Biology and survival of extremely halophilic archaeon Haloarcula marismortui RR12 isolated from Mumbai salterns, India in response to salinity stress.

Insights into Diversity and Imputed Metabolic Potential of Bacterial Communities in the Continental Shelf of Agatti Island.

Description of Domibacillus indicus sp. nov., isolated from ocean sediments and emended description of the genus Domibacillus.

Geochemistry Shapes Bacterial Communities and their Metabolic Potentials in Tertiary Coalbed

Response of Haloalkaliphilic Archaeon Natronococcus Jeotgali RR17 to Hypergravity