Stress-responsive gene regulation conferring salinity tolerance in wheat inoculated with ACC deaminase producing facultative methylotrophic actinobacterium.

Microbes enhance crop resilience to abiotic stresses, aiding agricultural sustainability amid rising global land salinity. While microbes have proven effective via seed priming, soil amendments, and foliar sprays in diverse crops, their mechanisms remain less explored. This study explores the utilization of ACC deaminase-producing Nocardioides sp. to enhance wheat growth in saline environments and the molecular mechanisms underlying Nocardioides sp.-mediated salinity tolerance in wheat. The Nocardioides sp. inoculated seeds were grown under four salinity regimes viz., 0 dS m-1, 5 dS m-1, 10 dS m-1, and 15 dS m-1, and vegetative growth parameters including shoot-root length, germination percentage, seedling vigor index, total biomass, and shoot-root ratio were recorded. The Nocardioides inoculated wheat plants performed well under saline conditions compared to uninoculated plants and exhibited lower shoot:root (S:R) ratio (1.52 ± 0.14 for treated plants against 1.84 ± 0.08 for untreated plants) at salinity level of 15 dS m-1 and also showed improved biomass at 5 dS m-1 and 10 dS m-1. Furthermore, the inoculated plants also exhibited higher protein content viz., 22.13 mg g-1, 22.10 mg g-1, 22.63 mg g-1, and 23.62 mg g-1 fresh weight, respectively, at 0 dS m-1, 5 dS m-1, 10 dS m-1, and 15 dS m-1. The mechanisms were studied in terms of catalase, peroxidase, superoxide dismutase, and ascorbate peroxidase activity, free radical scavenging potential, in-situ localization of H2O2 and superoxide ions, and DNA damage. The inoculated seedlings maintained higher enzymatic and non-enzymatic antioxidant potential, which corroborated with reduced H2O2 and superoxide localization within the tissue. The gene expression profiles of 18 stress-related genes involving abscisic acid signaling, salt overly sensitive (SOS response), ion transporters, stress-related transcription factors, and antioxidant enzymes were also analyzed. Higher levels of stress-responsive gene transcripts, for instance, TaABARE (~+7- and +10-fold at 10 dS m-1 and 15 dS m-1); TaHAk1 and hkt1 (~+4- and +8-fold at 15 dS m-1); antioxidant enzymes CAT, MnSOD, POD, APX, GPX, and GR (~+4, +3, +5, +4, +9, and +8 folds and), indicated actively elevated combat mechanisms in inoculated seedlings. Our findings emphasize Nocardioides sp.-mediated wheat salinity tolerance via ABA-dependent cascade and salt-responsive ion transport system. This urges additional study of methylotrophic microbes to enhance crop abiotic stress resilience.

Fungal Genomic Resources for Strain Identification and Diversity Analysis of 1900 Fungal Species.

Identification and diversity analysis of fungi is greatly challenging. Though internal transcribed spacer (ITS), region-based DNA fingerprinting works as a "gold standard" for most of the fungal species group, it cannot differentiate between all the groups and cryptic species. Therefore, it is of paramount importance to find an alternative approach for strain differentiation. Availability of whole genome sequence data of nearly 2000 fungal species are a promising solution to such requirement. We present whole genome sequence-based world's largest microsatellite database, FungSatDB having >19M loci obtained from >1900 fungal species/strains using >4000 assemblies across globe. Genotyping efficacy of FungSatDB has been evaluated by both in-silico and in-vitro PCR. By in silico PCR, 66 strains of 8 countries representing four continents were successfully differentiated. Genotyping efficacy was also evaluated by in vitro PCR in four fungal species. This approach overcomes limitation of ITS in species, strain signature, and diversity analysis. It can accelerate fungal genomic research endeavors in agriculture, industrial, and environmental management.

Mitigation of Salinity Stress in Wheat Seedlings Due to the Application of Phytohormone-Rich Culture Filtrate Extract of Methylotrophic Actinobacterium Nocardioides sp. NIMMe6.

Salinity stress is an important plant growth limiting factor influencing crop productivity negatively. Microbial interventions for salinity stress mitigation have invited significant attention due to the promising impacts of interactive associations on the intrinsic mechanisms of plants. We report the impact of microbial inoculation of a halotolerant methylotrophic actinobacterium (Nocardioides sp. NIMMe6; LC140963) and seed coating of its phytohormone-rich bacterial culture filtrate extract (BCFE) on wheat seedlings grown under saline conditions. Different plant-growth-promoting (PGP) attributes of the bacterium in terms of its growth in N-limiting media and siderophore and phytohormone [indole-3-acetic acid (IAA) and salicylic acid] production influenced plant growth positively. Microbial inoculation and priming with BCFE resulted in improved germination (92% in primed seeds at 10 dS m-1), growth, and biochemical accumulation (total protein 42.01 and 28.75 mg g-1 in shoot and root tissues at 10 dS m-1 in BCFE-primed seeds) and enhanced the activity level of antioxidant enzymes (superoxide dismutase, catalase, peroxidase, and ascorbate peroxidase) to confer stress mitigation. Biopriming with BCFE proved impactful. The BCFE application has further influenced the overexpression of defense-related genes in the seedlings grown under salinity stress condition. Liquid chromatography-mass spectrometry-based characterization of the biomolecules in the BCFE revealed quantification of salicylate and indole-3-acetate (Rt 4.978 min, m/z 138.1 and 6.177 min, 129.1), respectively. The high tolerance limit of the bacterium to 10% NaCl in the culture media suggested its possible survival and growth under high soil salinity condition as microbial inoculant. The production of a high quantity of IAA (45.6 µg ml-1 of culture filtrate) by the bacterium reflected its capability to not only support plant growth under salinity condition but also mitigate stress due to the impact of phytohormone as defense mitigators. The study suggested that although microbial inoculation offers stress mitigation in plants, the phytohormone-rich BCFE from Nocardioides sp. NIMMe6 has potential implications for defense against salinity stress in wheat.

Kinetic Study of the Biodegradation of Acephate by Indigenous Soil Bacterial Isolates in the Presence of Humic Acid and Metal Ions.

Many bacteria have the potential to use specific pesticides as a source of carbon, phosphorous, nitrogen and sulphur. Acephate degradation by microbes is considered to be a safe and effective method. The overall aim of the present study was to identify acephate biodegrading microorganisms and to investigate the degradation rates of acephate under the stress of humic acid and most common metal ions Fe(III) and copper Cu(II). Pseudomonas azotoformanss strain ACP1, Pseudomonas aeruginosa strain ACP2, and Pseudomonas putida ACP3 were isolated from acephate contaminated soils. Acephate of concentration 100 ppm was incubated with separate strain inoculums and periodic samples were drawn for UV-visible, FTIR (Fourier-transform infrared spectroscopy) and MS (Mass Spectrometry) analysis. Methamidophos, S-methyl O-hydrogen phosphorothioamidate, phosphenothioic S-acid, and phosphenamide were the major metabolites formed during the degradation of acephate. The rate of degradation was applied using pseudo-first-order kinetics to calculate the half-life (t1/2) values, which were 14.33-16.72 d-1 (strain(s) + acephate), 18.81-21.50 d-1 (strain(s) + acephate + Cu(II)), 20.06 -23.15 d-1 (strain(s) + acephate + Fe(II)), and 15.05-17.70 d-1 (strains + acephate + HA). The biodegradation efficiency of the three bacterial strains can be ordered as P. aeruginosa > P. putida > P. azotoformans. The present study illustrated the decomposition mechanism of acephate under different conditions, and the same may be applied to the removal of other xenobiotic compounds.

Microbial inoculation in rice regulates antioxidative reactions and defense related genes to mitigate drought stress.

Microbial inoculation in drought challenged rice triggered multipronged steps at enzymatic, non-enzymatic and gene expression level. These multifarious modulations in plants were related to stress tolerance mechanisms. Drought suppressed growth of rice plants but inoculation with Trichoderma, Pseudomonas and their combination minimized the impact of watering regime. Induced PAL gene expression and enzyme activity due to microbial inoculation led to increased accumulation of polyphenolics in plants. Enhanced antioxidant concentration of polyphenolics from microbe inoculated and drought challenged plants showed substantially high values of DPPH, ABTS, Fe-ion reducing power and Fe-ion chelation activity, which established the role of polyphenolic extract as free radical scavengers. Activation of superoxide dismutase that catalyzes superoxide (O2-) and leads to the accumulation of H2O2 was linked with the hypersensitive cell death response in leaves. Microbial inoculation in plants enhanced activity of peroxidase, ascorbate peroxidase, glutathione peroxidase and glutathione reductase enzymes. This has further contributed in reducing ROS burden in plants. Genes of key metabolic pathways including phenylpropanoid (PAL), superoxide dismutation (SODs), H2O2 peroxidation (APX, PO) and oxidative defense response (CAT) were over-expressed due to microbial inoculation. Enhanced expression of OSPiP linked to less-water permeability, drought-adaptation gene DHN and dehydration related stress inducible DREB gene in rice inoculated with microbial inoculants after drought challenge was also reported. The impact of Pseudomonas on gene expression was consistently remained the most prominent. These findings suggested that microbial inoculation directly caused over-expression of genes linked with defense processes in plants challenged with drought stress. Enhanced enzymatic and non-enzymatic antioxidant reactions that helped in minimizing antioxidative load, were the repercussions of enhanced gene expression in microbe inoculated plants. These mechanisms contributed strongly towards stress mitigation. The study demonstrated that microbial inoculants were successful in improving intrinsic biochemical and molecular capabilities of rice plants under stress. Results encouraged us to advocate that the practice of growing plants with microbial inoculants may find strategic place in raising crops under abiotic stressed environments.

Rhizosphere Metagenomics of Paspalum scrobiculatum L. (Kodo Millet) Reveals Rhizobiome Multifunctionalities.

Multifunctionalities linked with the microbial communities associated with the millet crop rhizosphere has remained unexplored. In this study, we are analyzing microbial communities inhabiting rhizosphere of kodo millet and their associated functions and its impact over plant growth and survival. Metagenomics of Paspalum scrobiculatum L.(kodo millet) rhizopshere revealed taxonomic communities with functional capabilities linked to support growth and development of the plants under nutrient-deprived, semi-arid and dry biotic conditions. Among 65 taxonomically diverse phyla identified in the rhizobiome, Actinobacteria were the most abundant followed by the Proteobacteria. Functions identified for different genes/proteins led to revelations that multifunctional rhizobiome performs several metabolic functions including carbon fixation, nitrogen, phosphorus, sulfur, iron and aromatic compound metabolism, stress response, secondary metabolite synthesis and virulence, disease, and defense. Abundance of genes linked with N, P, S, Fe and aromatic compound metabolism and phytohormone synthesis-along with other prominent functions-clearly justifies growth, development, and survival of the plants under nutrient deprived dry environment conditions. The dominance of actinobacteria, the known antibiotic producing communities shows that the kodo rhizobiome possesses metabolic capabilities to defend themselves against biotic stresses. The study opens avenues to revisit multi-functionalities of the crop rhizosphere for establishing link between taxonomic abundance and targeted functions that help plant growth and development in stressed and nutrient deprived soil conditions. It further helps in understanding the role of rhizosphere microbiome in adaptation and survival of plants in harsh abiotic conditions.

Metaproteomic data of maize rhizosphere for deciphering functional diversity.

Metaproteomics is a powerful tool for obtaining data on all proteins recovered directly from environmental samples at a given time. It provides a direct evidence of functional diversity and structure among microbiota present in niches and significant insights into microbial activity together with metabolomics, which is the study of the intermediate and end-products of cellular processes. Metaproteomics is a comparatively new approach which is facing a number of empirical, technical, computational and experimental design challenges that needs to be addressed. Presently only little efforts have been made to have information on microbial proteins in rhizospheric soil of maize through metagemonics approach but there is no direct evidence on functions of microbial community in this very important niche. Since rhizosphere microbiome plays important role in plant growth and development the present study is conducted to optimize the metaproteomic extraction protocol from maize rhizosphere and analyse functionality of microbial communities. We present metaproteome data from maize rhizospheric soil. Isolation of metaproteome from maize rhizosphere collected from ICAR-IISS, Mau experimental Farm was done with the standardized protocol at our laboratory and metaproteome analysis was done with the standardized pipeline. In total 696 proteins with different functions representing 244 genus and 393 species were identified. The proteome data provides direct evidence on the biological processes in soil ecosystem and is the first reported reference data from maize rhizosphere. The LC MS/MS proteomic data are available via ProteomeXchange with identifier PXD014519.

Microbial Pyrrolnitrin: Natural Metabolite with Immense Practical Utility.

Pyrrolnitrin (PRN) is a microbial pyrrole halometabolite of immense antimicrobial significance for agricultural, pharmaceutical and industrial implications. The compound and its derivatives have been isolated from rhizospheric fluorescent or non-fluorescent pseudomonads, Serratia and Burkholderia. They are known to confer biological control against a wide range of phytopathogenic fungi, and thus offer strong plant protection prospects against soil and seed-borne phytopathogenic diseases. Although chemical synthesis of PRN has been obtained using different steps, microbial production is still the most useful option for producing this metabolite. In many of the plant-associated isolates of Serratia and Burkholderia, production of PRN is dependent on the quorum-sensing regulation that usually involves N-acylhomoserine lactone (AHL) autoinducer signals. When applied on the organisms as antimicrobial agent, the molecule impedes synthesis of key biomolecules (DNA, RNA and protein), uncouples with oxidative phosphorylation, inhibits mitotic division and hampers several biological mechanisms. With its potential broad-spectrum activities, low phototoxicity, non-toxic nature and specificity for impacts on non-target organisms, the metabolite has emerged as a lead molecule of industrial importance, which has led to developing cost-effective methods for the biosynthesis of PRN using microbial fermentation. Quantum of work narrating focused research efforts in the emergence of this potential microbial metabolite is summarized here to present a consolidated, sequential and updated insight into the chemistry, biology and applicability of this natural molecule.

Cyanobacterial phylogenetic analysis based on phylogenomics approaches render evolutionary diversification and adaptation: an overview of representative orders.

Phylogenetic studies based on a definite set of marker genes usually reconstruct evolutionary relationships among the prokaryotic species. Based on specific target sequences, such studies represent variations and allow identification of similarities or dissimilarities in organisms. With the advent of completely sequenced genomes and accumulation of information on whole prokaryotic genomes, phylogenetic reconstructions should be considered more reliable if they are ideally based on entire genomes to resolve phylogenetic interest. We applied phylogenomics approaches taking into account completely sequenced cyanobacterial genomes to reconstruct underlying species that represented major taxonomic classes and belonged to distinctly different habitats (freshwater, marine, soils, and rocks). We did not rely on describing phylogeny of all representative class of cyanobacterial species on the basis of only ribosomal gene, 16S rDNA gene. In contrast, we analyzed combined molecular marker and phylogenomics approaches (genome alignment, gene content and gene order, composition vector and protein domain content) for accurately inferring phylogenetic relationship of species. We have shown that this approach reflects the impact of evolution on the organisms and considers connects with the ecological adaptation in cyanobacteria in different habitats. Analysis revealed that the members from marine habitat occupy different profile than those from freshwater. Impact of GC content and genomic repetitiveness over the diversification of cyanobacterial species and their possible role in adaptation was also reflected. Members occupying similar habitats cover more evolutionary distance together and also evolve various strategies for adaptation and survival either through genomic repetitiveness or preferences for genes of particular functions or modified GC content. Genomes undergo different changes for their adaptation in diverse habitats.

Trichoderma mediate early and enhanced lignifications in chickpea during Fusarium oxysporum f. sp. ciceris infection.

Lignifications in secondary cell walls play a significant role in defense mechanisms of plants against the invading pathogens. In the present study, we investigated Trichoderma strain specific lignifications in chickpea plants pre-treated with 10 potential Trichoderma strains and subsequently challenged with the wilt pathogen Fusarium oxysporum f. sp. ciceris (Foc). Trichoderma-induced lignifications in chickpea were observed through histochemical staining and expression of some genes of the lignin biosynthetic pathway. Lignifications were observed in transverse sections of shoots near the soil line through histochemical staining and expression pattern of the target genes was observed in root tissues through semi quantitative RT-PCR at different time intervals after inoculation of F. oxysporum f. sp. ciceris. Lignin deposition and expression pattern of the target genes were variable in each treatment. Lignifications were enhanced in all 10 Trichoderma strain treated and F. oxysporum f. sp. ciceris challenged chickpea plants. However, four Trichoderma strains viz., T-42, MV-41, DFL, and RO, triggered significantly high lignifications compared to the other six strains. Time course studies showed that effective Trichoderma isolates induced lignifications very early compared to the other strains and the process of lignifications nearly completes within 6 days of pathogen challenge. Thus, from the results it can be concluded that effective Trichoderma strains trigger lignifications very early in chickpea under Foc challenge and provide better protection to chickpea plants.

Bacterial diversity in rhizosphere of Paspalum scrobiculatum L. (kodo millet) is revealed with shotgun metagenome sequencing and data analysis.

Rhizosphere bacterial communities of kodo millet plant was analyzed from a large metagenome sequence dataset. Plant rhizosphere samples of kodo millet was collected in replicates and the metagenomic sequence data were obtained through shotgun sequencing. Overall sequences in the dataset were 476,649 comprising total read length of 179,349,372 base pairs. Taxonomic data analysis led to characterize α-diversity of 107 species. Dominance of actinobacteria followed by unclassified sequences (derived from Bacteria) was recorded. Raw data along with the analysis result is publicly available from the MG-RAST server with ID mgm4761530.3.

Metatranscriptome Analysis Deciphers Multifunctional Genes and Enzymes Linked With the Degradation of Aromatic Compounds and Pesticides in the Wheat Rhizosphere.

Agricultural soils are becoming contaminated with synthetic chemicals like polyaromatic compounds, petroleum hydrocarbons, polychlorinated biphenyls (PCBs), phenols, herbicides, insecticides and fungicides due to excessive dependency of crop production systems on the chemical inputs. Microbial degradation of organic pollutants in the agricultural soils is a continuous process due to the metabolic multifunctionalities and enzymatic capabilities of the soil associated communities. The plant rhizosphere with its complex microbial inhabitants and their multiple functions, is amongst the most live and dynamic component of agricultural soils. We analyzed the metatranscriptome data of 20 wheat rhizosphere samples to decipher the taxonomic microbial communities and their multifunctionalities linked with the degradation of organic soil contaminants. The analysis revealed a total of 21 different metabolic pathways for the degradation of aromatic compounds and 06 for the xenobiotics degradation. Taxonomic annotation of wheat rhizosphere revealed bacteria, especially the Proteobacteria, actinobacteria, firmicutes, bacteroidetes, and cyanobacteria, which are shown to be linked with the degradation of aromatic compounds as the dominant communities. Abundance of the transcripts related to the degradation of aromatic amin compounds, carbazoles, benzoates, naphthalene, ketoadipate pathway, phenols, biphenyls and xenobiotics indicated abundant degradation capabilities in the soils. The results highlighted a potentially dominant role of crop rhizosphere associated microbial communities in the remediation of contaminant aromatic compounds.

Antioxidant properties and polyphenolic content in terrestrial cyanobacteria.

Cell-free extracts of twenty terrestrial cyanobacteria were evaluated for their antioxidant properties in terms of free-radical scavenging (DPPH and ABTS) and metal chelating activity and deoxyribose protection. Extract of Anabaena constricta was the most prominent antioxidant agent (IC50 for DPPH activity 0.91 mg ml-1, ABTS 0.23 mg ml-1, deoxyribose protection 0.63 mg ml-1 and Fe+2-ion chelating 0.9 mg ml-1). The extracts of cyanobacterial species contained high quantity of total phenol and total flavonoid that were supposed to impart prominent antioxidant properties. Cyanobacterial species also showed fairly high PAL activity. We reported varied quantities of polyphenolics gallic, chlorogenic, caffeic, vanillic and ferulic acids and flavonoids rutin, quercetin and kaempferol in cyanobacterial extracts. The presence of these polyphenolics was linked with the free radical scavenging, metal chelating and antioxidative damage protecting properties of the organisms. Cyanobacteria are the most feasible, promising and alternative candidates for searching out new chemical leads for industrial applications in pharmaceuticals, neutraceuticals and biomolecules of importance. Presence of biomolecules such as polyphenolics and their connection with the prominent biological functions (e.g., antioxidant properties) make these organisms a potential source of secondary metabolites with predominant biological activities. Additionally, dominant presence of polyphenols as antioxidant agents in cyanobacterial species may reflect their adaptation strategies against abiotic stresses for their ecological success in different habitats.

Abiotic Stress Responses and Microbe-Mediated Mitigation in Plants: The Omics Strategies.

Abiotic stresses are the foremost limiting factors for agricultural productivity. Crop plants need to cope up adverse external pressure created by environmental and edaphic conditions with their intrinsic biological mechanisms, failing which their growth, development, and productivity suffer. Microorganisms, the most natural inhabitants of diverse environments exhibit enormous metabolic capabilities to mitigate abiotic stresses. Since microbial interactions with plants are an integral part of the living ecosystem, they are believed to be the natural partners that modulate local and systemic mechanisms in plants to offer defense under adverse external conditions. Plant-microbe interactions comprise complex mechanisms within the plant cellular system. Biochemical, molecular and physiological studies are paving the way in understanding the complex but integrated cellular processes. Under the continuous pressure of increasing climatic alterations, it now becomes more imperative to define and interpret plant-microbe relationships in terms of protection against abiotic stresses. At the same time, it also becomes essential to generate deeper insights into the stress-mitigating mechanisms in crop plants for their translation in higher productivity. Multi-omics approaches comprising genomics, transcriptomics, proteomics, metabolomics and phenomics integrate studies on the interaction of plants with microbes and their external environment and generate multi-layered information that can answer what is happening in real-time within the cells. Integration, analysis and decipherization of the big-data can lead to a massive outcome that has significant chance for implementation in the fields. This review summarizes abiotic stresses responses in plants in-terms of biochemical and molecular mechanisms followed by the microbe-mediated stress mitigation phenomenon. We describe the role of multi-omics approaches in generating multi-pronged information to provide a better understanding of plant-microbe interactions that modulate cellular mechanisms in plants under extreme external conditions and help to optimize abiotic stresses. Vigilant amalgamation of these high-throughput approaches supports a higher level of knowledge generation about root-level mechanisms involved in the alleviation of abiotic stresses in organisms.

Genome-wide comparative analysis of codon usage bias and codon context patterns among cyanobacterial genomes.

With the increasing accumulation of genomic sequence information of prokaryotes, the study of codon usage bias has gained renewed attention. The purpose of this study was to examine codon selection pattern within and across cyanobacterial species belonging to diverse taxonomic orders and habitats. We performed detailed comparative analysis of cyanobacterial genomes with respect to codon bias. Our analysis reflects that in cyanobacterial genomes, A- and/or T-ending codons were used predominantly in the genes whereas G- and/or C-ending codons were largely avoided. Variation in the codon context usage of cyanobacterial genes corresponded to the clustering of cyanobacteria as per their GC content. Analysis of codon adaptation index (CAI) and synonymous codon usage order (SCUO) revealed that majority of genes are associated with low codon bias. Codon selection pattern in cyanobacterial genomes reflected compositional constraints as major influencing factor. It is also identified that although, mutational constraint may play some role in affecting codon usage bias in cyanobacteria, compositional constraint in terms of genomic GC composition coupled with environmental factors affected codon selection pattern in cyanobacterial genomes.

Functional profiling of cyanobacterial genomes and its role in ecological adaptations.

With the availability of complete genome sequences of many cyanobacterial species, it is becoming feasible to study the broad prospective of the environmental adaptation and the overall changes at transcriptional and translational level in these organisms. In the evolutionary phase, niche-specific competitive forces have resulted in specific features of the cyanobacterial genomes. In this study, functional composition of the 84 different cyanobacterial genomes and their adaptations to different environments was examined by identifying the genomic composition for specific cellular processes, which reflect their genomic functional profile and ecological adaptation. It was identified that among cyanobacterial genomes, metabolic genes have major share over other categories and differentiation of genomic functional profile was observed for the species inhabiting different habitats. The cyanobacteria of freshwater and other habitats accumulate large number of poorly characterized genes. Strain specific functions were also reported in many cyanobacterial members, of which an important feature was the occurrence of phage-related sequences. From this study, it can be speculated that habitat is one of the major factors in giving the shape of functional composition of cyanobacterial genomes towards their ecological adaptations.

StressMicrobesInfo: Database of Microorganisms Responsive to Stress Conditions.

Microorganisms are continuously exposed to numerous stress conditions and had evolved with numerous evolutionary adaptations and physiological acclimation mechanisms against stress effects. Any information related to the microbes responsive to stress conditions will help scientists working in the area of stress biology. Currently, there is lack of information resource on this aspect and for getting information about microbes susceptible or tolerant to different environmental changes, literature searching is the only option. Here, we present a database StressMicrobesInfo that was developed with a mandate to provide information about microbes responding to various biotic and abiotic stress conditions. This database currently contains information about 183 microbes along with a brief detail for each. StressMicrobesInfo will facilitate researchers working on stress-related microbes as a starting point and will facilitate them with the microbes which are susceptible or resistant towards particular stress conditions.

ChloroMitoSSRDB 2.00: more genomes, more repeats, unifying SSRs search patterns and on-the-fly repeat detection.

Organelle genomes evolve rapidly as compared with nuclear genomes and have been widely used for developing microsatellites or simple sequence repeats (SSRs) markers for delineating phylogenomics. In our previous reports, we have established the largest repository of organelle SSRs, ChloroMitoSSRDB, which provides access to 2161 organelle genomes (1982 mitochondrial and 179 chloroplast genomes) with a total of 5838 perfect chloroplast SSRs, 37 297 imperfect chloroplast SSRs, 5898 perfect mitochondrial SSRs and 50 355 imperfect mitochondrial SSRs across organelle genomes. In the present research, we have updated ChloroMitoSSRDB by systematically analyzing and adding additional 191 chloroplast and 2102 mitochondrial genomes. With the recent update, ChloroMitoSSRDB 2.00 provides access to a total of 4454 organelle genomes displaying a total of 40 653 IMEx Perfect SSRs (11 802 Chloroplast Perfect SSRs and 28 851 Mitochondria Perfect SSRs), 275 981 IMEx Imperfect SSRs (78 972 Chloroplast Imperfect SSRs and 197 009 Mitochondria Imperfect SSRs), 35 250 MISA (MIcroSAtellite identification tool) Perfect SSRs and 3211 MISA Compound SSRs and associated information such as location of the repeats (coding and non-coding), size of repeat, motif and length polymorphism, and primer pairs. Additionally, we have integrated and made available several in silico SSRs mining tools through a unified web-portal for in silico repeat mining for assembled organelle genomes and from next generation sequencing reads. ChloroMitoSSRDB 2.00 allows the end user to perform multiple SSRs searches and easy browsing through the SSRs using two repeat algorithms and provide primer pair information for identified SSRs for evolutionary genomics.Database URL: http://www.mcr.org.in/chloromitossrdb.

Looking into the genome of Thermosynechococcus elongatus (thermophilic cyanobacteria) with codon selection and usage perspective.

Genome analysis of thermophilic cyanobacterium, Thermosynechococcus elongatus BP-1 revealed factors ruling choices of codons in this organism. Multiple parameters like Nc, GC3s, RSCU, Codon Adaptation Index (CAI), optimal and rare codons, codon-pair context and amino acid usage were analysed and compositional constraint was identified as major factor. Wide range of Nc values for the same GC3 content suggested the role of translational selection. Mutational bias is suggested at synonymous position. Among optimal codons for translation, most were GC-ending. Seven codons (AGA, AGG, AUA, UAA, UAG, UCA and UGA) were found to have least occurrence in the entire genome and except stop codons all were A-ending (exception AGG). Most widely used codon-pair in the genome are G-ending or C-ending and A-ending or U-ending codons make pair with G-ending or C-ending codons. Amino acids which are largely distributed in T. elongatus tend to use G-ending or C-ending codons most frequently. Findings showed cumulative role of translational selection, translational accuracy and gene expression levels with mutational bias as key player in codon selection pattern of this organism.

Whole genome phylogeny of Prochlorococcus marinus group of cyanobacteria: genome alignment and overlapping gene approach.

Prochlorococcus is the smallest known oxygenic phototrophic marine cyanobacterium dominating the mid-latitude oceans. Physiologically and genetically distinct P. marinus isolates from many oceans in the world were assigned two different groups, a tightly clustered high-light (HL)-adapted and a divergent low-light (LL-) adapted clade. Phylogenetic analysis of this cyanobacterium on the basis of 16S rRNA and other conserved genes did not show consistency with its phenotypic behavior. We analyzed phylogeny of this genus on the basis of complete genome sequences through genome alignment, overlapping-gene content and gene-order approach. Phylogenetic tree of P. marinus obtained by comparing whole genome sequences in contrast to that based on 16S rRNA gene, corresponded well with the HL/LL ecotypic distinction of twelve strains and showed consistency with phenotypic classification of P. marinus. Evidence for the horizontal descent and acquisition of genes within and across the genus was observed. Many genes involved in metabolic functions were found to be conserved across these genomes and many were continuously gained by different strains as per their needs during the course of their evolution. Consistency in the physiological and genetic phylogeny based on whole genome sequence is established. These observations improve our understanding about the adaptation and diversification of these organisms under evolutionary pressure.