An overview of Parafrankia (Nod+/Fix+) and Pseudofrankia (Nod+/Fix-) interactions through genome mining and experimental modeling in co-culture and co-inoculation of Elaeagnus angustifolia.

In many frankia, the ability to nodulate host plants (Nod+) and fix nitrogen (Fix+) is a common strategy. However, some frankia within the Pseudofrankia genus lack one or two of these traits. This phenomenon has been consistently observed across various actinorhizal nodule isolates, displaying Nod- and/or Fix- phenotypes. Yet, the mechanisms supporting the colonization and persistence of these inefficient frankia within nodules, both with and without symbiotic strains (Nod+/Fix+), remain unclear. It is also uncertain whether these associations burden or benefit host plants. This study delves into the ecological interactions between Parafrankia EUN1f and Pseudofrankia inefficax EuI1c, isolated from Elaeagnus umbellata nodules. EUN1f (Nod+/Fix+) and EuI1c (Nod+/Fix-) display contrasting symbiotic traits. While the prediction suggests a competitive scenario, the absence of direct interaction evidence implies that the competitive advantage of EUN1f and EuI1c is likely contingent on contextual factors such as substrate availability and the specific nature of stressors in their respective habitats. In co-culture, EUN1f outperforms EuI1c, especially under specific conditions, driven by its nitrogenase activity. Iron-depleted conditions favor EUN1f, emphasizing iron's role in microbial competition. Both strains benefit from host root exudates in pure culture, but EUN1f dominates in co-culture, enhancing its competitive traits. Nodulation experiments show that host plant preferences align with inoculum strain abundance under nitrogen-depleted conditions, while consistently favoring EUN1f in nitrogen-supplied media. This study unveils competitive dynamics and niche exclusion between EUN1f and EuI1c, suggesting that host plant may penalize less effective strains and even all strains. These findings highlight the complex interplay between strain competition and host selective pressure, warranting further research into the underlying mechanisms shaping plant-microbe-microbe interactions in diverse ecosystems. IMPORTANCE: While Pseudofrankia strains typically lack the common traits of ability to nodulate the host plant (Nod-) and/or fix nitrogen (Fix-), they are still recovered from actinorhizal nodules. The enigmatic question of how and why these unconventional strains establish themselves within nodule tissue, thriving either alongside symbiotic strains (Nod+/Fix+) or independently, while considering potential metabolic costs to the host plant, remains a perplexing puzzle. This study endeavors to unravel the competitive dynamics between Pseudofrankia inefficax strain EuI1c (Nod+/Fix-) and Parafrankia strain EU1Nf (Nod+/Fix+) through a comprehensive exploration of genomic data and empirical modeling, conducted both in controlled laboratory settings and within the host plant environment.

Development of a novel sensitive single-tube nested PCR assay for the detection of African swine fever virus.

African swine fever (ASF) is a highly fatal and contagious viral disease caused by African swine fever virus (ASFV). It has caused significant economic losses to the swine industry and poses a serious threat to food security worldwide. Diagnostic tests with high sensitivity are essential for the effective management of ASF. Here, we describe a single-tube nested PCR (STN-PCR) assay for the detection of ASFV in which two consecutive amplification steps are carried out within a single tube. Two pairs of primers (outer and inner) were designed to target the p72 gene of ASFV. The primer concentrations, annealing temperatures, and number of amplification cycles were optimized to ensure the consecutive utilization of outer and inner primer pairs during amplification while minimizing the likelihood of amplicon contamination. In comparison with two conventional endpoint PCR assays (one of which is recommended by the World Organization for Animal Health), the newly developed STN-PCR assay demonstrated a 100-fold improvement in the limit of detection (LOD), detecting 100 copies of ASFV genomic DNA, whereas the endpoint PCR assays could detect no fewer than 10,000 copies. The clinical performance of the STN-PCR assay was validated using 95 tissue samples suspected of being positive for ASFV, and the assay showed 100% specificity. A Cohen's kappa value of 0.91 indicated perfect agreement between the assays. This new STN-PCR assay is a potentially valuable tool that will facilitate the control of ASF.

Weak Universality Induced by Q=±2e Charges at the Deconfinement Transition of a (2+1)-Dimensional U(1) Lattice Gauge Theory.

Matter-free lattice gauge theories (LGTs) provide an ideal setting to understand confinement to deconfinement transitions at finite temperatures, which is typically due to the spontaneous breakdown (at large temperatures) of the center symmetry associated with the gauge group. Close to the transition, the relevant degrees of freedom (Polyakov loop) transform under these center symmetries, and the effective theory depends on only the Polyakov loop and its fluctuations. As shown first by Svetitsky and Yaffe, and subsequently verified numerically, for the U(1) LGT in (2+1) dimensions, the transition is in the 2D XY universality class, while for the Z_{2} LGT, it is in the 2D Ising universality class. We extend this classic scenario by adding higher charged matter fields and show that the critical exponents γ and ν can change continuously as a coupling is varied, while their ratio is fixed to the 2D Ising value. While such weak universality is well known for spin models, we demonstrate this for LGTs for the first time. Using an efficient cluster algorithm, we show that the finite temperature phase transition of the U(1) quantum link LGT in the spin S=1/2 representation is in the 2D XY universality class, as expected. On the addition of Q=±2e charges distributed thermally, we demonstrate the occurrence of weak universality.

Novel sensitive isothermal-based diagnostic technique for the detection of African swine fever virus.

A rapid, simple, and sensitive diagnostic technique for the detection of African swine fever virus (ASFV) nucleic acid was developed for testing clinical samples in the field or resource-constrained settings. In the current study, the saltatory rolling-circle amplification (SRCA) technique was used for the first time to detect ASFV. The technique was developed using World Organization for Animal Health (WOAH)-approved primers targeting the p72 gene of the ASFV genome. The assay can be performed within 90 minutes at an isothermal temperature of 58°C without a requirement for sophisticated instrumentation. The results can be interpreted by examination with the naked eye with the aid of SYBR Green dye. This assay exhibited 100% specificity, producing amplicons only from ASFV-positive samples, and there was no cross-reactivity with other pathogenic viruses and bacteria of pigs that were tested. The lower limits of detection of SRCA, endpoint PCR, and real-time PCR assays were 48.4 copies/µL, 4.84 × 103 copies/µL, and 4.84 × 103 copies/µL, respectively. Thus, the newly developed SRCA assay was found to be 100 times more sensitive than endpoint and real-time PCR assays. Clinical tissue samples obtained from ASFV-infected domestic pigs and other clinical samples collected during 2020-22 from animals with suspected ASFV infection were tested using the SRCA assay, and a 100% accuracy rate, negative predictive value, and positive predictive value were demonstrated. The results indicate that the SRCA assay is a simple yet sensitive method for the detection of ASFV that may improve the diagnostic capacity of field laboratories, especially during outbreaks. This novel diagnostic technique is completely compliant with the World Health Organization's "ASSURED" criteria advocated for disease diagnosis, as it is affordable, specific, sensitive, user-friendly, rapid and robust, equipment-free, and deliverable. Therefore, this SRCA assay may be preferable to other complex molecular techniques for diagnosing African swine fever.

Computational profiling of natural compounds as promising inhibitors against the spike proteins of SARS-CoV-2 wild-type and the variants of concern, viral cell-entry process, and cytokine storm in COVID-19.

The continuous spread and evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the rapid surge in infection cases in the coronavirus disease 2019 (COVID-19) evoke a dire need for effective therapeutics. In this study, we explored the inhibitory potential of a library of 605 phytocompounds, selected from Indian medicinal plants with reported antiviral and anti-inflammatory activities, against the receptor-binding domain of spike proteins of the SARS-CoV-2 wild-type and the variants of concern, including variants B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma), B.1.617.2 (Delta), and B.1.1.529 (Omicron). Our approach was based on extensive molecular docking, assessment of drug-likeness, and robust molecular dynamics simulations. We also identified promising inhibitory candidates against the host (human) proteins associated with SARS-CoV-2 spike activation and attachment, namely, ACE2 receptor, proteases TMPRSS2 and CTSL, and the endocytic regulator AAK1. In addition, we screened promising inhibitory compounds against the human proinflammatory cytokines- IL-6, IL-1ß, TNF-α, and IFN-γ, that are associated with the adverse cytokine storm in COVID-19 patients. Our analysis returned an encouraging list of promising inhibitory candidates that includes: abietatriene against the spike proteins of the SARS-CoV-2 wild-type and the variants of concern; taraxerol against the human ACE2, CTSL and TNF-α; ß-amyrin against the human TMPRSS2; cynaroside against the human AAK1 and IL-1ß; and friedelin against the human IL-6 and IFN-γ. Our findings provide substantial evidence for the inhibitory potential of these compounds and encourage further in vitro and in vivo studies to validate their use as safe and effective therapeutics against COVID-19.

Fragmentation dynamics of doubly charged camphor molecule following C 1s Auger decay.

The fragmentation dynamics of the gas-phase, doubly charged camphor molecule, formed by Auger decay following carbon 1s ionisation, using soft X-ray synchrotron radiation, is presented in this work. The technique of velocity map imaging combined with a photoelectron-photoion-photoion coincidence (VMI-PEPIPICO) is used for both electron energy and ion momentum (in-sequence) measurements. The experimental study is complemented by molecular dynamics simulation, performed with an NVT (moles, volume, and temperature) ensemble. Velocity Verlet algorithms were used for time integration at various internal energies. These simulations validate observed dissociation pathways. From these, we successfully deduce that the internal energy of the doubly charged molecular ion has a significant contribution to the fragmentation mechanism. Notably, a prominent signature of the internal energy was observed in the experimentally determined energies of the neutral fragment in these deferred charge separation pathways, entailing a more detailed theoretical study to uncover the exact dissociation dynamics.

Development and evaluation of a novel polymerase spiral reaction based testing technique for same-day visual detection of Campylobacter coli in pork.

The developed polymerase spiral reaction-based technique specifically amplified the ceuE gene of C. coli and involved a three-step centrifugation method for DNA extraction. PSR, real-time and end-point PCR were able to detect 62 fg, 620 fg and 6.2 pg C. coli DNA/tube, respectively. PSR detection limits for artificially contaminated pork samples without enrichment, with 12 h enrichment and after 24 h enrichment were 1000 CFU/g, 100 CFU/g, and 10 CFU/g samples, respectively which were ten times better than real-time PCR. The detection performance of PSR (with 12 h enrichment) was also compared to culture (ISO10272-1:2017) method using 75 naturally-contaminated samples, which revealed the sensitivity, specificity, PPV, NPV and accuracy of 100% (95%CI, 73.2%-100%), 98.4% (95%CI, 90%-99.9%), 93.3% (95%CI, 66%-99.6%), 100% (95%CI, 92.5%-100%) and 98.7% (95%CI, 92.8%-99.9%), respectively. The advantage and novelty of this assay are its equipment-free nature, dye-based interpretation by the naked eye, and the requirement of one enzyme and one primer pair. This assay could be a better alternative to other molecular methods and may help in reducing the possible troubles (e.g., gastroenteritis, hospitalization, or death) of belated detection of C. coli in food products. This is the primary report applying the PSR for C. coli detection.

A natural derivative from ethnomedicinal mushroom potentiates apoptosis, autophagy and attenuates cell migration, via fine tuning the Akt signaling in human lung adenocarcinoma cells (A549).

Although comprehensive exertions have been made in late decades for treating advanced lung cancer with inclusive therapies but efficient anti-lung cancer therapeutics are statically inadequate in the clinics. Hence, compelling novel anti-lung cancer drugs are considerably desired. This backdrop enticed us to unveil anticancer efficacy of astrakurkurol, derivative of wild edible mushroom against lung cancer, whose effects have not yet been described. Mechanistic analysis disclosed that sensitizing effect of astrakurkurol is due to cell cycle arrest at G0/G1 phase, increased level of Fas, FADD, decreased ratio of Bax/Bcl-2, and increased cleaved form of caspase 9, 8, and 3. Apart from the induction of apoptosis, it was demonstrated for the first time that astrakurkurol induced an autophagic response as evidenced by the development of acidic vesicular organelles (AVOs) with up-regulation of beclin-1, Atg7, and downregulated p62. Apoptosis and autophagy can be sparked by the same stimuli, which was as evident from the astrakurkurol-induced inactivation of PI3K/AKT signaling. The thorough scanning of the mechanism of crosstalk between apoptosis and autophagy is requisite for prosperous anticancer remedy. Triterpenoid has evidently intensified cytotoxicity, induced apoptosis and autophagy on A549 cells. Besides astrakurkurol could also curb migration and regress the size of tumor in ex ovo xenograft model. All these findings put forth astrakurkurol as a convincing novel anti-cancer agent, for scrutinizing the lung cancer therapies and as a robust contender for future in vitro and in vivo analysis.

Prevalence, toxinotyping, antimicrobial susceptibility and biofilm-forming ability of Clostridium perfringens isolated from free-living rodents and shrews.

BACKGROUND AND OBJECTIVES: Clostridium perfringens (C. perfringens), is a spore-forming and toxin-producing pathogenic Gram-positive rod-shaped bacterium with immense public health/zoonotic concern. Rodents are well-known reservoirs and vectors for a large number of zoonoses and strong links have been recognized between synanthropic rodents and foodborne disease outbreaks throughout the world. To date, no study has been conducted for studying the prevalence of C. perfringens in rodents and shrews. In this study, we investigated faecal samples from free-living rodents and shrews trapped in Meghalaya, a North-eastern hill state of India for the presence of virulent and antimicrobial-resistant C. perfringens. METHODS: A total of 122 animals comprising six species of rodents and one species of shrews were trapped: Mus musculus (n = 15), Mus booduga (n = 7), Rattus rattus (n = 9), Rattus norvegicus (n = 3), Bandicota indica (n = 30), Bandicota bengalensis (n = 32) and Suncus murinus (n = 26). The faecal swabs were collected and processed for the isolation of C. perfringens. Toxinotyping was done using PCR. Antimicrobial susceptibility testing and biofilm forming ability testing were done using Kirby Bauer disc diffusion method and crystal violet assay. RESULTS: C. perfringens was isolated from 27 of the 122 faecal swabs (22.1%), from six species of rodents and shrews. Five of the host species were rodents, Bandicota bengalensis (25%), Bandicota indica (16.7%), Rattus norvegicus (33.3%), Mus musculus (13.3%), Mus booduga (42.8%) and Suncus murinus (shrew) (29.6%). The common toxinotype was type A (59.2%) followed by Type A with beta2 toxin (33.3%), Type C (3.7%) and Type C with beta2 toxin (3.7%). None of the isolates harboured cpe, etx, iap, and NetB genes and therefore none was typed as either B, D, E, F, or G. Nine isolates (33.3%) turned out to be multi-drug resistant (MDR), displaying resistance to three or more categories of antibiotics tested. Twenty-three out of twenty-seven isolates (85.2%) were forming biofilms. CONCLUSION: Globally, this is the first study to report the prevalence of C. perfringens and its virulence profile and antimicrobial resistance in free-living rodents and shrews. The rodents and shrews can potentially contaminate the food and environment and can infect humans and livestock with multi-drug resistant/virulent Type A and Type C C. perfringens.

Quantum Scars from Zero Modes in an Abelian Lattice Gauge Theory on Ladders.

We consider the spectrum of a U(1) quantum link model where gauge fields are realized as S=1/2 spins and demonstrate a new mechanism for generating quantum many-body scars (high-energy eigenstates that violate the eigenstate thermalization hypothesis) in a constrained Hilbert space. Many-body dynamics with local constraints has attracted much attention due to the recent discovery of nonergodic behavior in quantum simulators based on Rydberg atoms. Lattice gauge theories provide natural examples of constrained systems since physical states must be gauge invariant. In our case, the Hamiltonian H=O_{kin}+λO_{pot}, where O_{pot} (O_{kin}) is diagonal (off-diagonal) in the electric flux basis, contains exact midspectrum zero modes at λ=0 whose number grows exponentially with system size. This massive degeneracy is lifted at any nonzero λ but some special linear combinations that simultaneously diagonalize O_{kin} and O_{pot} survive as quantum many-body scars, suggesting an "order-by-disorder" mechanism in the Hilbert space. We give evidence for such scars and show their dynamical consequences on two-leg ladders with up to 56 spins, which may be tested using available proposals of quantum simulators. Results on wider ladders point towards their presence in two dimensions as well.

A novel in situ methodology for visual detection of Clostridium perfringens in pork harnessing saltatory rolling circle amplification.

Clostridium perfringens (C. perfringens), a prolific toxin-producing anaerobe is an important foodborne pathogen with a huge public health concern. Rapid and on-site detection of C. perfringens is of specific importance in developing countries. In the present study, saltatory rolling circle amplification (SRCA) assay was developed for culture-independent, rapid and visual detection of C. perfringens and evaluated in meat with pork as a model. The specificity of the SRCA assay was ascertained by using 62 C. perfringens and 18 non- C. perfringens strains. The analytical sensitivity of the developed SRCA, conventional and real-time PCR assays were 80 fg, 800 fg and 800 fg DNA per tube, respectively. The limit of detection of the SRCA assay was 80 CFU/g of pork in the absence of enrichment and 8 CFU/g after short enrichment of 6 h. The detection limits of 80 CFU/g and 8 CFU/g of pork were attained within 120 min and 8 h, respectively. Real-world or field relevancy of the developed assay was evaluated by screening 82 raw and processed pork samples. As the developed assay is simple, user-friendly, cost-effective and sophisticated-equipment free, it would be more suitable for on-site testing of C. perfringens in foods. To our information, this is the first report to apply SRCA for the detection of C. perfringens.

Structural Insight into the Binding of Cyanovirin-N with the Spike Glycoprotein, Mpro and PLpro of SARS-CoV-2: Protein-Protein Interactions, Dynamics Simulations and Free Energy Calculations.

The emergence of COVID-19 continues to pose severe threats to global public health. The pandemic has infected over 171 million people and claimed more than 3.5 million lives to date. We investigated the binding potential of antiviral cyanobacterial proteins including cyanovirin-N, scytovirin and phycocyanin with fundamental proteins involved in attachment and replication of SARS-CoV-2. Cyanovirin-N displayed the highest binding energy scores (-16.8 ± 0.02 kcal/mol, -12.3 ± 0.03 kcal/mol and -13.4 ± 0.02 kcal/mol, respectively) with the spike protein, the main protease (Mpro) and the papainlike protease (PLpro) of SARS-CoV-2. Cyanovirin-N was observed to interact with the crucial residues involved in the attachment of the human ACE2 receptor. Analysis of the binding affinities calculated employing the molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) approach revealed that all forms of energy, except the polar solvation energy, favourably contributed to the interactions of cyanovirin-N with the viral proteins. With particular emphasis on cyanovirin-N, the current work presents evidence for the potential inhibition of SARS-CoV-2 by cyanobacterial proteins, and offers the opportunity for in vitro and in vivo experiments to deploy the cyanobacterial proteins as valuable therapeutics against COVID-19.

Development of cost-effective quantitative PCR method for parallel detection of porcine circovirus2 and porcine parvovirus in perspective of North-eastern India.

Pig farming performs as an intricate part in the socio-economic situation in the north-eastern region of India. This region contributes 38% (3.95 million) of total pigs in India. In spite of this, the region unables to flourish as an enterprise as per the expectation due to a low productivity rate. Porcine infectious pathogens like porcine cirovirus2 (PCV2) and porcine parvovirus (PPV) have a direct economic impact on pig farming through slow growth rate, abortion, and mortality and ultimately maximize the production cost by increasing the usage of antibiotic or antiviral drugs. The veterinary diagnostic infrastructure is a fundamental aspect of the development of livestock status by rapid and effective detection of pathogens. Quantitative PCR (qPCR) is a precise and fast-track technique used for the routine diagnostic method. Hence, we developed a highly precise and comparatively cost-effective SYBR Green reporter dye-based qPCR assay for parallel identification of PCV2 and PPV. In the present assay, the correlation coefficient (R2) value was 0.99, and 10 copies of the gene/µl were the least limit of detection (LOD) concerning both viruses. Melt curve analysis of this study represented PCV2-specific melt curve (Tm) at 81.2 °C and PPV-specific melt curve (Tm) at 73.5 °C. Therefore, the assay easily differentiates the true positive amplicons of PCV2 and PPV through specific Tm values. Among the 50 field samples, 26 (52%) samples were PCV2 positive, 18 (36%) samples PPV positive, and 11 (22%) samples were co-infected of both the viruses. This method is cost-effective, precise, and sensitive to diagnose the concurrent or individual infection of the PCV2 and PPV in the pig. Hence, considering the impact of pig farming in the north-eastern part of the country, the present assay gives an unprecedented achievement in disease diagnosis.

Development of a novel and rapid polymerase spiral reaction (PSR) assay to detect Salmonella in pork and pork products.

The polymerase spiral reaction (PSR), a novel isothermal method for targeted DNA amplification, was effectively applied to detect Salmonella in artificially spiked pork. The specificity of the developed PSR was tested using 16 Salmonella and 15 non-Salmonella strains. The PSR assay was 10-fold more sensitive than conventional end-point PCR, having a sensitivity comparable to real-time PCR. The limit of detection of the developed assay was 4 × 103 per gram of pork without enrichment and 4 CFU per gram after a 6 h enrichment. The detection of 4 CFU per gram of pork was achieved within 8 h. The PSR assay was successful, and accurate in comparison to microbiological methods, in detecting Salmonella in 11 of 76 commercial pork samples. Therefore the positive predictive value, negative predictive value and accuracy rate of the developed assay were 100%. Considering its rapidity, user-friendliness, simplicity, cost-effectiveness and equipment-free nature, this PSR assay is a promising tool for the food industry for the detection of Salmonella and prevention of Salmonella outbreaks and recalls.

Hindered alignment in ultrashort, intense laser-induced fragmentation of O2.

Molecules ionized by intense (10-100 TW/cm2) and ultrashort (tens of femtoseconds) laser fields undergo rotation and alignment mediated through their polarizability. The expected alignment is indeed observed in the case of O2 molecules ionized by intense laser pulses of 800 nm wavelength and 25 fs duration, as observed through velocity imaging of the fragments. Strikingly, when 35 fs pulses of 400 nm wavelength of comparable intensity are employed, an anomalous hindering of this alignment is observed. In both cases, we propose dissociation pathways for the energetic ions consistent with the recorded kinetic energy distributions. Using a semiclassical model of induced rotation of the molecular ion that involves polarizabilities of the participating excited states, both behaviors are reproduced. The model suggests that the difference in the observations can be attributed to a transient negative polarizability in an intermediate state of the proposed pathway.

Comparative genomics of Mycobacterium reveals evolutionary trends of M. avium complex.

Mycobacterium is gram positive, slow growing, disease causing Actinobacteria. Beside potential pathogenic species, Mycobacterium also contains opportunistic pathogens as well as free living non-pathogenic species. Disease related various analyses on Mycobacterium tuberculosis are very widespread. However, genomic study of overall Mycobacterium species for understanding the selection pressure on genes as well as evolution of the organism is still illusive. MLSA and 16s rDNA based analysis has been generated for 241 Mycobacterium strains and a detailed analysis of codon and amino acid usage bias of mycobacterial genes, their functional analysis have been done. Further the evolutionary features of M. avium complex also have been revealed. Mycobacterial genes are moderately GC rich showed higher expression level in PPs and significant negative correlation with biosynthetic cost of proteins. Translational selection pressure was observed in mycobacterial genes. MAC showed close relationship with NPs and higher evolutionary rate in MAC revealed their constant evolving nature.

Prevalence, molecular typing and antibiotic resistance of Clostridium perfringens in free range ducks in Northeast India.

This study reports faecal prevalence of Clostridium perfringens in free range ducks in North East India for the first time. We also report C. perfringens type A carrying cpb2 and cpe and type C carrying cpb2 and cpe strains in these ducks. Notably, a high prevalence (17.5%) of enterotoxin carrying C. perfringens strains and low antimicrobial resistance were observed.

Contrasted evolutionary constraints on carbohydrate active enzymes (CAZymes) in selected Frankia strains.

Carbohydrate active enzymes (CAZymes) are capable of breaking complex polysaccharides into simpler form. In plant-host-associated microorganisms CAZymes are known to be involved in plant cell wall degradation. However, the biology and evolution of Frankia CAZymes are largely unknown. In the present study, we took a genomic approach to evaluate the presence and putative roles of CAZymes in Frankia. The CAZymes were found to be potentially highly expressed (PHX) proteins and contained more aromatic amino acids, which increased their biosynthetic energy cost. These energy rich amino acids were present in the active sites of CAZymes aiding in their carbohydrate binding capacity. Phylogenetic and evolutionary analyses showed that, in Frankia strains with the capacity to nodulate host plants, CAZymes were evolving slower than the other PHX genes, whereas similar genes from non-nodulating (or ineffectively nodulating) Frankia strains showed little variation in their evolutionary constraints compared to other PHX genes. Thus, the present study revealed the persistence of a strong purifying selection on CAZymes of Frankia indicating their crucial role.

A novel phylogenetic tree based on the presence of protein domains in selected actinobacteria.

Protein functional domains are semi-autonomous parts of proteins capable of functioning independently. One protein may contain several domains and one domain may be present in different protein sequences. Thus, protein domains represent the niche specific adaptive nature of an organism. We hypothesized that the presence and absence of protein domains in an organism could be used to make a phylogenetic tree, which may better depict the biotope (niche). Here, we selected 100 actinobacteria and built a phylogenetic tree depending upon the presence and absence of protein domains. Strains of different genera from the same niche were found to cluster together suggesting niche specific domain acquisition among selected strains. Thus, the domain based phylogeny clustered the selected actinobacteria mainly according to their niche rather than their taxonomic classification.

An update on the taxonomy of the genus Frankia Brunchorst, 1886, 174AL.

Since the recognition of the name Frankia in the Approved Lists of bacterial names (1980), few amendments have been given to the genus description. Successive editions of Bergey's Manual of Systematics of Archaea and Bacteria have broadly conflicting suprageneric treatments of the genus without any advances for subgeneric classification. This review focuses on recent results from taxongenomics and phenoarray approaches to the positioning and the structuring of the genus Frankia. Based on phylogenomic analyses, Frankia should be considered the single member of the family Frankiaceae within the monophyletic order, Frankiales. A polyphasic strategy incorporating genome to genome data and omniLog® phenoarrays, together with classical approaches, has allowed the designation and an amended description of a type strain of the type species Frankia alni, and the recognition of at least 10 novel species covering symbiotic and non symbiotic taxa within the genus. Genome to phenome data will be shortly incorporated in the scheme for proposing novel species including those recalcitrant to isolation in axenic culture.