Comparative analysis of prokaryotic microbiomes in high-altitude active layer soils: insights from Ladakh and global analogues using In-Silico approaches.

The active layer is the portion of soil overlaying the permafrost that freezes and thaws seasonally. It is a harsh habitat in which a varied and vigorous microbial population thrives. The high-altitude active layer soil in northern India is a unique and important cryo-ecosystem. However, its microbiology remains largely unexplored. It represents a unique reservoir for microbial communities with adaptability to harsh environmental conditions. In the Changthang region of Ladakh, the Tsokar area is a high-altitude permafrost-affected area situated in the southern part of Ladakh, at a height of 4530 m above sea level. Results of the comparison study with the QTP, Himalayan, Alaskan, Russian, Canadian and Polar active layers showed that the alpha diversity was significantly higher in the Ladakh and QTP active layers as the environmental condition of both the sites were similar. Moreover, the sampling site in the Ladakh region was in a thawing condition at the time of sampling which possibly provided nutrients and access to alternative nitrogen and carbon sources to the microorganisms thriving in it. Analysis of the samples suggested that the geochemical parameters and environmental conditions shape the microbial alpha diversity and community composition. Further analysis revealed that the cold-adapted methanogens were present in the Ladakh, Himalayan, Polar and Alaskan samples and absent in QTP, Russian and Canadian active layer samples. These methanogens could produce methane at slow rates in the active layer soils that could increase the atmospheric temperature owing to climate change.

Validated checklist for assessing communication skills in undergraduate medical students: bridging the gap for effective doctor-patient interactions.

Communication skills are fundamental in healthcare, but assessing them among medical students presents challenges. In the Indian context, the lack of a specific assessment tool further compounds the issue. Thus this study aimed to develop and validate an observation-based communication skills checklist tailored to Phase I Bachelor of Medicine and Bachelor of Surgery (MBBS) students. The checklist was developed using both inductive and deductive approaches and underwent rigorous testing to ensure its reliability and validity. After piloting, the finalized version was administered to 84 Phase I MBBS students. Results indicated a critical content validity ratio of 0.78, face validity of 0.80, and an impressive Cronbach's alpha of 0.91, indicating good internal consistency and reliability of the checklist. The students scored over 80% in all checklist domains, except for empathy (73%) and support (74%), highlighting areas for potential improvement. Nonetheless, about 75% of students expressed satisfaction with the checklist's communication skills assessment. The feedback from faculty members was positive, as they found the checklist was easy to use, quick, and effective for evaluating communication skills. Consequently, the checklist's introduction has been well received by both students and faculty. In conclusion, the developed checklist proves to be an effective and valid instrument for assessing communication skills in Phase I MBBS students. By integrating this tool into observed station clinical examinations, medical educators can comprehensively evaluate students' communication behaviors. Moreover, the checklist serves as a valuable resource for bridging the gap between theoretical knowledge and practical application, enabling future physicians to excel in doctor-patient interactions, a crucial aspect of patient-centered care.NEW & NOTEWORTHY This article presents a highly unique and novel approach by introducing a structured checklist for communication skill assessment in medical students. Its rigorous validation process ensures reliability and effectiveness, while its adaptation to sociocultural norms highlights its relevance and applicability. The user-friendly design with a single-page layout and dichotomous scale further enhances its practicality in objective structured clinical examinations. The developed checklist equips educators with a valuable resource to assess and improve students' communication abilities.

Metal-organic frameworks (MOFs) based luminescent and electrochemical sensors for food contaminant detection.

With the increasing population, food toxicity has become a prevalent concern due to the growing contaminants of food products. Therefore, the need for new materials for toxicant detection and food quality monitoring will always be in demand. Metal-organic frameworks (MOFs) based on luminescence and electrochemical sensors with tunable porosity and active surface area are promising materials for food contaminants monitoring. This review summarizes and studies the most recent progress on MOF sensors for detecting food contaminants such as pesticides, antibiotics, toxins, biomolecules, and ionic species. First, with the introduction of MOFs, food contaminants and materials for toxicants detection are discussed. Then the insights into the MOFs as emerging materials for sensing applications with luminescent and electrochemical properties, signal changes, and sensing mechanisms are discussed. Next, recent advances in luminescent and electrochemical MOFs food sensors and their sensitivity, selectivity, and capacities for common food toxicants are summarized. Further, the challenges and outlooks are discussed for providing a new pathway for MOF food contaminant detection tools. Overall, a timely source of information on advanced MOF materials provides materials for next-generation food sensors.

Tuning the Photometric Properties of Ternary Sm3+ Complexes Involving Mixed-Ligands.

This research article deals with the synthesis of ternary Sm3+ complexes with 6,8-dichlorochromone-3-carboxaldehyde through solution-precipitation method. The photometric properties of resultant complexes were tuned by coordinating N-donor heterocyclic ligands with Sm3+ ion. The emission spectra, obtained in the visible region have been studied. Under optical excitation of 370 nm, the complexes displayed characteristic Sm3+-centered emission peaks at ~ 563, 600 and 647 nm in solution as well as in powder state. The complexes showed thermal stability up to 175 °C. The complexes delivered quantum yield as high as 7.91% and longest emission lifetime of 0.564 ms. The color coordinates of the complexes, located in deep orange (in solution) and red (in powder) spectral region, matched well with the Society of Motion Picture and Television Engineers and European Broadcasting Union. The properties of complexes have been investigated to a significant extent due to their easy synthesis and potential applications as orange-red light emitter in a wide range of photonic applications such as display devices, OLEDs, dashboards, optical systems.

Comparative Metagenomics of the Active Layer and Permafrost from Low-Carbon Soil in the Canadian High Arctic.

Approximately 87% of the Arctic consists of low-organic carbon mineral soil, but knowledge of microbial activity in low-carbon permafrost (PF) and active layer soils remains limited. This study investigated the taxonomic composition and genetic potential of microbial communities at contrasting depths of the active layer (5, 35, and 65 cm below surface, bls) and PF (80 cm bls). We showed microbial communities in PF to be taxonomically and functionally different from those in the active layer. 16S rRNA gene sequence analysis revealed higher biodiversity in the active layer than in PF, and biodiversity decreased significantly with depth. The reconstructed 91 metagenome-assembled genomes showed that PF was dominated by heterotrophic, fermenting Bacteroidota using nitrite as their main electron acceptor. Prevalent microbes identified in the active layer belonged to bacterial taxa, gaining energy via aerobic respiration. Gene abundance in metagenomes revealed enrichment of genes encoding the plant-derived polysaccharide degradation and metabolism of nitrate and sulfate in PF, whereas genes encoding methane/ammonia oxidation, cold-shock protein, and two-component systems were generally more abundant in the active layer, particularly at 5 cm bls. The results of this study deepen our understanding of the low-carbon Arctic soil microbiome and improve prediction of the impacts of thawing PF.

Thaumarchaea Genome Sequences from a High Arctic Active Layer.

The role of archaeal ammonia oxidizers often exceeds that of bacterial ammonia oxidizers in marine and terrestrial environments but has been understudied in permafrost, where thawing has the potential to release ammonia. Here, three thaumarchaea genomes were assembled and annotated from metagenomic data sets from carbon-poor Canadian High Arctic active-layer cryosols.

Metagenome-Assembled Genome of USCα AHI, a Potential High-Affinity Methanotroph from Axel Heiberg Island, Canadian High Arctic.

Metagenomic sequencing of active-layer cryosols from the Canadian High Arctic has yielded a nearly complete genome for an atmospheric CH4-oxidizing bacterium belonging to upland soil cluster α (USCα). This genome contains genes involved in CH4 metabolism, H2 metabolism, and multiple carbon assimilation pathways.

Emergence of Orientia tsutsugamushi as an important cause of Acute Encephalitis Syndrome in India.

BACKGROUND: Acute Encephalitis Syndrome (AES) is a major seasonal public health problem in Bihar, India. Despite efforts of the Bihar health department and the Government of India, burden and mortality of AES cases have not decreased, and definitive etiologies for the illness have yet to be identified. OBJECTIVES: The present study was undertaken to study the specific etiology of AES in Bihar. METHODS: Cerebrospinal fluid and/or serum samples from AES patients were collected and tested for various pathogens, including viruses and bacteria by ELISA and/or Real Time PCR. FINDINGS: Of 540 enrolled patients, 33.3% (180) tested positive for at least one pathogen of which 23.3% were co-positive for more than one pathogen. Most samples were positive for scrub typhus IgM or PCR (25%), followed by IgM positivity for JEV (8.1%), WNV (6.8%), DV (6.1%), and ChikV (4.5%).M. tuberculosis and S. pneumoniae each was detected in ~ 1% cases. H. influenzae, adenovirus, Herpes Simplex Virus -1, enterovirus, and measles virus, each was detected occasionally. The presence of Scrub typhus was confirmed by PCR and sequencing. Bihar strains resembled Gilliam-like strains from Thailand, Combodia and Vietnam. CONCLUSION: The highlights of this pilot AES study were detection of an infectious etiology in one third of the AES cases, multiple etiologies, and emergence of O. tsutsugamushi infection as an important causative agent of AES in India.

Metagenomes of microbial communities in arsenic- and pathogen-contaminated well and surface water from bangladesh.

The contamination of drinking water from both arsenic and microbial pathogens occurs in Bangladesh. A general metagenomic survey of well water and surface water provided information on the types of pathogens present and may help elucidate arsenic metabolic pathways and potential assay targets for monitoring surface-to-ground water pathogen transport.

Metagenomes from thawing low-soil-organic-carbon mineral cryosols and permafrost of the canadian high arctic.

Microbial release of greenhouse gases from thawing permafrost is a global concern. Seventy-six metagenomes were generated from low-soil-organic-carbon mineral cryosols from Axel Heiberg Island, Nunavut, Canada, during a controlled thawing experiment. Permafrost thawing resulted in an increase in anaerobic fermenters and sulfate-reducing bacteria but not methanogens.

Draft genome sequences of 10 strains of the genus exiguobacterium.

High-quality draft genome sequences were determined for 10 Exiguobacterium strains in order to provide insight into their evolutionary strategies for speciation and environmental adaptation. The selected genomes include psychrotrophic and thermophilic species from a range of habitats, which will allow for a comparison of metabolic pathways and stress response genes.

Integrated metagenomics and metatranscriptomics analyses of root-associated soil from transgenic switchgrass.

The benefits of using transgenic switchgrass with decreased levels of caffeic acid 3-O-methyltransferase (COMT) as biomass feedstock have been clearly demonstrated. However, its effect on the soil microbial community has not been assessed. Here we report metagenomic and metatranscriptomic analyses of root-associated soil from COMT switchgrass compared with nontransgenic counterparts.

Commercial DNA extraction kits impact observed microbial community composition in permafrost samples.

The total community genomic DNA (gDNA) from permafrost was extracted using four commercial DNA extraction kits. The gDNAs were compared using quantitative real-time PCR (qPCR) targeting 16S rRNA genes and bacterial diversity analyses obtained via 454 pyrosequencing of the 16S rRNA (V3 region) amplified in single or nested PCR. The FastDNA(®) SPIN (FDS) Kit provided the highest gDNA yields and 16S rRNA gene concentrations, followed by MoBio PowerSoil(®) (PS) and MoBio PowerLyzer™ (PL) kits. The lowest gDNA yields and 16S rRNA gene concentrations were from the Meta-G-Nome™ (MGN) DNA Isolation Kit. Bacterial phyla identified in all DNA extracts were similar to that found in other soils and were dominated by Actinobacteria, Firmicutes, Gemmatimonadetes, Proteobacteria, and Acidobacteria. Weighted UniFrac and statistical analyses indicated that bacterial community compositions derived from FDS, PS, and PL extracts were similar to each other. However, the bacterial community structure from the MGN extracts differed from other kits exhibiting higher proportions of easily lysed ß- and γ-Proteobacteria and lower proportions of Actinobacteria and Methylocystaceae important in carbon cycling. These results indicate that gDNA yields differ between the extraction kits, but reproducible bacterial community structure analysis may be accomplished using gDNAs from the three bead-beating lysis extraction kits.

Pseudomonas fluorescens HK44: lessons learned from a model whole-cell bioreporter with a broad application history.

Initially described in 1990, Pseudomonas fluorescens HK44 served as the first whole-cell bioreporter genetically endowed with a bioluminescent (luxCDABE) phenotype directly linked to a catabolic (naphthalene degradative) pathway. HK44 was the first genetically engineered microorganism to be released in the field to monitor bioremediation potential. Subsequent to that release, strain HK44 had been introduced into other solids (soils, sands), liquid (water, wastewater), and volatile environments. In these matrices, it has functioned as one of the best characterized chemically-responsive environmental bioreporters and as a model organism for understanding bacterial colonization and transport, cell immobilization strategies, and the kinetics of cellular bioluminescent emission. This review summarizes the characteristics of P. fluorescens HK44 and the extensive range of its applications with special focus on the monitoring of bioremediation processes and biosensing of environmental pollution.

Complete genome sequence of Thauera aminoaromatica strain MZ1T.

Thauera aminoaromatica strain MZ1T, an isolate belonging to genus Thauera, of the family Rhodocyclaceae and the class the Betaproteobacteria, has been characterized for its ability to produce abundant exopolysaccharide and degrade various aromatic compounds with nitrate as an electron acceptor. These properties, if fully understood at the genome-sequence level, can aid in environmental processing of organic matter in anaerobic cycles by short-circuiting a central anaerobic metabolite, acetate, from microbiological conversion to methane, a critical greenhouse gas. Strain MZ1T is the first strain from the genus Thauera with a completely sequenced genome. The 4,496,212 bp chromosome and 78,374 bp plasmid contain 4,071 protein-coding and 71 RNA genes, and were sequenced as part of the DOE Community Sequencing Program CSP_776774.

Draft genome sequence of the polycyclic aromatic hydrocarbon-degrading, genetically engineered bioluminescent bioreporter Pseudomonas fluorescens HK44.

Pseudomonas fluorescens strain HK44 (DSM 6700) is a genetically engineered lux-based bioluminescent bioreporter. Here we report the draft genome sequence of strain HK44. Annotation of ∼6.1 Mb of sequence indicates that 30% of the traits are unique and distributed over five genomic islands, a prophage, and two plasmids.

Reductive dehalogenation mediated initiation of aerobic degradation of 2-chloro-4-nitrophenol (2C4NP) by Burkholderia sp. strain SJ98.

Burkholderia sp. strain SJ98 (DSM 23195) was previously isolated and characterized for degradation and co-metabolic transformation of a number nitroaromatic compounds. In the present study, we evaluated its metabolic activity on chlorinated nitroaromatic compounds (CNACs). Results obtained during this study revealed that strain SJ98 can degrade 2-chloro-4-nitrophenol (2C4NP) and utilize it as sole source of carbon, nitrogen, and energy under aerobic conditions. The cells of strain SJ98 removed 2C4NP from the growth medium with sequential release of nearly stoichiometric amounts of chloride and nitrite in culture supernatant. Under aerobic degradation conditions, 2C4NP was transformed into the first intermediate that was identified as p-nitrophenol by high-performance liquid chromatography, LCMS-TOF, and GC-MS analyses. This transformation clearly establishes that the degradation of 2C4NP by strain SJ98 is initiated by "reductive dehalogenation"; an initiation mechanism that has not been previously reported for microbial degradation of CNAC under aerobic conditions.

Chryseomicrobium imtechense gen. nov., sp. nov., a new member of the family Planococcaceae.

A Gram-stain-positive, rod-shaped, yellow, non-motile, non-spore-forming, strictly aerobic bacterial strain, designated MW 10(T), was isolated from seawater of the Bay of Bengal, India, and was subjected to a polyphasic taxonomic study. Analysis of the 16S rRNA gene sequence revealed that strain MW 10(T) showed highest similarity to the type strains of Psychrobacillus psychrodurans (96.15 %) and Psychrobacillus psychrotolerans (96.01 %) and showed less than 96 % similarity to members of the genera Paenisporosarcina, Planococcus, Sporosarcina and Planomicrobium. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain MW 10(T) formed a clade separate from members of closely related genera. The morphological, physiological and chemotaxonomic characteristics of strain MW 10(T) differed from those of members of closely related genera. The major fatty acid in strain MW 10(T) was iso-C(15 : 0) and the menaquinones were MK-7 (48.4 %), MK-8 (32.3 %), MK-7(H(2)) (13.7 %) and MK-6 (5.6 %). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unknown phospholipid, an unknown lipid and an unknown glycolipid. The cell-wall peptidoglycan type was l-Lys-d-Asp. The genomic DNA G+C content (53.4 mol%) of strain MW 10(T) was significantly different from those of members of closely related genera. On the basis of its morphological, physiological and chemotaxonomic characteristics as well as our phylogenetic analysis, we conclude that strain MW 10(T) is a member of a novel genus and species, for which the name Chryseomicrobium imtechense gen. nov., sp. nov., is proposed. The type strain of Chryseomicrobium imtechense is MW 10(T) ( = MTCC 10098(T)  = JCM 16573(T)).

Biodegradation: gaining insight through proteomics.

Biodegradation, a generic term used to describe methodologies to affect cleanup of environmental pollutants, has come up as an improved substitute for ineffective and expensive physico-chemical remediation methods. However, lack of information about the factors controlling the growth and metabolism of microorganisms in the polluted environment often limits its implementation. Recent advances in the understanding of biogeochemical processes and genomics have opened up new perspectives towards new opportunities of pollution abatement. High throughput genomic techniques have revolutionized the remediation process leading to breakthroughs in characterizing proteomes, metabolomes and phenotypes for organisms, communities and populations. These new techniques have allowed us to address longstanding questions regarding the molecular mechanisms that may control the mineralization processes and have an in-depth understanding of microbial community structure and stress responses. In order to explore insights of biodegradation this article discusses ways in which proteomics may be able to meet challenges in biodegradation.

p-Nitrophenol degradation via 4-nitrocatechol in Burkholderia sp. SJ98 and cloning of some of the lower pathway genes.

Microbial degradation studies have pointed toward the occurrence of two distinct PNP catabolic pathways in Gram positive and Gram negative bacteria. The former involves 4-nitrocatechol (4-NC), 1,2,4-benzenetriol (BT), and maleylacetate (MA) as major degradation intermediates, whereas the later proceeds via formation of 1,4-benzoquinone (BQ) and hydroquinone (HQ). In the present study we identified a Gram negative organism viz. Burkholderia sp. strain SJ98 that degrades PNP via 4NC, BT, and MA. A 6.89 Kb genomic DNA fragment of strain SJ98 that encompasses seven putatively identified ORFs (orfA, pnpD, pnpC, orfB, orfC, orfD, and orfE) was cloned. PnpC is benzenetriol dioxygenase belonging to the intradiol dioxygenase superfamily, whereas PnpD is identified as maleylacetate reductase, a member of the Fe-ADH superfamily showing NADH dependent reductase activity. The in vitro activity assays carried out with purified pnpC and pnpD (btd and mar) gene products transformed BT to MA and MA to beta-ketoadipate, respectively. The cloning, sequencing, and characterization of these genes along with the functional PNP degradation studies ascertained the involvement of 4-NC, BT, and MA as degradation intermediates of PNP pathway in this strain. This is one of the first conclusive reports for 4-NC and BT mediated degradation of PNP in a Gram negative organism.