Potential plant growth promoting traits and bioacidulation of rock phosphate by thiosulfate oxidizing bacteria isolated from crop plants

Thiosulfate oxidizing bacteria isolated from crop plants were tested for their traits related to plant growth promotion and their ability to solubilize Morocco rock phosphate (RP) through oxidation of thiosulfate to sulfuric acid. All the tested strains grew in Nfb medium (except Dyella ginsengisoli) and possessed beta-1,3 glucanase activity (except Burkholderia kururiensis). Of the fourteen tested strains, 2 were found positive for siderophore production, 3 each for phytohormones (IAA), and salicylic acid production. Based on qualitative and quantitative assays, 5 strains were found to efficiently solubilize tri-calcium phosphate in Pikovskaya's medium. Nine strains exhibited ACC (1-aminocyclopropane-1-carboxylate) deaminase activity. In gnotobiotic experiments, Pandoraea sputorum ATSB28 which possessed the lowest ACC deaminase (0.44 nM of alpha-Keto butyrate formed min(-1) mg of protein(-1)) activity increased the primary root length of canola by 166%. Inoculation of Pandoraea sp. strain ATSB30 in mixture containing RP and thiosulfate significantly enhanced the water extractable-P (1147 microg P g RP(-1)) and bicarbonate extractable-P (1144 microg P g RP(-1)) on day 45. Glucose amendment resulted in increased RP solubilization as compared to glucose unamended treatments. Thiosulfate oxidizing bacteria tested in this study possessed at least one or more plant growth promoting traits apart from thiosulfate oxidation and solubilized the RP.     

Chromate reducing and plant growth promoting activities of psychrotrophic Rhodococcus erythropolis MtCC 7,905.

A psychrotrophic bacterial strain resistant to 300 mg l(-1) of Cr(6+) was isolated from metal contaminated soil samples from a site situated in the Indian Himalayan Region. Based on 16 S rRNA analysis the isolate showed maximum similarity to Rhodococcus erythropolis. Rhodococcus erythropolis MTCC 7,905 reduced substantial amounts of Cr(6+) to Cr(3+) at 10 degrees C and showed plant growth promotion. The isolate offer promise as inoculant to promote plant growth of pea (Pisum sativum) in the presence of toxic Cr(6+) concentration. To the best of our knowledge this is the first report on a psychrotrophic strain belonging to species R. erythropolis and its functional characterization to reduce Cr(6+ )and promote plant growth at low temperature.     

Molecular characterization of the extracellular matrix in a Pseudomonas putida dsbA mutant: implications for acidic stress defense and plant growth promotion

The Pseudomonas putida dsbA mutant displays enhanced extracellular matrix production, which promotes biofilm formation. Here we confirmed that the extracellular matrix consists of both capsular polysaccharides and exopolysaccharides. However, the carbohydrate composition of the P. putida dsbA mutant matrix was shown to be similar to that of the wild-type strain. Our data indicate that the overproduced matrix itself, rather than alterations in the matrix composition, promotes biofilm formation in the P. putida dsbA mutant. Moreover, the mutant was more sensitive than the wild-type to alkali stress (pH 9.0 to 10.0), but not to acidic stress (pH 5.0). Interestingly, acidic stress stimulated polysaccharide production and pellicle formation, while these changes were recovered to the level of the wild-type under alkali conditions in the P. putida dsbA mutant. Enhanced biofilm formation of the dsbA mutant increased the efficiency with which P. putida attached to tomato and pepper seeds, which have longer germinated roots than the wild-type strain. This phenomenon could not be observed in the cucumber plant, which suggests that each plant seed has a different effect on the attachment of P. putida. Interestingly, this increased attachment to plant seeds resulted in more root colonization and plant growth promotion. The findings of this study suggested that the overproduced extracellular matrix caused by deletion of the dsbA gene could have pleiotropic effect on P. putida phenotypes, including acidic stress defense and plant growth promotion.     

Genotypic characterization of thermophilic bacilli: A study on new soil isolates and several reference strains

A genotypic study using amplified ribosomal DNA restriction analysis (ARDRA), random amplified polymorphic DNA fingerprinting (RAPD) and ribosomal spacer analysis (RSA) in comparison with DNA-DNA reassociation experiments was carried out with 85 thermophilic Bacillus isolates from uncultivated soil of 14 different geographical areas and seventeen reference strains representing defined thermophilic Bacillus species. This approach permitted the attribution of 51 % of the new isolates to the Bacillus thermoleovorans group and the identification of 40% of the new isolates as B. “thermodenitrificans”. Moreover, 2 strains were assigned to B. pallidus species and 1 isolate to B. thermosphaericus species. The remaining 6% of our thermophilic isolates from soil, constituting 2 DNA-DNA homology groups, are still unidentified. A detailed genotypic characterization of the heterogeneous species of B. thermoleovorans and B. stearothermophilus was also presented.     

Diversity of protease-producing marine bacteria from sub-antarctic environments

From seawater and the intestines of benthonic organisms collected from the Beagle Channel, Argentina, 230 marine bacteria were isolated. Cultivable bacteria were characterized and classified as psychrotolerant, whereas few isolates were psychrophiles. These isolates were capable of producing proteases at 4 and 15 °C under neutral (pH 7.0), alkaline (pH 10.0) and acidic (pH 4.5) conditions on different media, revealing 62, 33 and 22% producers at cold and 84, 47 and 33% producers at low temperatures, respectively. More protease-producing strains (67%) were detected when isolated from benthic invertebrates as compared to seawater (33%), with protease production under neutral conditions resulting in milk protein hydrolysis halos between 27 and 30 ± 2 mm in diameter. Using sterile 0.22 μm membrane filters, 29 isolates exhibiting extracellular protease activity were detected. These were grouped into six operational taxonomic units by restriction analysis and identified based on 16S rDNA as γ-proteobacteria of the genera Pseudoalteromonas, Pseudomonas, Shewanella, Alteromonas, Aeromonas, and Serratia. Plasmids were found to be harbored by eight strains, mainly within the isolates from benthonic organisms.     

Lactovum miscens gen. nov., sp. nov., an aerotolerant, psychrotolerant, mixed-fermentative anaerobe from acidic forest soil

An aerotolerant, psychrotolerant anaerobe, anNAG3, was isolated from an acidic forest floor solution (in situ pH of 4.5). Cells of anNAG3 stained Gram-positive did not form spores, and were not motile. Cells were ovoid, approximately 1 microm long and 0.7 microm wide, mostly in pairs, and contained a multi-layered cell wall and intracytoplasmic membranes. Growth was observed at pH 3.5-7.5 and 0-35 degrees C. Glucose, galactose, fructose, mannitol, glucosamine, N-acetylglucosamine, cellobiose, and maltose supported growth. Lactate, ethanol, formate, and acetate were end products. H(2) and CH(4) were not detected, and only very minor amounts of CO(2) were produced. The relative amount of a particular product was dependent on the substrate utilized, and product profiles indicated that (i) sugars were initially metabolized to pyruvate via glycolysis, and (ii) lactate dehydrogenase and pyruvate-formate lyase were responsible for the subsequent metabolism of pyruvate. O(2) was not significantly utilized and was not toxic to growth. anNAG3 did not contain detectable membranous or cytoplasmic cytochromes. Nitrate, sulfate, and Fe(III) were not dissimilated. Thus, anNAG3 was characterized as an aerotolerant, non-acetogenic chemoorganotroph with a mixed-fermentative metabolism. The G + C content of the DNA was 37.6 mol%. The similarity of the 16S rRNA gene sequence of anNAG3 to that of its closest phylogenetic relatives (which were in the genera Lactococcus and Streptococcus) approximated 88-89%, indicating that anNAG3 constitutes the type species of a new genus. Based on the collective properties of anNAG3, it is proposed that anNAG3 be termed Lactovum miscens.     

Loss of all plastid ndh genes in Gnetales and conifers: extent and evolutionary significance for the seed plant phylogeny

The exact phylogenetic position of Gnetales, a small, highly modified group of gymnosperms with an accelerated rate of molecular evolution, is one of the most challenging issues for seed plant systematics. Recent results from entire plastid genome (ptDNA) sequencing revealed the absence of the entire suite of plastid ndh genes in several species of Gnetales and the pine family (Pinaceae) potentially highlighting a major structural feature linking these two groups—concerted loss of all plastid genes for the NADH dehydrogenase complex. However, the precise extent of ndh gene loss in gymnosperms has not been surveyed. Using a slot-blot hybridization method, we probed all 11 ndh genes in 162 species from 70 of 85 gymnosperm genera. We find that all ndh genes are absent across Gnetales and Pinaceae, but not in any other group of gymnosperms. This feature represents either a major synapomorphy for a clade consisting of these two lineages or, less likely, a convergent loss. Our survey substantially extends previous inferences based on more limited sampling and, if the former evolutionary interpretation is correct, it provides additional support for the contentious “gnepine” hypothesis, which places Gnetales as sister to Pinaceae. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Nitrogen fixing bacteria in the family Acetobacteraceae and their role in agriculture

For centuries, the Acetobacteraceae is known as a family that harbors many species of organisms of biotechnological importance for industry. Nonetheless, since 1988 representatives of this family have also been described as nitrogen fixing bacteria able to plant growth promotion by a variety of mechanisms. Nitrogen fixation is a biological process that guarantees that the atmospheric N₂ is incorporated into organic matter by several bacterial groups. Most representatives of this group, also known as diazotrophic, are generally associated with soil rhizosphere of many plants and also establishing a more specific association living inside roots, leaves, and others plants tissues as endophyte. Their roles as plant growth‐promoting microorganisms are generally related to increase in plant biomass, phosphate and other mineral solubilization, and plant pathogen control. Here, we report many of these plant growth‐promoting processes related to nitrogen fixing species already described in Acetobacteraceae family, especially Gluconacetobacter diazotrophicus and their importance to agriculture. In addition, a brief review of the state of art of the phylogenetics, main physiological and biochemical characteristics, molecular and functional genomic data of this group of Acetobacteraceae is presented.

     

Identification,phylogeny and expression analysis of suppressors of cytokine signaling in channel catfish

The suppressors of cytokine signaling (SOCS) family genes play important roles in regulating a variety of signal transduction pathways that are involved in immunity, growth and development. Because of their importance, they have been extensively studied in mammalian species, but they have not been systematically studied among teleost fish species. In this study, a total of 12 SOCS genes were characterized to understand the molecular mechanisms of SOCS function in channel catfish. Phylogenetic analyses suggested that all SOCS were clustered into two main clusters. Further syntenic analysis confirmed the phylogenetic analyses and allowed the annotation of SOCS genes in channel catfish. This work, for the first time, determined the expression profiles of the 12 SOCS genes after bacterial infections with Flavobacterium columnare and Edwardsiella ictaluri in channel catfish. The SOCS1a and SOCS3a were significantly up-regulated at 4 h after F. columnare challenge in the gill, but were down-regulated at later stages of pathogenesis. Similarly, SOCS1a and CISH were significantly up-regulated at 3 h in intestine under E. ictaluri infection, but were down-regulated at later stages of pathogenesis at 24 h and 3 days after infection. These expression patterns may indicate that SOCS genes could be induced in acute immune responses after bacterial infections, but the massive cytokine expression, especially chemokine expression after the first day of infection may have had negative feedback leading to the overall down-regulation of the expression of SOCS genes. Moreover, the differential expression patterns of SOCS genes in the catfish gill and intestine after F. columnare and E. ictaluri infection demonstrated that the regulation of SOCS gene expression was both tissue-specific and time-dependent. Taken together, these results suggested that SOCS genes were involved in immune responses to bacterial invasions, and these results set the foundation for future studies of SOCS gene functions.     

Diversity of the exoproteome of Fusarium graminearum grown on plant cell wall

The exoproteome of the fungus Fusarium graminearum grown on glucose and on hop (Humulus lupulus, L.) cell wall has been investigated. The culture medium was found to contain a higher quantity of proteins and the proteins are more diverse when the fungus is grown on cell wall. Using both 1D and 2D electrophoresis followed by mass spectrometry analysis and protein identification based on similarity searches, 84 unique proteins were identified in the cell wall-grown fungal exoproteome. Many are putatively implicated in carbohydrate metabolism, mainly in cell wall polysaccharide degradation. The predicted carbohydrate-active enzymes fell into 24 different enzymes classes, and up to eight different proteins within a same class are secreted. This indicates that fungal metabolism becomes oriented towards synthesis and secretion of a whole arsenal of enzymes able to digest almost the complete plant cell wall. Cellobiohydrolase is one of the only four proteins found both after growth on glucose and on plant cell wall and we propose that this enzyme could act as a sensor of the extracellular environment. Extensive knowledge of this very diverse F. graminearum exoproteome is an important step towards the full understanding of Fusarium/plants interactions. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Molecular evolution and phylogeny of dengue type 4 virus in the Caribbean

We sequenced the E gene and adjacent prM/M and NS1 junctions (1940 bp) of 48 Dengue-4 (DEN-4) isolates collected between 1981 and 1999 from 8 Caribbean islands and from 7 South and Central American countries. Phylogenetic analysis confirms a single introduction in the early 1980s and a high degree of gene flow resulting in a pattern of evolution defined more by time period than geographic origin, especially within the Caribbean basin. A modern Caribbean clade consisting of four distinct lineages has arisen, comprised of isolates from Caribbean islands and nearby regions of South America. This clade is defined by three amino acid substitutions in the E (aa 163 and 351) and NS1 (aa 52) proteins. These findings highlight the importance of migration and gene flow in dengue viral change and suggest that efforts to understand disease dynamics in the Caribbean basin need to focus at regional, rather than local scales.     

The actin gene of the glaucocystophyte Cyanophora paradoxa: analysis of the coding region and introns, and an actin phylogeny of eukaryotes

We isolated the actin gene of the glaucocystophyte alga Cyanophora paradoxa and analyzed the coding region and its introns. Phylogenetic analyses of the actin coding region and the inferred protein sequence in data sets containing 47 other actin sequences show Cyanophora to be a member of the eukaryotic crown-group radiation in agreement with ribosomal DNA sequence analyses. Four of the five Cyanophora actin introns are relatively short (55–59 nt) and occupy novel positions in a catalogue of actin introns containing 56 distinct sites. The fifth intron has a length of 171 nt and occurs also in actin genes from green algae and the crustacean Artemia. Received: 4 December 1996 / Accepted: 5 February 1997