Rhizosphere impact bacterial community structure in the tea (Camellia sinensis (L.) O. Kuntze.) estates of Darjeeling, India

India contributes 28% of the world's tea production, and the Darjeeling tea of India is a world-famous tea variety known for its unique quality, flavor, and aroma. This study analyzed the spatial distribution of bacterial communities in the tea rhizosphere of six different tea estates at different altitudes. The organic carbon, total nitrogen, and available phosphate were higher in the rhizosphere soils than the bulk soils, irrespective of the sites. Alpha and beta diversities were significantly (p<0.05) higher in the bulk soil than in the rhizosphere. Among the identified phyla, the predominant ones were Proteobacteria, Actinobacteria, and Acidobacteria. At the genus level, only 4 out of 23 predominant genera (>1% relative abundance) could be classified viz. Candidatus Solibacter (5.36±0.36%), Rhodoplanes (4.87±0.3%), Candidatus Koribacter (2.3±0.67%), Prevotella (1.49±0.26%). The rhizosphere effect was prominent evident from the significant depletion of more ASVs (n=39) compared to enrichment (n=11). The functional genes also exhibit a similar trend with the enrichment of N2 fixation genes, disease suppression, and Acetoine synthesis. Our study reports that the rhizobiome of tea is highly selective by reducing the alpha and beta diversity while enriching the significant functional genes. This article is protected by copyright. All rights reserved.

Molecular and culture-based surveys of metabolically active hydrocarbon-degrading archaeal communities in Sundarban mangrove sediments

Archaea remain important players in global biogeochemical cycles worldwide, including in the highly productive mangrove estuarine ecosystems. In the present study, we have explored the diversity, distribution, and function of the metabolically active fraction of the resident archaeal community of the Sundarban mangrove ecosystem, using both culture-independent and culture-dependent approaches. To evaluate the diversity and distribution pattern of the active archaeal communities, RNA based analysis of the 16S rRNA gene was performed on an Illumina platform. The active Crenarchaeal community was observed to remain constant while active Euryarchaeal community underwent considerable change across the sampling sites depending on varying anthropogenic factors. Haloarchaea were the predominant group in hydrocarbon polluted sediments, leading us to successfully isolate eleven p-hydroxybenzoic acid degrading haloarchaeal species. The isolates could also survive in benzoic acid, naphthalene, and o-phthalate. Quantitative estimation of p-hydroxybenzoic acid degradation was studied on select isolates, and their ability to reduce COD of polluted saline waters of Sundarban was also evaluated. To our knowledge, this is the first ever study combining culture-independent (Next Generation sequencing and metatranscriptome) and culture-dependent analyses for an assessment of archaeal function in the sediment of Sundarban.

Effective rhizoinoculation and biofilm formation by arsenic immobilizing halophilic plant growth promoting bacteria (PGPB) isolated from mangrove rhizosphere: A step towards arsenic rhizoremediation

Arsenic (As) uptake by plants is largely influenced by the presence of microbial consortia and their interactions with As. In the coastal region of Bengal deltaic plain of Eastern India, the As-contaminated groundwater is frequently used for irrigation purposes resulting in an elevated level of soil As in agricultural lands. The health hazards associated with As necessitates development of cost-effective remediation strategies to reclaim contaminated agricultural lands. Among the available technologies developed in recent times, bioremediation using bacteria has been found to be the most propitious. In this study, two As-resistant halophilic bacterial strains Kocuria flava AB402 and Bacillus vietnamensis AB403 were isolated, identified and characterized from mangrove rhizosphere of Sundarban. The isolates, AB402 and AB403, could tolerate 35mM and 20mM of arsenite, respectively. The effect of As on the exopolysaccharide (EPS) synthesis, biofilm formation, and root association was evaluated for both the bacterial strains. Arsenic adsorption on the cell surfaces and intracellular accumulation in both the bacterial strains were promising under culture conditions. Moreover, both the strains when used as inoculum, not only promoted the growth of rice seedlings but also decreased As uptake and accumulation in plants.

Genome-Guided Insights into the Plant Growth Promotion Capabilities of the Physiologically Versatile Bacillus aryabhattai Strain AB211

Bacillus aryabhattai AB211 is a plant growth promoting, Gram-positive firmicute, isolated from the rhizosphere of tea (Camellia sinensis), one of the oldest perennial crops and a major non-alcoholic beverage widely consumed all over the world. The whole genome of B. aryabhattai AB211 was sequenced, annotated and evaluated with special focus on genomic elements related to plant microbe interaction. It’s genome sequence reveals the presence of a 5,403,026 bp chromosome. A total of 5226 putative protein-coding sequences, 16 rRNA, 120 tRNA, 8 ncRNAs, 58 non-protein coding genes, and 11 prophage regions were identified. Genome sequence comparisons between strain AB211 and other related environmental strains of B. aryabhattai, identified about 3558 genes conserved among all B. aryabhattai genomes analyzed. Most of the common genes involved in plant growth promotion activities were found to be present within core genes of all the genomes used for comparison, illustrating possible common plant growth promoting traits shared among all the strains of B. aryabhattai. Besides the core genes, some genes were exclusively identified in the genome of strain AB211. Functional annotation of the genes predicted in the strain AB211 revealed the presence of genes responsible for mineral phosphate solubilization, siderophores, acetoin, butanediol, exopolysaccharides, flagella biosynthesis, surface attachment/biofilm formation, and indole acetic acid production, most of which were experimentally verified in the present study. Genome analysis and experimental evidence suggested that AB211 has robust central carbohydrate metabolism implying that this bacterium can efficiently utilize the root exudates and other organic materials as an energy source. Genes for the production of peroxidases, catalases, and superoxide dismutases, that confer resistance to oxidative stresses in plants were identified in AB211 genome. Besides these, genes for heat shock tolerance, cold shock tolerance, glycine-betaine production, and antibiotic/heavy metal resistance that enable bacteria to survive biotic/abiotic stress were also identified. Based on the genome sequence information and experimental evidence as presented in this study, strain AB211 appears to be metabolically diverse and exhibits tremendous potential as a plant growth promoting bacterium.

Improvements to the SMO algorithm for SVM regression

This paper points out an important source of inefficiency in Smola and Schölkopf's sequential minimal optimization (SMO) algorithm for support vector machine (SVM) regression that is caused by the use of a single threshold value. Using clues from the KKT conditions for the dual problem, two threshold parameters are employed to derive modifications of SMO for regression. These modified algorithms perform significantly faster than the original SMO on the datasets tried.

Robust sparse hyperplane classifiers: application to uncertain molecular profiling data

Molecular profiling studies can generate abundance measurements for thousands of transcripts, proteins, metabolites, or other species in, for example, normal and tumor tissue samples. Treating such measurements as features and the samples as labeled data points, sparse hyperplanes provide a statistical methodology for classifying data points into one of two categories (classification and prediction) and defining a small subset of discriminatory features (relevant feature identification). However, this and other extant classification methods address only implicitly the issue of observed data being a combination of underlying signals and noise. Recently, robust optimization has emerged as a powerful framework for handling uncertain data explicitly. Here, ideas from this field are exploited to develop robust sparse hyperplanes, i.e., classification and relevant feature identification algorithms that are resilient to variation in the data. Specifically, each data point is associated with an explicit data uncertainty model in the form of an ellipsoid parameterized by a center and covariance matrix. The task of learning a robust sparse hyperplane from such data is formulated as a second order cone program (SOCP). Gaussian and distribution-free data uncertainty models are shown to yield SOCPs that are equivalent to the SCOP based on ellipsoidal uncertainty. The real-world utility of robust sparse hyperplanes is demonstrated via retrospective analysis of breast cancer related transcript profiles. Data-dependent heuristics are used to compute the parameters of each ellipsoidal data uncertainty model. The generalization performance of a specific implementation, designated "robust LIKNON," is better than its nominal counterpart. Finally, the strengths and limitations of robust sparse hyperplanes are discussed.

Integrated analysis of transcript profiling and protein sequence data

Transcript profiling can be used to elucidate the molecular and cellular mechanisms involved in ageing and cancer. A recent study of human gastrointestinal stromal tumours (GISTs) with mutations in the KIT gene, Cancer Res. 61 (2001) 8624 exemplifies a common type of investigation. cDNA microarrays were used to generate measurements for 1987 clones in two types of tissues: 13 KIT mutation-positive GISTs and 6 spindle cell tumours from locations outside the gastrointestinal tract. Statistical problems associated with such two-class, high-dimensional profiling data include simultaneous classification and relevant feature identification, probabilistic clustering and protein sequence family modelling. Here, the GIST data were reexamined using specific solutions to these problems, namely sparse hyperplanes, nai;ve Bayes models and profile hidden Markov models respectively. The integrated analysis of molecular profiling and sequence data highlighted 6 clones that may be of clinical and experimental interest. The protein encoded by one of these putative biomarkers defined a novel protein family present in diverse eucarya. The family may be involved in chromosome segregation and/or stability. One family member is a potential biomarker identified recently from a retrospective analysis of transcript profiles for sporadic breast cancer samples from patients with poor and good prognosis, Signal Process. (in press).

Developmental expression of alcohol dehydrogenase (ADH3) in zebrafish (Danio rerio)

Alcohol dehydrogenase (ADH) is the primary enzyme responsible for metabolism of ethanol to acetaldehyde. One class of ADH has been described in fish, and has been found to be structurally similar to mammalian class III ADH (glutathione-dependent formaldehyde dehydrogenase) but functionally similar to class I ADH (primarily responsible for ethanol metabolism). We have cloned a cDNA by RT-PCR from zebrafish (Danio rerio) liver representing the zebrafish ADH3 gene product, with a coding region of 1131 nucleotides. The deduced amino acid sequences share 90% identity to ADH3 from the marine fish Sparus aurata, and 82 and 81% identity to the mouse and human sequences, respectively. Using a quantitative competitive RT-PCR assay, ADH3 mRNA was detected at all timepoints analyzed and was lowest between 8 and 24 h postfertilization. Thus, differential ADH3 expression may be at least partly responsible for temporal variations in the sensitivity of zebrafish embryos to developmental alcohol exposure.

Mean Field Methods for a Special Class of Belief Networks

The chief aim of this paper is to propose mean-field approximations for a broad class of Belief networks, of which sigmoid and noisy-or networks can be seen as special cases. The approximations are based on a powerful mean-field theory suggested by Plefka. We show that Saul, Jaakkola and Jordan' s approach is the first order approximation in Plefka's approach, via a variational derivation. The application of Plefka's theory to belief networks is not computationally tractable. To tackle this problem we propose new approximations based on Taylor series. Small scale experiments show that the proposed schemes are attractive.

Improvements to Platt's SMO Algorithm for SVM Classifier Design

This article points out an important source of inefficiency in Platt's sequential minimal optimization (SMO) algorithm that is caused by the use of a single threshold value. Using clues from the KKT conditions for the dual problem, two threshold parameters are employed to derive modifications of SMO. These modified algorithms perform significantly faster than the original SMO on all benchmark data sets tried.

Peptide from a prokaryotic adhesin blocks leukocyte migration in vitro and in vivo

The integrin CD11b/CD18 promotes leukocyte extravasation during inflammation. Filamentous hemagglutinin (FHA) of Bordetella pertussis binds to CD11b/CD18, raising the possibility that peptides derived from FHA might inhibit leukocyte migration. The Arg-Gly-Asp (RGD) sequence of FHA has been suggested to modulate binding of ligands to CD11b/CD18. Peptides derived from this region inhibited adherence and transendothelial migration of neutrophils in vitro and prevented recruitment of leukocytes into the cerebrospinal fluid in an experimental model of meningitis in rabbits. The mechanism of the antiinflammatory effect may involve modulation of the activity of CD11b/CD18 through peptide interaction with the leukocyte response integrin/integrin-associated protein complex.

Inhibition of leukocyte-endothelial cell interactions and inflammation by peptides from a bacterial adhesin which mimic coagulation factor X

Factor X (factor ten) of the coagulation cascade binds to the integrin CD11b/CD18 during inflammation, initiating procoagulant activity on the surface of leukocytes (Altieri, D.C., O.R. Etingin, D.S. Fair, T.K. Brunk, J.E. Geltosky, D.P. Hajjar, and T. S. Edgington. 1991. Science [Wash.DC]. 254:1200-1202). Filamentous hemagglutinin (FHA), an adhesin of Bordetella pertussis also binds to the CD11b/CD18 integrin (Relman D., E. Tuomanen, S. Falkow, D.T. Golenbock, K. Saukkonen, and S.D. Wright. 1990. Cell. 61:1375-1382). FHA and the CD11b/CD18 binding loops of Factor X share amino acid sequence similarity. FHA peptides similar to Factor X binding loops inhibited 125I-Factor X binding to human neutrophils and prolonged clotting time. In addition, ETKEVDG and its Factor X analogue prevented transendothelial migration of leukocytes in vitro and reduced leukocytosis and blood brain barrier disruption in vivo. Interference with leukocyte migration by a coagulation-based peptide suggests a novel strategy for antiinflammatory therapy.

The cell wall mediates pneumococcal attachment to and cytopathology in human endothelial cells

Streptococcus pneumoniae interacts with vascular endothelial cells during the course of bacteremia. In this study, we characterized the initial attachment of pneumococci to human endothelial cells (EC) and the response of the endothelium to this interaction. Pneumococci adhered to EC in a dose-dependent fashion. Attachment was rapid, with the majority of bacteria attached by 30 min. No difference was found between the attachment of unencapsulated (R6) and encapsulated (SIII) strains. Purified pneumococcal cell wall components competitively inhibited attachment of R6 by a maximum of 60% in a dose-dependent manner. Following attachment of pneumococci or exposure of EC to pneumococcal cell wall, pronounced changes in EC morphology ensued, resulting in striking separation of the cells of the monolayer and, eventually, destruction of the cells. The cytopathic effects of the cell wall were inhibited by antibodies to interleukin-1 but not to tumor necrosis factor. Both antibodies were required to neutralize the cytopathology caused by intact pneumococci. We conclude that pneumococci attach rapidly to human EC and that the cell wall is important in this interaction. Intact pneumococci and pneumococcal cell wall induce profound morphologic changes in human EC, leading to loss of barrier integrity. These cytopathic effects are likely to be cytokine mediated.

Induction of procoagulant activity on human endothelial cells by Streptococcus pneumoniae

The inflammatory response in infection caused by gram-negative organisms involves induction of procoagulant activity (PCA) on human endothelial cells. Although infections caused by gram-positive organisms are also associated with fibrin formation and thrombosis, the bacterial determinants inducing PCA are unknown. This study shows that intact pneumococci and the pneumococcal cell wall efficiently induce PCA on human endothelial cells. Upon exposure of endothelial cells to pneumococci, PCA was first detectable at 30 min, peaked at 2 h, and disappeared by 6 h. The specific activities of encapsulated and unencapsulated strains for induction of PCA were equivalent. Purified pneumococcal cell walls were as potent as endotoxin in induction of PCA. The ability to induce a procoagulant state on endothelial cells is a new biological activity of gram-positive cell walls which promotes the participation of the coagulation cascade in the inflammatory response to disease caused by gram-positive organisms.