Biology subjects

Sarkar, J.

Publications and source records attributed to Sarkar, J..

15 recordsLinked to original sources

bioRxiv2026

Sustained presence of metabolically active mesophiles in the boiling vent-water of a low-salinity, slightly-alkaline, sulfate-rich geothermal spring characterized by an inequitable ecology of hyperthermophiles and thermophiles

Geothermal vent-heads exclusively support the proliferation of (hyper)thermophilic microorganisms. However, diverse mesophiles are stochastically thrust into these ecosystems by local geodynamic forces, and their population-level responses to the unfamiliar stressor hold critical implications for lifes intrinsic resilience to biophysical adversities. Here, we report a time-course exploration of the boiling vent-water of a Trans-Himalayan geothermal spring to determine the population dynamics, in situ functionalities, and potential ecological roles of mesophilic incomers in the context of indigenous (hyper)thermophiles. The temporally-consistent (hyper)thermophilic core-community, predominated in turn by a few Aquificia and Thermoproteota, was delineated as metagenome-assembled genomes. Mesophiles/moderate-thermophiles were identified as MAGs and/or pure-cultures, and whether temporally-consistent/inconsistent, had far lower prevalence. Overall, in situ transcriptional activity and prevalence had significant positive correlation; but many species exhibited high activity despite low prevalence and vice versa, implicating the decoupling of global metabolism from growth/proliferation. Bulked metatranscriptomic signatures identified the (hyper)thermophiles as primary producers of the ecosystem. Populations of mesophiles and moderate-thermophiles were apparently active, but not growing, in situ, with some being engaged in environment detoxification, and production of nutrients, metabolites and protective-biomolecules wanting in the (hyper)thermophiles. The findings engender an unprecedented portrayal of geothermal-vents as multi-community ecosystems where unfamiliar immigrants provide critical metabolic services.

microbiology↗

bioRxiv2026

ProteoMapper: Alignment-Aware Identification and Quantitative Analysis of Contextual Motif-Domain Patterns in Protein Families

Protein function depends on interactions between structural domains and regulatory motifs. Yet current tools analyze these elements separately, hindering investigation of disease mutations affecting evolutionarily conserved, structurally constrained motifs. We present ProteoMapper, a computational framework integrating HMMER-based domain annotation with user-defined motif detection to quantify motif-domain spatial relationships in protein families. ProteoMapper introduces two discovery metrics: (1) positional conservation scoring, identifying motifs at identical alignment coordinates in [≥] N% of sequences (default 60%), indicating purifying selection; (2) Motif-Domain Coverage Score (MDCS), quantifying motif embedding within Pfam domains (MDCS=1: fully embedded; MDCS=0: extra-domain). The platform processes Excel-formatted alignments without programming requirements, delivering color-coded reports with conserved motif positions, domain boundaries, and MDCS values. Parallel execution of sequence batches enables rapid analysis (8 motifs were searched in 150 sequences with complete Pfam scanning in <6 seconds on standard hardware). Validation across three protein families confirmed technical accuracy and biological insight. In PLATZ transcription factors (24 proteins), domain predictions achieved 0.94 mean intersection-over-union versus published annotations, exactly reproducing 22 of 23 reported spans. In Arabidopsis ERD6-like sugar transporters (17 proteins), MDCS analysis revealed canonical PROSITE signatures PS00216 and PS00217 are equally domain-embedded (MDCS=1.0) but evolutionarily divergent. PS00217 shows positional conservation (58.8% of sequences) while PS00216 exhibits dispersal, suggesting subfunctionalization. In tomato actin-depolymerizing factors (11 proteins), domain detection achieved 100% sensitivity with >93% positional concordance. ProteoMapper enables hypothesis-driven investigation of evolutionary constraints, regulatory mechanisms, and variant effect prediction in biomedical and functional proteomics. Source code, documentation, and test results with datasets at https://github.com/sifullah0/ProteoMapper.

bioinformatics↗

bioRxiv2025

Psychrophilic and cryophilic bacterial copiotrophs from a Trans-Himalayan lake-desert ecosystem as biogeothermometers of warming, mitigators of perturbation, and candidates for biodegradation

A Trans-Himalayan lake-desert ecosystem was explored for the low-to-high temperature adaptations of native copiotrophic psychrophiles that have the potentials for rendering substantive carbon remineralization under natural and/or anthropogenically influenced conditions of high organic matter delivery to the environment. Overall 27 species, classified across 15 genera of Actinomycetota, Bacillota, Bacteroidota, and Pseudomonadota, were isolated from the brackish-water and sediment-surface of Tso Moriri (a massive lacustrine body on the Changthang plateau that remains frozen for approximately one third of the year), and the fine talus covering a lake-side rocky mountain. In Luria broth, all the isolates grew at 4{degrees}C and 15{degrees}C; 13 of them grew, while 14 retained 19-99% cells in metabolically-active state, at -10{degrees}C; 23, 11, and none grew at 28{degrees}C, 37{degrees}C, and 42{degrees}C respectively. A Cryobacterium was most heat-susceptible, whereas some -10{degrees}C-growing Arthrobacter, Microbacterium, Paenarthrobacter, Pseudomonas and Streptomyces were most warming-resilient, among the present isolates. Catabolizing different simple/complex organic compounds, all isolates accomplished low/moderate/high growths at 4{degrees}C; 20 performed low growths at -10{degrees}C. Taxonomy/phylogeny did not determine the isolates growth/survival across the temperature-range tested. Lake-water and rock-dust isolates had the widest, while lake-sediment-dwellers had the narrowest, temperature-window for growth/survival. Rock-dust and lake-water isolates had more genes for low and high temperature adaptations, compared to the lake-sediment isolates. In co-cultures, most actinobacterial isolates inhibited the growth of mesophilic bacteria from warmer ecosystems, plus non-actinobacteria and actinobacteria from native/adjoining habitats. The data hold implications for biodegradation in cold/frigid territories, negative feedback control/reversal of warming, and microbiome protection from infiltration amidst climate change. IMPORTANCEPhylogenetically diverse, cold-adapted copiotrophic bacteria were retrieved from a Trans-Himalayan lake-desert ecosystem, and tested for chemoorganoheterotrophic growth at temperatures between -10{degrees}C and 42{degrees}C. Albeit growth dwindled at [≥]28{degrees}C, most of the isolates thrived on simple as well as complex organic substances under freezing condition, which makes them prospective constituents of biodegradation reactors suitable for high-altitude/latitude deployment. In the natural habitats of the psychrophilic isolates, cessation of organotrophic activities at elevated temperatures would stop simple fatty acids and CO2 production, which in turn would preempt methanogenesis, undo greenhouse effect, and reverse environmental thawing (usher cooling). Such negative feedback control of homeostasis is fraught with the danger of microbiome takeover by thermally-better-adapted foreign organisms. Consequently, ecosystem preservation rests on the native microfloras ability to resist external invasion. At 28{degrees}C, majority of the actinobacterial isolates inhibited bacteria from discrete higher-temperature ecosystems; they can, therefore, be viewed as the defenders of the cold/frigid ecosystem.

microbiology↗

bioRxiv2024

Co-existence of plasmid-mediated blaNDM-1 and blaNDM-5 in Escherichia coli sequence type 167 and ST101 and their discrimination through restriction digestion

The concurrent presence of multiple New Delhi metallo-{beta}-lactamase (blaNDM) variants within an isolate often goes undetected without the use of next-generation sequencing. This study detects and characterizes dual blaNDM-variants in Escherichia coli through Sanger and whole-genome sequencing. Additionally, a rapid identification method utilizing restriction digestion was designed for detecting variants carrying M154L mutation. Antibiotic susceptibility, minimal inhibitory concentration for meropenem and ertapenem, PCR and Sanger sequencing of blaNDM along with genome sequencing using Ilumina and Nanopore technology were conducted. Transmissibility and replicon types of blaNDM-harbouring plasmids were evaluated. Restriction digestion using restriction enzyme, BtsCI was developed to distinguish between blaNDM-1 and variants possessing M154L mutations. Two isolates belonging to phylogroups A; ST167 and B1; ST101 and resistant to meropenem and ertapenem ([≥]16mg/L) were recovered from the blood of a neonate and the rectal swab of a pregnant woman respectively. blaNDM was detected by PCR, and Sanger sequences of blaNDM showed two peaks at 262 (G & T) and 460 (A & C) nucleotide positions indicative of more than one blaNDM variant. Hybrid assembly confirmed co-existence of blaNDM-1 and blaNDM-5 in each isolate. blaNDM-1 was located on IncY (ST167) and IncHI1A/HI1B (ST101), while blaNDM-5 was on a IncFIA/FII (ST167) and IncC (ST101) plasmids. Digestion with BtsC1 could discriminate blaNDM-1 and blaNDM-5. Co-existence of multiple blaNDMS, blaNDM-1 and blaNDM-5 in epidemic clones of E. coli is concerning. Restriction digestion method and Sanger sequencing can facilitate quick identification of dual blaNDM variants in single isolate. ImportanceThe global dissemination of antimicrobial resistance genes is a serious concern. One such gene, blaNDM, has spread all across the globe via plasmids. blaNDM confers resistance against all {beta}-lactam antibiotics except monobactams. Most of the earlier literature reported presence of single blaNDM variants. However, this study reports the prevalence of dual blaNDM variants (blaNDM-1 and blaNDM-5) located on two separate plasmids identified in two distinct E. coli epidemic clones ST167 and ST101; isolated from a septicaemic neonate and a pregnant mother respectively. blaNDM-5 differs from blaNDM-1 due to presence of two point mutations i.e., V88L and M154L. This study detected dual blaNDM-variants through Sanger sequences and further validated through hybrid-genome assembly. Detection of multiple blaNDM-variants in a single isolate remains difficult until genome sequencing or southern blotting are carried out. Hence, a simple restriction digestion method was devised for rapid screening of dual blaNDM-variants containing M154L mutation.

microbiology↗

bioRxiv2023

Extremely oligotrophic and complex organic compounds degrading microaerobic bacteria from Arabian Sea oxygen minimum zone sediments

Sediments underlying marine hypoxic zones are huge sinks of unreacted complex organic matter, where despite acute O2-limitation obligately aerobic bacteria thrive, and steady depletion of organic carbon takes place within a few meters below the seafloor. However, little knowledge exists about the sustenance and complex carbon degradation potentials of aerobic chemoorganotrophs in these sulfidic ecosystems. We isolated and characterized a number of aerobic bacterial chemoorganoheterotrophs from across a [~]3 m sediment horizon underlying the perennial hypoxic zone of the eastern Arabian Sea. High levels of sequence correspondence between the isolates genomes and the habitats metagenomes and metatranscriptomes illustrated that the strains were widespread and active across the sediment-cores explored. The isolates catabolized several complex organic compounds of marine and terrestrial origins in the presence of high or low, but not zero, O2. Some of them could also grow anaerobically on yeast extract or acetate by reducing nitrate and/or nitrite. Fermentation did not support growth, but enabled all the strains to maintain a fraction of their cell populations over prolonged anoxia. Under extreme oligotrophy, limited growth followed by protracted stationary phase was observed for all the isolates at low cell density, amid high or low, but not zero, O2 concentration. While population control and maintenance could be particularly useful for the strains survival in the critically carbon-depleted layers below the explored sediment-depths (core-bottom organic carbon: 0.5-1.0 % w/w), metagenomic data suggested that in situ anoxia could be surmounted via potential supplies of cryptic O2 from previously-reported sources such as Nitrosopumilus species.

microbiology↗

bioRxiv2023

High diversity of Proteobacteria amid the dominance of a few Aquificae species in the vent-water of a Trans-Himalayan sulfur-borax hot spring

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 x 104 mL-1; live:dead cell ratio 1.7) thriving in the boiling (85{degrees}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 Ponds 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 Ponds vent-water have strains growing in the laboratory at >45{degrees}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 Ponds 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.

genomics↗

bioRxiv2023

PERK arm of UPR selectively regulates ferroptosis in colon cancer cells by modulating the expression of SLC7A11 (System Xc-)

Ferroptosis, a genetically and biochemically distinct form of programmed cell death, is characterised by an iron-dependent accumulation of lipid peroxides. Therapy-resistant tumor cells display vulnerability toward ferroptosis. Endoplasmic Reticulum (ER) stress and Unfolded Protein Response (UPR) play a critical role in cancer cells to become therapy resistant. Tweaking the balance of UPR to make cancer cells susceptible to ferroptotic cell death could be an attractive therapeutic strategy. To decipher the emerging contribution of ER-stress in the ferroptotic process, we observe that ferroptosis inducer RSL3 promotes UPR (PERK, ATF6, and IRE1), along with overexpression of cystine-glutamate transporter SLC7A11 (System Xc-). Exploring the role of a particular UPR arm in modulating SLC7A11 expression and subsequent ferroptosis, we notice that PERK is selectively critical in inducing ferroptosis in colorectal carcinoma. PERK inhibition reduces ATF4 expression and recruitment to the promoter of SLC7A11 and results in its downregulation. Loss of PERK function not only primes cancer cells for increased lipid peroxidation but also limits in vivo colorectal tumor growth, demonstrating active signs of ferroptotic cell death in situ. Further, by performing TCGA data mining and using colorectal cancer patient samples, we demonstrate that the expression of PERK and SLC7A11 is positively correlated. Overall, our experimental data indicate that PERK is a negative regulator of ferroptosis and loss of PERK function sensitizes colorectal cancer cells to ferroptosis. Therefore, small molecule PERK inhibitors hold huge promise as novel therapeutics and their potential can be harnessed against the apoptosis-resistant condition.

cancer biology↗

bioRxiv2022

Thermal endurance by a hot-spring-dwelling phylogenetic relative of the mesophilic Paracoccus

High temperature growth/survival was revealed in a phylogenetic relative (strain SMMA_5) of the mesophilic Paracoccus isolated from the 78-85{degrees}C water of a Trans- Himalayan sulfur-borax spring. After 12 h at 50{degrees}C, or 45 minutes at 70{degrees}C, in mineral salts thiosulfate (MST) medium, SMMA_5 retained [~]2% colony-forming units (CFUs), whereas comparator Paracoccus had 1.5% and 0% CFU left at 50{degrees}C and 70{degrees}C respectively. After 12 h at 50{degrees}C, the thermally-conditioned sibling SMMA_5_TC exhibited [~]1.5 time increase in CFU-count; after 45 minutes at 70{degrees}C, SMMA_5_TC had 7% of the initial CFU-count intact. 1000-times diluted Reasoners 2A medium, and MST supplemented with lithium, boron or glycine-betaine (solutes typical of the SMMA_5 habitat), supported higher CFU-retention/CFU-growth than MST. With or without lithium/boron/glycine-betaine in MST, a higher percentage of cells always remained viable (cytometry data), compared with what percentage remained capable of forming single colonies (CFU data). SMMA_5, compared with other Paracoccus, contained 335 unique genes, mostly for DNA replication/recombination/repair, transcription, secondary metabolites biosynthesis/transport/catabolism, and inorganic ion transport/metabolism. Its also exclusively enriched in cell wall/membrane/envelope biogenesis, and amino acid metabolism, genes. SMMA_5 and SMMA_5_TC mutually possessed 43 nucleotide polymorphisms, of which 18 were in protein-coding genes with 13 nonsynonymous and seven radical amino acid replacements. Such biochemical and biophysical mechanisms could be involved in thermal stress mitigation which streamline the cells energy and resources towards system-maintenance and macromolecule-stabilization, thereby relinquishing cell-division for cell-viability. Thermal conditioning apparently helped memorize those potential metabolic states which are crucial for cell-system maintenance, while environmental solutes augmented the indigenous stability-conferring mechanisms. IMPORTANCEFor a holistic understanding of microbial lifes high-temperature adaptation it is imperative to explore the biology of the phylogenetic relatives of mesophilic bacteria which get stochastically introduced to geographically and geologically diverse hot spring systems by local geodynamic forces. Here, in vitro endurance of high heat up to the extent of growth under special (habitat-inspired) conditions was discovered in a hot- spring-dwelling phylogenetic relative of the mesophilic Paracoccus species. Thermal conditioning, extreme oligotrophy, metabolic deceleration, presence of certain habitat- specific inorganic/organic solutes, and typical genomic specializations were found to be the major enablers of this conditional (acquired) thermophilicity. Feasibility of such phenomena across the taxonomic spectrum can well be paradigm-changing for the established scopes of microbial adaptation to the physicochemical extremes. Applications of conditional thermophilicity in microbial process biotechnology may be far reaching and multi-faceted.

microbiology↗

bioRxiv2022

Characterizing brain imaging features associated with ADAS-Cog13 sub-scores with 3D convolutional neural networks

To date, few advanced machine learning models have been developed for investigating the associations between features from brain imaging and individual Alzheimers disease (AD) related cognitive functional changes. Additionally, how these associations differ among different imaging modalities is unclear. Here we investigated 3D convolutional neural network (CNN) models which were trained to predict sub-scores in 13-item Alzheimers Disease Assessment Scale - Cognitive Subscale (ADAS-Cog13) based on MRI and FDG-PET brain imaging data obtained from the ADNI database. We found that each key ADAS-Cog13 sub-score was associated with a specific set of brain features within an imaging modality. Overall, sub-scores were strongly associated with structural changes of subcortical regions including amygdala, hippocampus, and putamen, and were associated with metabolic changes of cortical regions including the cingulated gyrus, occipital cortex, middle front gyrus, precuneus cortex, and the cerebellum. Our findings provided insights into complex AD etiology. Our analytical pipeline can also be utilized to study other brain diseases.

neuroscience↗

bioRxiv2020

Sedimentation rate and organic matter dynamics shape microbiomes across a continental margin

Marine sedimentation rate and bottom-water O2 concentration control the remineralization/sequestration of organic carbon across continental margins; but whether/how they shape microbiome architecture (the ultimate effector of all biogeochemical phenomena), across shelf/slope sediments, is unknown. Here we reveal distinct microbiome structures and functions, amidst comparable pore-fluid chemistries, along ~3 m sediment-horizons underlying the seasonal (shallow coastal) and perennial (deep sea) oxygen minimum zones (OMZs) of the Arabian Sea, situated across the western-Indian margin (water-depths: 31 m and, 530 and 580 m, respectively). Along the perennial- and seasonal-OMZ sediment-cores microbial communities were predominated by Gammaproteobacteria/Alphaproteobacteria and Euryarchaeota/Firmicutes respectively. As a perennial-OMZ signature, a cryptic methane production-consumption cycle was found to operate near the sediment-surface; overall diversity, as well as the relative abundances of simple-fatty-acids-requiring anaerobes (methanogens, anaerobic methane-oxidizers, sulfate-reducers and acetogens), peaked in the topmost sediment-layer and then declined via synchronized fluctuations until the sulfate-methane transition zone was reached. The entire microbiome profile was reverse in the seasonal-OMZ sediment-horizon. We discerned that in the perennial-OMZ sediments organic carbon deposited was higher in concentration, and marine components-rich, so it potentially degraded readily to simple fatty acids; lower sedimentation rate afforded higher O2 exposure time for organic matter degradation despite perennial hypoxia in the bottom-water; thus, the resultant abundance of reduced metabolites sustained multiple inter-competing microbial processes in the upper sediment-layers. Remarkably, the whole geomicrobial scenario was opposite in the sediments of the seasonal/shallow-water OMZ. Our findings create a microbiological baseline for understanding carbon-sulfur cycling across distinct marine depositional settings and water-colum n oxygenation regimes.

microbiology↗

bioRxiv2020

Salinomycin inhibits epigenetic modulator EZH2 to enhance Death Receptors in Colon Cancer Stem Cells

Drug resistance is one of the trademark features of Cancer Stem Cells (CSCs). We and others have recently shown that paucity of functional death receptors (DR4/5) on the cell surface of tumor cells is one of the major reasons for drug resistance, but their involvement in the context of in CSCs is poorly understood. By harnessing CSC specific cytotoxic function of salinomycin, we discovered a critical role of epigenetic modulator EZH2 in regulating the expression of DRs in colon CSCs. Our unbiased proteome profiler array approach followed by ChIP analysis of salinomycin treated cells indicated that the expression of DRs, especially DR4 is epigenetically repressed in colon CSCs. Concurrently, EZH2 knockdown demonstrated increased expression of DR4/DR5, significant reduction of CSC phenotype such as spheroid formation in-vitro and tumorigenic potential in-vivo in colon cancer. TCGA data analysis of human colon cancer clinical samples shows strong inverse correlation between EZH2 and DR4. Taken together, this study provides an insight about epigenetic regulation of DR4 in colon CSCs and advocates that drug resistant colon cancer can be therapeutically targeted by combining TRAIL and small molecule EZH2 inhibitors.

cancer biology↗

bioRxiv2019

Metabolically-active obligate aerobes in anoxic (sulfidic) marine sediments

Metabolically-active obligate aerobes are unheard-of in tightly-anoxic environments. Present culture-independent and culture-dependent investigations revealed aerobic microbial communities along two, ~3-meter-long sediment-cores underlying the eastern Arabian Sea oxygen minimum zone, where high H2S disallows O2 influx from the water-column. While genes for aerobic respiration by aa3-/cbb3-type cytochrome-c oxidases and cytochrome-bd ubiquinol oxidase, and aerobic oxidation of methane/ammonia/alcohols/thiosulfate/sulfite/organosulfur-compounds, were present across the cores, so were live aerobic, sulfur-chemolithoautotrophs and chemoorganoheterotrophs. The 8820-years-old, highly-sulfidic, methane-containing sediment-sample from 275 cmbsf of 530 mbsl yielded many such obligately-aerobic bacterial-isolates that died upon anaerobic incubation with alternative electron-acceptors/fermentative-substrates. Several metatranscriptomic reads from this sediment-sample matched aerobic-respiration-/oxidase-reaction-/transcription-/translation-/DNA-replication-/membrane-transport-/cell-division-related genes of the obligately-aerobic isolates, thereby corroborating their active aerobic metabolic-status in situ. Metagenomic and metatranscriptomic detection of perchlorate-/chlorate-reduction genes, plus anaerobic growth of an obligately-aerobic Halothiobacillus isolate in the presence of perchlorate and perchlorate-reducing-consortia, suggested that cryptic O2 produced by perchlorate-respirers could be sustaining obligately-aerobes in this environment.

microbiology↗

bioRxiv2019

Molecular mechanism of sulfur chemolithotrophy in the betaproteobacterium Pusillimonas ginsengisoli

Molecular mechanism of chemolithotrophic sulfur oxidation in Betaproteobacteria is less explored than that in Alphaproteobacteria. Here we carried out whole genome sequencing and analysis of a new betaproteobacterial isolate Pusillimonas ginsengisoli SBSA which oxidizes thiosulfate via formation tetrathionate as an intermediate. The 4.7-Mb SBSA genome was found to encompass a complete soxCDYZAXOB operon, plus one thiosulfate dehydrogenase (tsdA) and sulfite:acceptor oxidoreductase (sorAB) genes. Recombination-based knock-out of tsdA revealed that the entire thiosulfate oxidized by SBSA is first converted to tetrathionate, and no thiosulfate is directly converted to sulfate as typical of the Alphaproteobacterial Sox pathway whereas its tetrathionate-oxidizing ability was as good as that of the wild-type. The {triangleup}soxYZ knock-out mutant exhibited wild-type-like phenotype for thiosulfate/tetrathionate oxidation, whereas {triangleup}soxB oxidized thiosulfate only up to tetrathionate and had complete impairment of tetrathionate oxidation. However, substrate-dependent O2-consumption rate of whole cells, and sulfur-oxidizing enzyme activities of cell-free extracts, measured in the presence/absence of thiol-inhibitors/glutathione, indicated that glutathione plays a key role in SBSA tetrathionate oxidation. All the present findings collectively indicated that glutathione:tetrathionate coupling in Pusillimonas ginsengisoli may involve some unknown proteins other than thiol dehydrotransferase(ThdT), while subsequent oxidation of the potential glutathione:sulfodisulfane and sulfite molecules produced may proceed via soxBCD action.

microbiology↗

bioRxiv2019

Cryptic role of tetrathionate in the sulfur cycle: A study from Arabian Sea oxygen minimum zone sediments

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 Indias 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 M), 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.

microbiology↗

bioRxiv2019

Two pathways for thiosulfate oxidation in the alphaproteobacterial chemolithotroph Paracoccus thiocyanatus SST

Chemolithotrophic bacteria oxidize various sulfur species for energy and electrons, thereby operationalizing biogeochemical sulfur cycles in nature. The best-studied pathway of bacterial sulfur-chemolithotrophy, involving direct oxidation of thiosulfate to sulfate (without any free intermediate) by the SoxXAYZBCD multienzyme system, is apparently the exclusive mechanism of thiosulfate oxidation in facultatively chemolithotrophic alphaproteobacteria. Here we explore the molecular mechanisms of sulfur oxidation in the thiosulfate- and tetrathionate-oxidizing alphaproteobacterium Paracoccus thiocyanatus SST, and compare them with the prototypical Sox process characterized in Paracoccus pantotrophus. Our results revealed the unique case where, an alphaproteobacterium has Sox as its secondary pathway of thiosulfate oxidation, converting [~]10% of the thiosulfate supplied whilst 90% of the substrate is oxidized via a Tetrathionate-Intermediate pathway. Knock-out mutation, followed by the study of sulfur oxidation kinetics, showed that thiosulfate-to-tetrathionate conversion, in SST, is catalyzed by a thiosulfate dehydrogenase (TsdA) homolog that has far-higher substrate-affinity than the Sox system of this bacterium, which, remarkably, is also less efficient than the P. pantotrophus Sox. soxB-deletion in SST abolished sulfate-formation from thiosulfate/tetrathionate while thiosulfate-to-tetrathionate conversion remained unperturbed. Physiological studies revealed the involvement of glutathione in SST tetrathionate oxidation. However, zero impact of the knock-out of a thiol dehydrotransferase (thdT) homolog, together with no production of sulfite as an intermediate, indicated that tetrathionate oxidation in SST is mechanistically novel, and distinct from its betaproteobacterial counterpart mediated by glutathione, ThdT, SoxBCD and sulfite:acceptor oxidoreductase. All the present findings collectively highlight extensive functional diversification of sulfur-oxidizing enzymes across phylogenetically close, as well as distant, bacteria.

microbiology↗