Novel oceanic cyanobacterium isolated from Bangaram island with profound acid neutralizing ability is proposed as Leptolyngbya iicbica sp. nov. strain LK.

An acid-neutralizing, filamentous, non-heterocytous, marine cyanobacterium named 'LK' has been isolated from the seashore of Bangaram Island, an atoll of Lakshadweep, India, and is described here as a novel species. LK has been characterized using morphological, ecological, and genomic features. Based on 16S rRNA, whole-genome sequencing, and marker gene-based analysis, LK has been identified as a new species. LK clustered with Leptolyngbya-like strains belonging to the LPP group but diverged from Leptolyngbya sensu stricto, indicating the polyphyletic nature of the Leptolyngbya genus. Leptolyngbya sp. SIOISBB and Halomicronema sp. CCY15110 were identified as LK's two closest phylogenetic neighbors in various phylogenetic studies. The analysis of 16S rRNA, ITS secondary structures, and genome relatedness indices such as AAI, ANI, and gANI strongly support LK as a novel species of the Leptolyngbya genus. The mechanism behind acid neutralization in LK has been delineated, attributing it to a surface phenomenon most likely due to the presence of salts of calcium, magnesium, sodium, and potassium. We name LK as Leptolyngbya iicbica strain LK which is a novel species with prominent acidic pH-neutralizing properties.

Comparative transcriptome profiling provides insights into the growth promotion activity of Pseudomonas fluorescens strain SLU99 in tomato and potato plants.

The use of biocontrol agents with plant growth-promoting activity has emerged as an approach to support sustainable agriculture. During our field evaluation of potato plants treated with biocontrol rhizobacteria, four bacteria were associated with increased plant height. Using two important solanaceous crop plants, tomato and potato, we carried out a comparative analysis of the growth-promoting activity of the four bacterial strains: Pseudomonas fluorescens SLU99, Serratia plymuthica S412, S. rubidaea AV10, and S. rubidaea EV23. Greenhouse and in vitro experiments showed that P. fluorescens SLU99 promoted plant height, biomass accumulation, and yield of potato and tomato plants, while EV23 promoted growth in potato but not in tomato plants. SLU99 induced the expression of plant hormone-related genes in potato and tomato, especially those involved in maintaining homeostasis of auxin, cytokinin, gibberellic acid and ethylene. Our results reveal potential mechanisms underlying the growth promotion and biocontrol effects of these rhizobacteria and suggest which strains may be best deployed for sustainably improving crop yield.

Constitutional isomerism of the linkages in donor-acceptor covalent organic frameworks and its impact on photocatalysis.

When new covalent organic frameworks (COFs) are designed, the main efforts are typically focused on selecting specific building blocks with certain geometries and properties to control the structure and function of the final COFs. The nature of the linkage (imine, boroxine, vinyl, etc.) between these building blocks naturally also defines their properties. However, besides the linkage type, the orientation, i.e., the constitutional isomerism of these linkages, has rarely been considered so far as an essential aspect. In this work, three pairs of constitutionally isomeric imine-linked donor-acceptor (D-A) COFs are synthesized, which are different in the orientation of the imine bonds (D-C=N-A (DCNA) and D-N=C-A (DNCA)). The constitutional isomers show substantial differences in their photophysical properties and consequently in their photocatalytic performance. Indeed, all DCNA COFs show enhanced photocatalytic H2 evolution performance than the corresponding DNCA COFs. Besides the imine COFs shown here, it can be concluded that the proposed concept of constitutional isomerism of linkages in COFs is quite universal and should be considered when designing and tuning the properties of COFs.

Genome Analysis Coupled With Transcriptomics Reveals the Reduced Fitness of a Hot Spring Cyanobacterium Mastigocladus laminosus UU774 Under Exogenous Nitrogen Supplement.

The present study focuses on the stress response of a filamentous, AT-rich, heterocystous cyanobacterium Mastigocladus laminosus UU774, isolated from a hot spring, Taptapani, located in the eastern part of India. The genome of UU774 contains an indispensable fragment, scaffold_38, of unknown origin that is implicated during severe nitrogen and nutrition stress. Prolonged exposure to nitrogen compounds during starvation has profound adverse effects on UU774, leading to loss of mobility, loss of ability to fight pathogens, reduced cell division, decreased nitrogen-fixing ability, reduced ability to form biofilms, reduced photosynthetic and light-sensing ability, and reduced production of secreted effectors and chromosomal toxin genes, among others. Among genes showing extreme downregulation when grown in a medium supplemented with nitrogen with the fold change > 5 are transcriptional regulator gene WalR, carbonic anhydrases, RNA Polymerase Sigma F factor, fimbrial protein, and twitching mobility protein. The reduced expression of key enzymes involved in the uptake of phosphate and enzymes protecting oxygen-sensitive nitrogenases is significant during the presence of nitrogen. UU774 is presumed to withstand heat by overexpressing peptidases that may be degrading abnormally folded proteins produced during heat. The absence of a key gene responsible for heterocyst pattern formation, patS, and an aberrant hetN without a functional motif probably lead to the formation of a chaotic heterocyst pattern in UU774. We suggest that UU774 has diverged from Fischerella sp. PCC 9339, another hot spring species isolated in the United States.

Incipient Sympatric Speciation and Evolution of Soil Bacteria Revealed by Metagenomic and Structured Non-Coding RNAs Analysis.

Soil bacteria respond rapidly to changes in new environmental conditions. For adaptation to the new environment, they could mutate their genome, which impacts the alternation of the functional and regulatory landscape. Sometimes, these genetic and ecological changes may drive the bacterial evolution and sympatric speciation. Although sympatric speciation has been controversial since Darwin suggested it in 1859, there are several strong theoretical or empirical evidences to support it. Sympatric speciation associated with soil bacteria remains largely unexplored. Here, we provide potential evidence of sympatric speciation of soil bacteria by comparison of metagenomics from two sharply contrasting abutting divergence rock and soil types (Senonian chalk and its rendzina soil, and abutting Pleistocene basalt rock and basalt soil). We identified several bacterial species with significant genetic differences in the same species between the two soil types and ecologies. We show that the bacterial community composition has significantly diverged between the two soils; correspondingly, their functions were differentiated in order to adapt to the local ecological stresses. The ecologies, such as water availability and pH value, shaped the adaptation and speciation of soil bacteria revealed by the clear-cut genetic divergence. Furthermore, by a novel analysis scheme of riboswitches, we highlight significant differences in structured non-coding RNAs between the soil bacteria from two divergence soil types, which could be an important driver for functional adaptation. Our study provides new insight into the evolutionary divergence and incipient sympatric speciation of soil bacteria under microclimatic ecological differences.

Structurally directed thienylenevinylene self-assembly for improved charge carrier mobility: 2D sheets vs. 1D fibers.

High charge carrier mobility is a prerequisite for organic electronics for which molecular arrangement and morphology play a vital role. Herein, we report how the self-assembly of thienylenevinylenes T1 and T2 can achieve morphologically distinct nanostructures with improved charge carrier mobility. Morphological analysis revealed that T1 forms 2D nanosheets that further extend to an array of hierarchical pseudo-1D assemblies, whereas T2 results in 1D nanofibers. Flash photolysis - time resolved microwave conductivity and transient absorption spectroscopy (FP-TRMC and TAS) revealed that 1D fibers of T2 show 1.75 fold higher charge carrier mobility (9.2 × 10-2 cm2 V-1 s-1) when compared to the array of 2D sheets obtained from T1 (5.0 × 10-2 cm2 V-1 s-1). This simple approach can be extended to design self-assembled organic photoconducting materials for optoelectronic applications.

Ultra-fast single-crystal polymerization of large-sized covalent organic frameworks.

In principle, polymerization tends to produce amorphous or poorly crystalline materials. Efficiently producing high-quality single crystals by polymerization in solvent remains as an unsolved issue in chemistry, especially for covalent organic frameworks (COFs) with highly complex structures. To produce µm-sized single crystals, the growth time is prolonged to >15 days, far away from the requirements in practical applications. Here, we find supercritical CO2 (sc-CO2) accelerates single-crystal polymerization by 10,000,000 folds, and produces two-dimensional (2D) COF single crystals with size up to 0.2 mm within 2~5 min. Although it is the fastest single-crystal polymerization, the growth in sc-CO2 leads to not only the largest crystal size of 2D COFs, but also higher quality with improved photoconductivity performance. This work overcomes traditional concept on low efficiency of single-crystal polymerization, and holds great promise for future applications owing to its efficiency, industrial compatibility, environmental friendliness and universality for different crystalline structures and linkage bonds.

Reconstructing Draft Genomes Using Genome Resolved Metagenomics Reveal Arsenic Metabolizing Genes and Secondary Metabolites in Fresh Water Lake in Eastern India.

Rabindra Sarovar lake is an artificial freshwater lake in the arsenic infested eastern region of India. In this study, using the genome resolved metagenomics approach; we have deciphered the taxonomic diversity as well as the functional insights of the gene pools specific to this region. Initially, a total of 113 Metagenome Assembled Genomes (MAGs) were recovered from the two predominant seasons, that is, rainy (n = 50) and winter (n = 63). After bin refinement and de-replication, 27 MAGs (18 from Winter season and 9 from Rainy season) were reconstructed. These MAGs were either of high-quality (n = 10) or of medium quality (n = 17) that was determined based on genome completeness and contamination. These 27 MAGs spanning across 6 bacterial phyla and the most predominant ones were Proteobacteria, Bacteroidetes, and Cyanobacteria regardless of the season. Functional annotation across the MAGs suggested the existence of all known types of arsenic resistance and metabolism genes. Besides, important secondary metabolites such as zoocin_A, prochlorosin, and microcin were also abundantly present in these genomes. The metagenomic study of this lake provides the first insights into the microbiome composition and functional classification of the gene pools in two predominant seasons. The presence of arsenic metabolism and resistance genes in the recovered genomes is a sign of adaptation of the microbes to the arsenic contamination in this region. The presence of secondary metabolite genes in the lake microbiome has several implications including the potential use of these for the pharmaceutical industry.

Interplay of structural dynamics and electronic effects in an engineered assembly of pentacene in a metal-organic framework.

Charge carrier mobility is an important figure of merit to evaluate organic semiconductor (OSC) materials. In aggregated OSCs, this quantity is determined by inter-chromophoric electronic and vibrational coupling. These key parameters sensitively depend on structural properties, including the density of defects. We have employed a new type of crystalline assembly strategy to engineer the arrangement of the OSC pentacene in a structure not realized as crystals to date. Our approach is based on metal-organic frameworks (MOFs), in which suitably substituted pentacenes act as ditopic linkers and assemble into highly ordered π-stacks with long-range order. Layer-by-layer fabrication of the MOF yields arrays of electronically coupled pentacene chains, running parallel to the substrate surface. Detailed photophysical studies reveal strong, anisotropic inter-pentacene electronic coupling, leading to efficient charge delocalization. Despite a high degree of structural order and pronounced dispersion of the 1D-bands for the static arrangement, our experimental results demonstrate hopping-like charge transport with an activation energy of 64 meV dominating the band transport over a wide range of temperatures. A thorough combined quantum mechanical and molecular dynamics investigation identifies frustrated localized rotations of the pentacene cores as the reason for the breakdown of band transport and paves the way for a crystal engineering strategy of molecular OSCs that independently varies the arrangement of the molecular cores and their vibrational degrees of freedom.

Supramolecular Fullerene Tetramers Concocted with Porphyrin Boxes Enable Efficient Charge Separation and Delocalization.

Herein, we report a novel porphyrin/fullerene supramolecular cocrystal using a shape-persistent zinc-metalated porphyrin box (Zn-PB) and C60/C70. An unprecedented arrangement of a tightly packed square-planar core of four C60 or C70 surrounded by six cube-shaped Zn-PBs was observed. This unique packing promotes strong charge transfer (CT) interactions between the two components in the ground state and formation of charge-separated states with very long lifetimes in the excited state and enables unusually high photoconductivity. Quantum chemical calculations show that these features are enabled by delocalized orbitals that promote the CT, on one hand, and that are spatially separated from each other, on the other hand. This work may open a new avenue to design novel electron donor/acceptor architectures for artificial photosynthesis.

Identification of Prime Factors to Maximize the Photocatalytic Hydrogen Evolution of Covalent Organic Frameworks.

Visible-light-driven hydrogen (H2) production from water is a promising strategy to convert and store solar energy as chemical energy. Covalent organic frameworks (COFs) are front runners among different classes of organic photocatalysts. The photocatalytic activity of COFs depends on numerous factors such as the electronic band gap, crystallinity, surface area, exciton migration, stability of transient species, charge separation and transport, etc. However, it is challenging to fine tune all of these factors simultaneously to enhance the photocatalytic activity. Hence, in this report, an effort has been made to understand the interplay of these factors and identify the key factors for efficient photocatalytic H2 production through a structure-property-activity relationship. Careful molecular engineering allowed us to optimize all of the above plausible factors impacting the overall catalytic activities of a series of isoreticular COFs. The present study determines three prime factors: light absorption, charge carrier generation, and its transport, which influence the photocatalytic H2 production of COFs to a much greater extent than the other factors.

A new pentacyclic pyrylium fluorescent probe that responds to pH imbalance during apoptosis.

Efficient fluorophores with easy synthetic routes and fast responses are of great importance in clinical diagnostics. Herein, we report a new, rigid pentacyclic pyrylium fluorophore, PS-OMe, synthesised in a single step by a modified Vilsmeier-Haack reaction. Insights into the reaction mechanism facilitated a new reaction protocol for the efficient synthesis of PS-OMe which upon demethylation resulted in a "turn-on" pH sensor, PS-OH. This new fluorescent probe has been successfully used to monitor intracellular acidification at physiological pH. From the fluorescence image analysis, we were able to quantify the intracellular dynamic pH change during apoptosis. This new pH probe is a potential chemical tool for screening, drug discovery and dose determination in cancer therapy.

Reanalysis of Lactobacillus paracasei Lbs2 Strain and Large-Scale Comparative Genomics Places Many Strains into Their Correct Taxonomic Position.

Lactobacillus paracasei are diverse Gram-positive bacteria that are very closely related to Lactobacillus casei, belonging to the Lactobacillus casei group. Due to extreme genome similarities between L. casei and L. paracasei, many strains have been cross placed in the other group. We had earlier sequenced and analyzed the genome of Lactobacillus paracasei Lbs2, but mistakenly identified it as L. casei. We re-analyzed Lbs2 reads into a 2.5 MB genome that is 91.28% complete with 0.8% contamination, which is now suitably placed under L. paracasei based on Average Nucleotide Identity and Average Amino Acid Identity. We took 74 sequenced genomes of L. paracasei from GenBank with assembly sizes ranging from 2.3 to 3.3 MB and genome completeness between 88% and 100% for comparison. The pan-genome of 75 L. paracasei strains hold 15,945 gene families (21,5232 genes), while the core genome contained about 8.4% of the total genes (243 gene families with 18,225 genes) of pan-genome. Phylogenomic analysis based on core gene families revealed that the Lbs2 strain has a closer relationship with L. paracasei subsp. tolerans DSM20258. Finally, the in-silico analysis of the L. paracasei Lbs2 genome revealed an important pathway that could underpin the production of thiamin, which may contribute to the host energy metabolism.

Rod-like transition first or chain aggregation first? ordered aggregation of rod-like poly(p-phenyleneethynylene) chains in solution.

The rod-like configuration of conjugated polymer chains with its low energetic disorder is the key to utilizing the backbone as a highly electrically-conductive wire. An energetic disorder that is higher than 0.1 eV, coupled with vibronic modes of the chains, leads to the localization of charges. Herein, we have tracked precisely the rod-like transition of poly(p-phenyleneethynylene) (PPE) chains as a function of temperature in diluted solutions, and shown a steep increase in persistence length at 230 K. The resulting rod-like configuration of the PPE chains with its extended electronic conjugation exhibited an extremely small energetic disorder of ∼70 meV, and was stabilized by subsequent polymer aggregate formation.

Genome/transcriptome collection of plethora of economically important, previously unexplored organisms from India and abroad.

Genome and transcriptome sequencing data are extremely useful resources for researchers in carrying out biological experiments that involves cloning and characterizing genes. We are presenting here genome sequence data from different clades of life including photosynthetic prokaryotes; oomycetes pathogens; probiotic bacteria; endophytic yeasts and filamentous fungus and pathogenic protozoa Leishmania donovani. In addition, we are also presenting paired control and treated stress response transcriptomes of Cyanobacteria growing in extreme conditions. The Cyanobacterial species that are included in this dataset were isolated from extreme conditions including desiccated monuments, hot springs and saline archipelagos. The probiotic Lactobacillus paracasei was isolated from Indian sub-continent. The Kala azar causing protozoan Leishmania donovani, whose early infectious stage is also included in this dataset. The endophyte Arthrinium malaysianum was isolated as a contaminant has significant bio-remediation property. Our collaborators have isolated endophyte Rhodotorula mucilaginosa JGTA1 from Jaduguda mines, West Bengal, India infested with Uranium. Our collaborators have isolated a heterozygous diploid oomycetes pathogen, Phytophthora ramorum causing sudden oak death in CA, USA coast is also part of the data. These dataset presents a unique heterogeneous collection from various sources that are analyzed using "Genome Annotator Light (GAL): A Docker-based package for genome analysis and visualization" (Panda et al., 2019) and are presented in a web site automatically created by GAL at http://www.eumicrobedb.org/cglab.

Haplotype-Phased Genome Assembly of Virulent Phytophthora ramorum Isolate ND886 Facilitated by Long-Read Sequencing Reveals Effector Polymorphisms and Copy Number Variation.

Phytophthora ramorum is a destructive pathogen that causes sudden oak death disease. The genome sequence of P. ramorum isolate Pr102 was previously produced, using Sanger reads, and contained 12 Mb of gaps. However, isolate Pr102 had shown reduced aggressiveness and genome abnormalities. In order to produce an improved genome assembly for P. ramorum, we performed long-read sequencing of highly aggressive P. ramorum isolate CDFA1418886 (abbreviated as ND886). We generated a 60.5-Mb assembly of the ND886 genome using the Pacific Biosciences (PacBio) sequencing platform. The assembly includes 302 primary contigs (60.2 Mb) and nine unplaced contigs (265 kb). Additionally, we found a 'highly repetitive' component from the PacBio unassembled unmapped reads containing tandem repeats that are not part of the 60.5-Mb genome. The overall repeat content in the primary assembly was much higher than the Pr102 Sanger version (48 versus 29%), indicating that the long reads have captured repetitive regions effectively. The 302 primary contigs were phased into 345 haplotype blocks and 222,892 phased variants, of which the longest phased block was 1,513,201 bp with 7,265 phased variants. The improved phased assembly facilitated identification of 21 and 25 Crinkler effectors and 393 and 394 RXLR effector genes from two haplotypes. Of these, 24 and 25 RXLR effectors were newly predicted from haplotypes A and B, respectively. In addition, seven new paralogs of effector Avh207 were found in contig 54, not reported earlier. Comparison of the ND886 assembly with Pr102 V1 assembly suggests that several repeat-rich smaller scaffolds within the Pr102 V1 assembly were possibly misassembled; these regions are fully encompassed now in ND886 contigs. Our analysis further reveals that Pr102 is a heterokaryon with multiple nuclear types in the sequences corresponding to contig 10 of ND886 assembly.

A unique life-strategy of an endophytic yeast Rhodotorula mucilaginosa JGTA-S1-a comparative genomics viewpoint.

Endophytic yeasts of genus Rhodotorula are gaining importance for their ability to improve plant growth. The nature of their interaction with plants, however, remains unknown. Rhodotorula mucilaginosa JGTA-S1 was isolated as an endophyte of Typha angustifolia and promoted growth in the host. To investigate the life-strategy of the yeast from a genomics perspective, we used Illumina and Oxford Nanopore reads to generate a high-quality annotated draft assembly of JGTA-S1 and compared its genome to three other Rhodotorula yeasts and the close relative Rhodosporidium toruloides. JGTA-S1 is a haploid yeast possessing several genes potentially facilitating its endophytic lifestyle such as those responsible for solubilizing phosphate and producing phytohormones. An intact mating-locus in JGTA-S1 raised the possibility of a yet unknown sexual reproductive cycle in Rhodotorula yeasts. Additionally, JGTA-S1 had functional anti-freezing genes and was also unique in lacking a functional nitrate-assimilation pathway-a feature that is associated with obligate biotrophs. Nitrogen-fixing endobacteria were found within JGTA-S1 that may circumvent this defective N-metabolism. JGTA-S1 genome data coupled with experimental evidence give us an insight into the nature of its beneficial interaction with plants.

Charge Carrier Polarity Modulation in Diketopyrrolopyrrole-Based Low Band Gap Semiconductors by Terminal Functionalization.

Organic semiconductors with variable charge carrier polarity are required for optoelectronic applications. Herein, we report the synthesis of three novel diketopyrrolopyrrole (DPP)-based D-A molecules having three different terminal groups (amide, ester, and dicyano) and study their electronic properties. An increase in electron acceptor strength from amide to dicyano leads to a bathochromic shift in absorption. Photoconductivity and field effect transistor (FET) measurements confirmed that a small increase in acceptor strength can result in a large change in the charge transport properties from p-type to n-type. The molecule with an amide group, DPP-amide, exhibited a moderate p-type mobility (1.3 × 10-2 cm2 V-1 s-1), whereas good n-type mobilities were observed for molecules with an ester moiety, DPP-ester (1.5 × 10-2 cm2 V-1 s-1), and with a dicyano group, DPP-DCV (1 × 10-2 cm2 V-1 s-1). The terminal functional group modification approach presented here is a simple and efficient method to alter the charge carrier polarity of organic semiconductors.

A Supramolecular Nanocomposite as a Near-Infrared-Transmitting Optical Filter for Security and Forensic Applications.

Visibly opaque but near-infrared (NIR)-transparent materials are an essential component for night-vision photography, security imaging, and forensic applications. Herein, the development of a novel supramolecular black dye from a diketopyrrolopyrrole (DPP)-based low-molecular-weight organogelator is described. In the solution state, the monomer of DPP-Amide exhibits a deep green color with a broad absorption in the visible region due to firm intramolecular charge transfer from the donor to the acceptor unit. Interestingly, due to the synergistic effect of H-bonding and π-stacking, DPP-Amide can form a black organogel in toluene with complete spectral coverage from 300 to 800 nm, and transmits beyond 850 nm. In the gel state, complete visible-spectrum coverage is achieved due to the simultaneous formation of both H- and J-type aggregates, which is confirmed via absorption studies. To create a free-standing NIR-transmitting elastomeric black filter, nanoscopic molecular aggregates of DPP-Amide (0.15 wt%) are embedded into a poly(dimethylsiloxane) matrix. This nanocomposite possesses high NIR transparency with good thermal and photostability for practical applications. Finally, the use of the developed material for NIR photography, security, and forensic-related applications is demonstrated.

An unprecedented amplification of near-infrared emission in a Bodipy derived π-system by stress or gelation.

We report an unprecedented strategy to generate and amplify near-infrared (NIR) emission in an organic chromophore by mechanical stress or gelation pathways. A greenish-yellow emitting film of π-extended Bodipy-1, obtained from n-decane, became orange-red upon mechanical shearing, with a 15-fold enhancement in NIR emission at 738 nm. Alternatively, a DMSO gel of Bodipy-1 exhibited a 7-fold enhancement in NIR emission at 748 nm with a change in emission color from yellow to orange-red upon drying. The reason for the amplified NIR emission in both cases is established from the difference in chromophore packing, by single crystal analysis of a model compound (Bodipy-2), which also exhibited a near identical emission spectrum with red to NIR emission (742 nm). Comparison of the emission features and WAXS and FT-IR data of the sheared n-decane film and the DMSO xerogel with the single crystal data supports a head-to-tail slipped arrangement driven by the N-H···F-B bonding in the sheared or xerogel states, which facilitates strong exciton coupling and the resultant NIR emission.