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Light-gated ion channel and ion pump rhodopsins are widely used as optogenetic tools and these can control the electrically excitable cells as (1) they are a single-component system i.e., their light sensing and ion-conducting functions are encoded by the 7-transmembrane domains and, (2) they show fast kinetics with small dark-thermal recovery time. In cellular signaling, a signal receptor, modulator, and the effector components are involved in attaining synchronous regulation of signaling. Optical modulation of the multicomponent network requires either receptor to effector encoded in a single ORF or direct modulation of the effector domain through bypassing all upstream players. Recently discovered modular rhodopsins like rhodopsin guanylate cyclase (RhoGC) and rhodopsin phosphodiesterase (RhoPDE) paves the way to establish a proof of concept for utilization of complex rhodopsin (modular rhodopsin) for optogenetic applications. Light sensor coupled modular system could be expressed in any cell type and hence holds great potential in the advancement of optogenetics 2.0 which would enable manipulating the entire relevant cell signaling system. Here, we had identified 50 novel modular rhodopsins with variant domains and their diverse cognate signaling cascades encoded in a single ORF, which are associated with specialized functions in the cells. These novel modular algal rhodopsins have been characterized based on their sequence and structural homology with previously reported rhodopsins. The presented novel modular rhodopsins with various effector domains leverage the potential to expand the optogenetic tool kit to regulate various cellular signaling pathways across the diverse biological model systems.

The adverse effects of chemical nitrogen fertilizers affecting soil fertility, water pollution and native microorganisms, particularly cyanobacteria, in wetland rice cultivation have drawn global attention towards the use of alternative sources like N2-fixing cyanobacteria as a biofertilizer for sustainable rice farming. Although chemical nitrogen fertilizers are extensively used for obtaining higher rice yield, they are likely to have a deleterious effect on the growth and N2-fixation of diazotrophs, including cyanobacteria. In addition, biocides (herbicides and insecticides) are widely being used in rice cultivation for optimizing crop yield, but these chemicals also affects non-target organisms adversely. There are several reports indicating impacts of these agrochemicals on cyanobacteria, but most such studies were carried out under laboratory conditions. This article reviews information from different field evaluations on the impact of agrochemicals on cyanobacteria along with rice crop in wetland rice field ecosystem.

Biocides (herbicides and insecticides) are intensively being used in rice cultivation, despite several adverse non-target effects on native cyanobacteria. Comparative effects of three herbicides (benthiocarb, butachlor, and 2,4-D) and four insecticides (furadon, phorate, methyl parathion, and ekalux) were studied at field-recommended doses. Field experiments of rice were carried out for three consecutive seasons in completely randomized block designs in both rainy and winter croppings at the Central Rice Research Institute, Cuttack, India. Toxicities of seven biocides individually to native cyanobacteria growing with rice crops in wetland fields were assessed for growth and acetylene reduction activity (ARA); several crop parameters of paddy were estimated concomitantly. It was observed that applications of butachlor and benthiocarb individually significantly decreased growth (15.86 and 17.50%), ARA (0.16 and 0.68%), and N-yield (0.26 and 0.85%) of the native cyanobacteria, whereas these parameters increased (24.04% in growth, 0.25% in ARA, and 0.40% in N-yield) due to the application of 2,4-D. Of the tested insecticides, furadon, phorate, and methyl parathion enhanced the growth (17.8, 10.7, and 11.7%), N2-fixation (0.10, 0.097, and 0.074%), and N-yield (0.16, 0.18, and 0.20%) of cyanobacteria, whereas ekalux had no significant effect on cyanobacteria. On the basis of cyanobacterial parameters, biocides could be recommended for rice crops in the order furadon < phorate < methyl parathion < ekalux. Applications of 2,4-D and furadon individually in comparison to the rest other biocides enhanced rice yield. These finding could help to revise integrated strategies of weed and pest management in wetland rice agriculture to save non-target soil microorganisms, particularly cyanobacteria.

Cyanobacteria maintain soil fertility by performing N2-fixation and act as a key biocatalyst in nitrogen cycle. Chemical N-fertilizers and pesticides as agrochemicals are intensively being used in rice farming to boost rice production, this work deals with the first hand information on their influence on native N2-fixing cyanobacteria, which play an important role in maintaining soil health. A field study was conducted for three consecutive seasons in water logged rice field to observe the influence of agrochemicals, urea, benthiocarb and carbofuran in isolation and in combinations on biomass, acetylene reduction activity (ARA) and N-yield of native cyanobacteria as well as, on growth and yield of rice. The ARA and N-yield followed almost same trend. It is discernible that both urea and benthiocarb had deleterious effects whereas, carbofuran was promoting effects on cyanobacterial growth, ARA and N-yield. The combination of all the three above agrochemicals was found inhibitory, but inhibition was comparatively less than that of urea or benthiocarb in isolation or urea plus benthiocarb treatments. It is concluded that the combination of agrochemicals was toxic, in comparison to the control, but was better than application of urea N or benthiocarb alone or with their combinations. It was recorded that along with rice straw and gain yields, panicle numbers were the maximum at the combination with treatments of benthiocarb+carbofuran. Adverse effects of used agrochemicals on cyanobacteria in wetland rice cultivation could be avoided by a prudent use of chemical N-fertilizers and pesticide(s) in combination.

Cyanobacteria, one of the most ancient groups of oxygenic photoautotrophs are ubiquitously found in almost all habitats on earth. Under nitrogen limitation, some of the cyanobacteria have the ability to differentiate a specialized cell called heterocyst which provides the microoxic environment favorable for proper functioning of oxygen-sensitive enzyme nitrogenase. In heterocystous cyanobacteria, nitrogenase complex is involved in N2 fixation which is also accompanied by hydrogen production. Today, the limited sources of fossil fuel prompt us to exploit various unconventional methods including hydrogen gas as an alternate source of energy. H2 gas is an environmentally clean and efficient alternative for energy. Several microorganisms including cyanobacteria can produce hydrogen. Therefore, this chapter first of all, highlights the basics of nitrogen assimilation and its regulation in cyanobacteria. It also deals and discusses in detail the nitrogenase and its involvement in H2 production. Further, the cyanobacterial hydrogenases and their role in hydrogen production and regulation have also been discussed. Various approaches used to enhance hydrogen production, like genetic and metabolic engineering, have been emphasized along with information on the different types of photobioreactor which are being used for a large-scale industrial production of hydrogen gas. Overall, this chapter summarizes the information about the nitrogenases and hydrogenases involved in H2 production in cyanobacteria and the technologies being utilized for increasing hydrogen production at industrial level. Understanding the underlying mechanisms of hydrogen production in cyanobacteria and improving production methods enable commercialization of molecular hydrogen as an efficient and environment-friendly energy source.

Cyanobacteria are a diverse group of Gram-negative oxygenic photoautotrophs and many of them have ability to perform nitrogen fixation in addition to carbon fixation. The demand of iron in cyanobacteria is exceptionally high due to its involvement in the function of a variety of crucial enzymes. Hence, iron acquisition process and its regulation is essential. The Fe2 +/Fe3 + imbalance in the cells causes severe abnormal changes and it needs to be regulated for proper growth and survival of cyanobacteria. Therefore, cyanobacteria have evolved complex metabolic pathways with different mechanisms to regulate intracellular levels of iron for their survival in a changing environment, by tightly regulating iron uptake. In cyanobacteria, iron uptake is regulated by TonB system which includes a barrel-shaped TonB-dependent transporter (TBDT), integral membrane protein ExbB, and the membrane-anchored periplasmic protein ExbD. At the center to this regulatory network of iron homeostasis is the ferric uptake regulator (Fur), which is a global iron regulator in prokaryotes including cyanobacteria. Considering the importance of availability of iron, understanding the complex iron homeostasis and associated regulatory mechanisms involving Fur is necessary and important. The complex regulatory mechanisms of iron homeostasis along with the basic understanding of the functioning of Fur protein and its interaction with other transcriptional regulator in cyanobacteria have been discussed in this chapter.

Simple Summary Mucociliary clearance constitutes an innate lung defense mechanism that is primarily driven by ciliated cells. Respiratory mucus traps pathogens entering the airways, and lung cilia propel them outward via their coordinated directional motion. Thus, damage to the component(s) of this apparatus will hamper its smooth functioning. Here, we update the cellular and molecular machinery that constitutes and regulates mucociliary clearance (MCC). We also describe several respiratory diseases arising due to genetic or acquired molecular shortcomings in the MCC. The past few decades have seen the emergence of novel viruses that inflame and damage the respiratory tract. Coronaviruses have been observed to disrupt the ciliated epithelium and abolish its integrity. Bearing in mind the havoc created by the ongoing pandemic, we outline the significance of the ciliated respiratory epithelium in defense against such microbial infections. We have predicted protein interaction networks depicting severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)-manifested implications on the molecular machinery regulating mucociliary clearance. Several proteins involved in the network were found to interact with SARS-CoV-2 viral proteins upon host infection. This review also emphasizes the importance of the proper management and surveillance of respiratory health in the elderly and patients with chronic respiratory diseases so that they do not bear the impact of a severe or lethal infection. Abstract Mucociliary defense, mediated by the ciliated and goblet cells, is fundamental to respiratory fitness. The concerted action of ciliary movement on the respiratory epithelial surface and the pathogen entrapment function of mucus help to maintain healthy airways. Consequently, genetic or acquired defects in lung defense elicit respiratory diseases and secondary microbial infections that inflict damage on pulmonary function and may even be fatal. Individuals living with chronic and acute respiratory diseases are more susceptible to develop severe coronavirus disease-19 (COVID-19) illness and hence should be proficiently managed. In light of the prevailing pandemic, we review the current understanding of the respiratory system and its molecular components with a major focus on the pathophysiology arising due to collapsed respiratory epithelium integrity such as abnormal ciliary movement, cilia loss and dysfunction, ciliated cell destruction, and changes in mucus rheology. The review includes protein interaction networks of coronavirus infection-manifested implications on the molecular machinery that regulates mucociliary clearance. We also provide an insight into the alteration of the transcriptional networks of genes in the nasopharynx associated with the mucociliary clearance apparatus in humans upon infection by severe acute respiratory syndrome coronavirus-2.

The diazotrophic cyanobacteria are known to play an important role in nitrogen economy of wetland rice ecosystem. Due to intensive use of nitrogenous fertilizers in rice cultivation, maintenance of soil health has become a challenging task. In this context, a systematic study was conducted in flooded rice field to determine the effects of different doses of commonly used urea and ammonium sulphate nitrogenous fertilizers on native cyanobacterial biomass, N2-fixation and N-yield at various stages of rice plants. The results clearly demonstrated that both urea and ammonium sulphate inhibited cyanobacterial growth and N2-fixation at different stages of rice crop. Maximum growth and N2-fixation were observed at heading stage of rice plant at 60 days after transplantation when compared with early and late stages of rice crop. Of the two fertilizers, urea was found more inhibitory to cyanobacteria and among the two seasons, these fertilizers were more inhibitory in the dry than in the wet season. This study suggests that N fertilizers need to be used judiciously in rice cultivation so that both cyanobacterial contribution and high rice yield are ensured.

In cyanobacterium Anabaena 7120, iron deficiency leads to oxidative stress with unavoidable consequences. Nitric oxide reduces pigment damage and supported the growth of Anabaena 7120 in iron-deficient conditions. Elevation in nitric oxide accumulation and reduced superoxide radical production justified the role of nitric oxide in alleviating oxidative stress in iron deficiency. Increased activities of antioxidative enzymes and higher levels of ROS scavengers (ascorbate, glutathione and thiol) in iron deficiency were also observed in the presence of nitric oxide. Nitric oxide also supported the membrane integrity of Anabaena cells and reduces protein and DNA damage caused by oxidative stress induced by iron deficiency. Results suggested that nitric oxide alleviates the damaging effects of oxidative stress induced by iron deficiency in cyanobacterium Anabaena 7120.

To unravel the existence of dominant bacterial population in the paddy fields of Eastern Uttar Pradesh, India and their relation to the prevailing soil physicochemistry using multivariate statistical analyses, a cumulative culture-independent 16S rRNA based Polymerase chain reaction-Denaturing gradient gel electrophoresis (PCR-DGGE) and a 16S-23S ribosomal intergenic spacer analysis (RISA) have been performed. Detrended correspondence analysis (DCA) and principal component analysis (PCA) biplot analyses were used to assess the relation between soil bacterial population and its physicochemistry. DCA analysis exhibited a strong dependence of bacterial existence on the soil physicochemical variables, such as organic matter, total nitrogen, inorganic nutrients, temperatures, and moisture status. Soil dehydrogenase activity (DHA) was assessed to check the metabolic activity of all soil samples which showed a range of 0.012–0.050 nmol TPF g−1 min−1 with significant variation (p

The efficacy of dihydroxamate siderophore in attenuation/mitigation of cadmium toxicity, an optimum level of cadmium under which cyanobacterium can grow and produce siderophore, complexation behaviour of cadmium and siderophore and kinetics of complexation along with in silico analysis have been investigated in paddy field cyanobacterium Anabaena oryzae under iron replete and deplete conditions. Results showed that cadmium concentration as 1.0 μM is optimum for growth as well as siderophore production in iron replete and deplete culture conditions. The complexation between cadmium–siderophore was evident in spectral scan. Kinetic studies as well as in silico docking analysis indicate that like iron, cadmium also forms a thermodynamically stable complex with siderophore. Thus our results suggest that the siderophore produced by Anabaena oryzae can act as a biological sequestering agent for the mitigation of cadmium metal ions from the paddy fields to improve crop productivity.

Comparative growth and N2-fixation of cyanobacteria, namely Aphanothece sp. (unicellular) and Gloeotrichia sp. (heterocystous, filamentous), were studied after their inoculation to rice crop in the absence and presence of urea nitrogen fertilizer. In the absence of N-fertilizer application (control), inoculation of both cyanobacterial species showed significant increase in growth and acetylene reduction activity (ARA), but gradual reduction in these parameters was observed at 30 and 60 kg N ha−1 of urea application. In inoculation of Gloeotrichia sp. at control, 30 and 60 kg N ha−1 increased grain yield significantly over uninoculated control in both wet and dry seasons, but grain yield with Aphanothece sp. inoculation was statistically similar to the control at N levels during both seasons. The inoculation study showed that heterocystous cyanobacteria contributed better than unicellular ones, and application of N-fertilizer adversely affected both growth and N2-fixation of native as well of inoculated cyanobacteria.

To investigate the physiology and taxonomic composition of the key players of nitrification and denitrification processes in paddy fields, culture dependent and independent studies have been carried out. A total of 28 bacterial strains have been screened in which six were capable of reducing nitrate and nitrite as well as having significant ammonium removal potential. 16S rRNA-PCR-DGGE-based molecular typing of enriched batch culture was done with time duration to explore and identify dominant and stable soil denitrifiers. Notably, three isolates namely PDN3, PDN19, PDN14 were found to be efficiently involved in the removal of 70.32, 71.46, and 81.50% of NH4 (+) and showed closest similarity (>98%) with Bacillus cereus, Bacillus subtilis, and Pseudomonas aeruginosa strains, respectively. The bacterial strain PDN14 showed maximum growth with highest ammonium removal rate (2.78 gN/(m(3) ·h) has also been characterized based on nosZ gene which showed similarity to uncultured γ- Proteobacteria, P. aeruginosa sp. B3. Median joining (MJ) network and rRNA secondary structure have been analyzed for their detailed taxonomic diversity and derived haplotype-based co-occurrence. Results demonstrated that such strains can serve as good candidate for in situ nitrogen transformation in paddy soils and improvingly characterized by physiological and detailed phylogenetic approaches.

Spore (akinete) formation in the heterocystous and branched filamentous cyanobacterium Fischerella muscicola involves a significant increase in cell size and formation of several endospores in each of the cells. In present study, the physico-chemical factors (pH, light sources, nutrient deficiency, nitrogen sources, carbon sources, and growth hormones) affecting the germination of spores of F. muscicola were examined. Increase in spore germination frequency was detected above pH 8 with maximum germination (46.04%) recorded at pH 9, whereas a significant decrease in germination was observed at pH 6 when compared to control (pH 7.6). Spore germination was not observed at pH 5. Among light sources germination frequency followed the following order, that is, red light (39.9%) > white light (33.8%) > yellow light (3.4%) > green light (1.3%) whereas germination did not take place in dark and blue light. Ammonium chloride (NH4 Cl) supported maximum (99.5%) germination frequency followed by calcium nitrate (Ca(NO3 )2 ), potassium nitrate (KNO3 ), and minimum germination was observed in urea. Nutrient (phosphorus, calcium, and magnesium) deficiency significantly enhanced the germination frequency with maximum increase in magnesium (Mg) deficient condition. Further, supplementation of carbon sources (glucose, fructose, and sodium acetate) and growth hormones (IAA and GA) also enhanced the germination frequency in this cyanobacterium. Therefore, it may be concluded that, those factors supporting higher germination frequency could be considered for successful production and use of this cyanobacterium in biofertilizer and other algal production technologies.

In Anabaena sp. PCC 7120, iron is an essential trace element and its availability determines proper functioning of several kinds of metabolisms. Iron deficiency leads to several unavoidable consequences including membrane damage. In the present study, we dealt with the impact of iron deficiency on NtcA (global nitrogen regulator)-dependent regulation of two important processes, i.e. fatty acid desaturation and heterocyte envelop formation in cyanobacterium Anabaena sp. PCC 7120. In Anabaena sp. PCC 7120, NtcA regulates fatty acid desaturation by regulating enzyme fatty acid desaturases. The NtcA-based regulation of fatty acid desaturation may be direct or indirect. Furthermore, the expression of genes involved in the heterocyte envelope polysaccharide (HEP) layer formation (hepABCK) and heterocyte-specific glycolipids (HGLs) synthesis (devH, hglEA , prpJ and devB) were also under the control of NtcA and reduced under iron deficiency background. The enhanced expression of furA and early downregulation of ntcA under iron deficiency is responsible for reduction in fatty acid desaturation as well as decrease in the expression of genes involved in HEP layer formation and HGL synthesis. Overall results confirmed that iron deficiency influences the NtcA-based regulation of fatty acid desaturation and heterocyte envelop formation in Anabaena sp. PCC 7120.

The Ferric uptake regulator (Fur) protein is a global iron regulator found in most prokaryotes. Although the Fur protein is involved in a variety of metabolic pathways, it is specifically known for the regulation of several iron responsive genes. It binds to the highly conserved sequences located in the upstream promoter region known as iron boxes, using ferrous ion as a co-repressor. Apart from that, the Fur protein is also directly/indirectly involved in a variety of other crucial physiological pathways. Hence, understanding the mechanism of action and the mechanistic pathways of iron regulation by Fur is necessary and important. The basic understanding of the functioning and properties of Fur protein along with its role, interaction and regulation at various levels in cyanobacteria has been discussed in detail.

Cyanobacteria sense the environmental phosphate level and respond accordingly with the help of a two component regulatory system SphS-SphR orthologous to PhoR-PhoB of E. coli, where SphS act as a sensor kinase and SphR as a response regulator. Under phosphate limiting condition SphS-SphR regulates the expression of many genes including genes which do not have the direct role in metabolism and transport of phosphate. Thus there is some crosstalk mechanism which connects this regulatory system to the other metabolic processes. Different types of enzymes and transporters are expressed by cyanobacteria under phosphate limitation to release and transport the phosphate from different organic compounds present in the environment. Genes encoding these enzymes and transporters contain Pho boxes in their promoter region where SphR binds and regulate their expression under phosphate limitation. The machinery and mechanism of regulation is not uniform in cyanobacteria as it varies in different groups according to their evolutionary adaptations. This review article is summarizing the reports on machinery and mechanism of organophosphate metabolism in cyanobacteria.

The cyanobacterium Anabaena sp. PCC 7120 was grown in presence and absence of iron to decipher the role of manganese in protection against the oxidative stress under iron starvation and growth, manganese uptake kinetics, antioxidative enzymes, lipid peroxidation, electrolyte leakage, thiol content, total peroxide, proline and NADH content was investigated. Manganese supported the growth of cyanobacterium Anabaena 7120 under iron deprived conditions where maximum uptake rate of manganese was observed with lower K(m) and higher V(max) values. Antioxidative enzymes were also found to be elevated in iron-starved conditions. Estimation of lipid peroxidation and electrolyte leakage depicted the role of manganese in stabilizing the integrity of the membrane which was considered as the prime target of oxygen free radicals in oxidative stress. The levels of total peroxide, thiol, proline and NADH content, which are the representative of oxidative stress response in Anabaena 7120, were also showed increasing trends in iron starvation. Hence, the results discerned, clearly suggested the role of manganese in protection against the oxidative stress in cyanobacterium Anabaena 7120 under iron starvation either due to its antioxidative properties or involvement as cofactor in a number of antioxidative enzymes.

Out of the various mycotoxigenic food and feed contaminant, the fungal species belonging to Penicillium genera, particularly Penicillium roqueforti is of great economic importance, and well known for its crucial role in the manufacturing of Roquefort and Gorgonzola cheese. The mycotoxicosis effect of this mold is due to secretion of several metabolites, of which PR toxin is of considerable importance, with regard to food quality and safety challenges issues. The food products and silages enriched with PR toxin could lead into damage to vital internal organs, gastrointestinal perturbations, carcinogenicity, immunotoxicity, necrosis, and enzyme inhibition. Moreover, it also has the significant mutagenic potential to disrupt/alter the crucial processes like DNA replication, transcription, and translation at the molecular level. The high genetic diversities in between the various strains of P. roqueforti persuaded their nominations with Protected Geographical Indication (PGI), accordingly to the cheese type, they have been employed. Recently, the biosynthetic mechanism and toxicogenetic studies unraveled the role of ari1 and prx gene clusters that cross-talk with the synthesis of other metabolites or involve other cross-regulatory pathways to negatively regulate/inhibit the other biosynthetic route targeted for production of a strain-specific metabolites. Interestingly, the chemical conversion that imparts toxic properties to PR toxin is the substitution/oxidation of functional hydroxyl group (-OH) to aldehyde group (-CHO). The rapid conversion of PR toxin to the other derivatives such as PR imine, PR amide, and PR acid, based on conditions available reflects their unstability and degradative aspects. Since the PR toxin-induced toxicity could not be eliminated safely, the assessment of dose-response and other pharmacological aspects for its safe consumption is indispensable. The present review describes the natural occurrences, diversity, biosynthesis, genetics, toxicological aspects, control and prevention strategies, and other management aspects of PR toxin with paying special attention on economic impacts with intended legislations for avoiding PR toxin contamination with respect to food security and other biosafety purposes.

Curcuma longa L., commonly known as turmeric, is a rhizomatous herb of the family Zingiberaceae. It is mostly used as a spice, a coloring agent and broadly used in traditional medicine such as Ayurveda, Unani, etc., Turmeric rhizomes interact with a large numbers of rhizosphere-associated microbial species, and some enter the plant tissue and act as endophytes. Both rhizospheric and endophytic species are directly or indirectly involved in growth promotion and disease management in plants and also play an important role in the modulation of morphological growth, secondary metabolite production, curcumin content, antioxidant properties, etc. The present review focuses on the rhizobacterial and endophytic bacterial and fungal populations associated with the turmeric.

Cyanobacteria are known to exhibit their efficiency in producing high concentrations of compounds of commercial value. Arthrospira is one such cyanobacterium which is considered as important source of protein (65%) and other nutrients. In present study, chemical mutagenesis using N-methyl-Ń-Nitro-nitrosoguanidine (NTG), a proven potent mutagen for cyanobacteria was used to bring stable and desirable alteration in Arthrospira platensis ARM 730. Three morphological mutants (G-1, G-2, and SF) were selected and characterized. The G-1 and G-2 were helical, more bluish in pigmentation than the wild type strain where G-1 also showed enlarged cell size. The SF mutant was an altered straight-filament having maximum biomass. Among three mutants, higher protein and phycocyanin contents were observed in G-1 and G-2 mutants whereas chlorophyll was less in these mutants as compared to wild type strain indicating change in the pigment ratio. Carotenoid content was higher in SF mutant as compared to wild type and other mutants. Variation in total sugar content was not observed in comparison to wild type strain. The analysis of amino acid spectrum of all the mutants and wild type showed significant increase in proline content. Overall, it is revealed from the results that G-1 and G-2 mutants showed higher biomass, phycocyanin, and protein contents in comparison to wild type which indicated their great potential to be used in food and pharmaceutical industries.

Iron deficiency ends up into several unavoidable consequences including damaging oxidative stress in cyanobacteria. NtcA is a global nitrogen regulator controls wide range of metabolisms in addition to regulation of nitrogen metabolism. In present communication, NtcA based regulation of iron homeostasis, ROS production and cellular phenotype under iron deficiency in Anabaena 7120 has been investigated. NtcA regulates the concentration dependent iron uptake by controlling the expression of furA gene. NtcA also regulated pigment synthesis and phenotypic alterations in Anabaena 7120. A significant increase in ROS production and corresponding reduction in the activities of antioxidative enzymes (SOD, CAT, APX and GR) in CSE2 mutant strain in contrast to wild type Anabaena 7120 also suggested the possible involvement of NtcA in protection against oxidative stress in iron deficiency. NtcA has no impact on the expression of furB and furC in spite of presence of consensus NtcA binding site (NBS) and -10 boxes in their promoter. NtcA also regulates the thylakoid arrangement as well as related photosynthetic and respiration rates under iron deficiency in Anabaena 7120. Overall results suggested that NtcA regulates iron acquisition and in turn protect Anabaena cells from the damaging effects of oxidative stress induced under iron deficiency.

Highly iterated palindromes (HIP) have been used as high resolution molecular markers for assessing the genetic variability and phylogenetic relatedness of heterocystous cyanobacteria (subsections IV and V) representing 12 genera of heterocystous cyanobacteria, collected from different geographical areas of India. DNA fingerprints generated using four HIP markers viz. HIP-AT, HIP-CA, HIP-GC, and HIP-TG showed 100 % polymorphism in all the heterocystous cyanobacteria studied and each marker produced unique and strain-specific banding pattern. Furthermore, phylogenetic affinities based on the dendrogram constructed using HIP DNA profiles of heterocystous cyanobacteria suggest the monophyletic origin of this entire heterocystous clade along with a clear illustration of the polyphyletic origin of the branched Stigonematalean order (Subsection V). In addition, phylogenetic affinities were validated by principal component analysis of the HIP fingerprints. The overall data obtained by both the phylogeny and principal component assessments proved that the entire heterocystous clade was intermixed, and there are immediate needs for classificatory reforms that satisfy morphological plasticity and environmental concerns.

Organisms can respond to varying light conditions using a wide range of sensory photoreceptors. These photoreceptors can be standalone proteins or represent a module in multidomain proteins, where one or more modules sense light as an input signal which is converted into an output response via structural rearrangements in these receptors. The output signals are utilized downstream by effector proteins or multiprotein clusters to modulate their activity, which could further affect specific interactions, gene regulation or enzymatic catalysis. The blue-light using flavin (BLUF) photosensory module is an autonomous unit that is naturally distributed among functionally distinct proteins. In this study, we identified 34 BLUF photoreceptors of prokaryotic and eukaryotic origin from available bioinformatics sequence databases. Interestingly, our analysis shows diverse BLUF-effector arrangements with a functional association that was previously unknown or thought to be rare among the BLUF class of sensory proteins, such as endonucleases, tet repressor family (tetR), regulators of G-protein signaling, GAL4 transcription family and several other previously unidentified effectors, such as RhoGEF, Phosphatidyl-Ethanolamine Binding protein (PBP), ankyrin and leucine-rich repeats. Interaction studies and the indexing of BLUF domains further show the diversity of BLUF-effector combinations. These diverse modular architectures highlight how the organism’s behaviour, cellular processes, and distinct cellular outputs are regulated by integrating BLUF sensing modules in combination with a plethora of diverse signatures. Our analysis highlights the modular diversity of BLUF containing proteins and opens the possibility of creating a rational design of novel functional chimeras using a BLUF architecture with relevant cellular effectors. Thus, the BLUF domain could be a potential candidate for the development of powerful novel optogenetic tools for its application in modulating diverse cell signaling.

To decipher an evolutionary lineage between two different but important bacterial groups, i.e., Pseudomonas strain (γ-Proteobacteria) and Frankia strain (actinobacteria) growing in the same ecological niche in and around of an actinorhizal plant Hippophae salicifolia D. Don, genetic diversity and comparative molecular phylogeny have been investigated using 16S rRNA gene sequences and computer-simulated and virtually directed restriction fragment length polymorphism (RFLP) through 10 restriction enzymes. Bayesian and coalescent analyses on the basis of 16S rRNA gene sequences suggested three major groups with close proximity between Pseudomonas and Frankia isolates. This result has been further validated based on the data observed through similarity coefficient value and computational RFLP. Principal component analysis and Mandel h and k statistical analysis also confirmed and strengthen the findings. Approximately 458 aligned sequence of all the taxa were used to decipher nucleotide diversity, polymorphism and gene flow between these taxa. Thus, our results suggest for a possible co-evolution or a heterologous gene transfer of distantly related microbial forms. Further, our study also advocate for the use of computer aided, virtual RFLP analysis as a cost effective and rapid identification tool. Electronic supplementary material The online version of this article (doi:10.1007/s13205-016-0488-5) contains supplementary material, which is available to authorized users.

To investigate the physiology and taxonomic composition of the key players of nitrification and denitrification processes in paddy fields, culture dependent and independent studies have been carried out. A total of 28 bacterial strains have been screened in which six were capable of reducing nitrate and nitrite as well as having significant ammonium removal potential. 16S rRNA-PCR-DGGE-based molecular typing of enriched batch culture was done with time duration to explore and identify dominant and stable soil denitrifiers. Notably, three isolates namely PDN3, PDN19, PDN14 were found to be efficiently involved in the removal of 70.32, 71.46, and 81.50% of NH4 (+) and showed closest similarity (98%) with Bacillus cereus, Bacillus subtilis, and Pseudomonas aeruginosa strains, respectively. The bacterial strain PDN14 showed maximum growth with highest ammonium removal rate (2.78 gN/(m(3) ·h) has also been characterized based on nosZ gene which showed similarity to uncultured γ- Proteobacteria, P. aeruginosa sp. B3. Median joining (MJ) network and rRNA secondary structure have been analyzed for their detailed taxonomic diversity and derived haplotype-based co-occurrence. Results demonstrated that such strains can serve as good candidate for in situ nitrogen transformation in paddy soils and improvingly characterized by physiological and detailed phylogenetic approaches.

The cyanobacterium Anabaena sp. PCC 7120 was grown in presence and absence of iron to decipher the role of manganese in protection against the oxidative stress under iron starvation and growth, manganese uptake kinetics, antioxidative enzymes, lipid peroxidation, electrolyte leakage, thiol content, total peroxide, proline and NADH content was investigated. Manganese supported the growth of cyanobacterium Anabaena 7120 under iron deprived conditions where maximum uptake rate of manganese was observed with lower K(m) and higher V(max) values. Antioxidative enzymes were also found to be elevated in iron-starved conditions. Estimation of lipid peroxidation and electrolyte leakage depicted the role of manganese in stabilizing the integrity of the membrane which was considered as the prime target of oxygen free radicals in oxidative stress. The levels of total peroxide, thiol, proline and NADH content, which are the representative of oxidative stress response in Anabaena 7120, were also showed increasing trends in iron starvation. Hence, the results discerned, clearly suggested the role of manganese in protection against the oxidative stress in cyanobacterium Anabaena 7120 under iron starvation either due to its antioxidative properties or involvement as cofactor in a number of antioxidative enzymes.