Selection of phytotoxin producing rhizobacteria

In order to select phytotoxin producing rhizobacteria to control weed plants, twenty five bacterial strains previously isolated from the rhizospheres of various plants were grown in a liquid medium and, after cell removal by centrifugation, the liquid phases were freeze-dried and the products were extracted with ethyl acetate/methanol. The extracts were concentrated to dryness under vacuum and dissolved in water and sucrose solution to be submitted to in vitro assays of lettuce (Lactuca sativa L.) seed germination and wheat (Triticum aestivum L.) coleoptile growth. Although most samples affected coleoptile growth, only those from four strains reduced lettuce seed germination. Two strains of Bacillus cereus, one strain of B. pumilus and one of Stenotrophoonas altophilia were the most promising microorganisms for producing phytotoxin and, consequently, for the development of new weed control products.

Com o objetivo de selecionar rizobactérias produtoras de fitotoxinas para uso no controle de plantas daninhas, vinte e cinco isolados bacterianos previamente obtidos das rizosferas de diferentes plantas foram cultivados em meio líquido e, após remoção das células por centrifugação, as fases líquidas foram liofilizadas e os resíduos obtidos foram submetidos à extração com acetato de etila/metanol. Os extratos foram concentrados sob vácuo até secura e dissolvidos em água e solução de sacarose para serem submetidos a testes in vitro de germinação de sementes de alface (Lactuca sativa L.) e de crescimento de coleóptilos de trigo (Triticum aestivum L.). Embora a maior parte das amostras tenha desfavorecido o crescimento dos coleóptilos de trigo, somente as provenientes de quatro isolados reduziram a germinação das sementes de alface. Dois isolados de Bacillus cereus, um isolado de B. pumilus e um de Stenotrophomonas maltophilia foram os microrganismos mais promissores para a produção de fitotoxinas, com possibilidade de uso no desenvolvimento de novos produtos para o controle de plantas daninhas.

Selection of phytotoxin producing rhizobacteria.

In order to select phytotoxin producing rhizobacteria to control weed plants, twenty five bacterial strains previously isolated from the rhizospheres of various plants were grown in a liquid medium and, after cell removal by centrifugation, the liquid phases were freeze-dried and the products were extracted with ethyl acetate/methanol. The extracts were concentrated to dryness under vacuum and dissolved in water and sucrose solution to be submitted to in vitro assays of lettuce (Lactuca sativa L.) seed germination and wheat (Triticum aestivum L.) coleoptile growth. Although most samples affected coleoptile growth, only those from four strains reduced lettuce seed germination. Two strains of Bacillus cereus, one strain of B. pumilus and one of Stenotrophoonas altophilia were the most promising microorganisms for producing phytotoxin and, consequently, for the development of new weed control products.

Biosurfactants, bioemulsifiers and exopolysaccharides from marine microorganisms.

Marine biosphere offers wealthy flora and fauna, which represents a vast natural resource of imperative functional commercial grade products. Among the various bioactive compounds, biosurfactant (BS)/bioemulsifiers (BE) are attracting major interest and attention due to their structural and functional diversity. The versatile properties of surface active molecules find numerous applications in various industries. Marine microorganisms such as Acinetobacter, Arthrobacter, Pseudomonas, Halomonas, Myroides, Corynebacteria, Bacillus, Alteromonas sp. have been studied for production of BS/BE and exopolysaccharides (EPS). Due to the enormity of marine biosphere, most of the marine microbial world remains unexplored. The discovery of potent BS/BE producing marine microorganism would enhance the use of environmental biodegradable surface active molecule and hopefully reduce total dependence or number of new application oriented towards the chemical synthetic surfactant industry. Our present review gives comprehensive information on BS/BE which has been reported to be produced by marine microorganisms and their possible potential future applications.

In silico comparison of bacterial strains using mutual information.

Fast-sequencing throughput methods have increased the number of completely sequenced bacterial genomes to about 400 by December 2006, with the number increasing rapidly. These include several strains. In silico methods of comparative genomics are of use in categorizing and phylogenetically sorting these bacteria. Various word-based tools have been used for quantifying the similarities and differences between entire genomes. The simple di-nucleotide frequency comparison, codon specificity and k-mer repeat detection are among some of the well-known methods. In this paper, we show that the Mutual Information function, which is a measure of correlations and a concept from Information Theory, is very effective in determining the similarities and differences among genome sequences of various strains of bacteria such as the plant pathogen Xylella fastidiosa, marine Cyanobacteria Prochlorococcus marinus or animal and human pathogens such as species of Ehrlichia and Legionella. The short-range three-base periodicity, small sequence repeats and long-range correlations taken together constitute a genome signature that can be used as a technique for identifying new bacterial strains with the help of strains already catalogued in the database. There have been several applications of using the Mutual Information function as a measure of correlations in genomics but this is the first whole genome analysis done to detect strain similarities and differences.

Thermobacillus composti sp. nov., a moderately thermophilic bacterium isolated from a composting reactor.

A Gram-negative, rod-shaped, spore-forming and moderately thermophilic bacterium, strain KWC4(T), was isolated from a composting reactor. Cells of strain KWC4(T) were 2.0-5.0 microm long and 0.5-0.7 microm in diameter. Strain KWC4(T) grew aerobically at 32-61 degrees C, with optimal growth occurring at 50 degrees C. It grew at pH 5.6-10.1, with optimal growth at around pH 9.0. The optimum NaCl concentration for growth was almost 0 % (w/v), but strain KWC4(T) was moderately halotolerant and was able to grow at NaCl concentrations up to 4.4 % (w/v). The DNA G+C content of strain KWC4(T) was 60.0 mol%. The major fatty acids were iso-16 : 0 (39.0 %) and anteiso-15 : 0 (33.3 %). Based on 16S rRNA gene sequence similarity data, strain KWC4(T) belonged to the genus Thermobacillus and was related to Thermobacillus xylanilyticus. However, strain KWC4(T) had a 38 bp insertion sequence located near the 3' end of its 16S rRNA gene that was not present in T. xylanilyticus. The 16S rRNA gene sequence similarity value between strain KWC4(T) and T. xylanilyticus was 95.7 %. The DNA-DNA hybridization value between strain KWC4(T) and T. xylanilyticus strain XE(T) was 66 %. On the basis of phenotypic and genotypic evidence, strain KWC4(T) (=DSM 18247(T)=JCM 13945(T)) is the type strain of a novel species, for which the name Thermobacillus composti sp. nov. is proposed.

Structural elucidation of phosphoglycolipids from strains of the bacterial thermophiles Thermus and Meiothermus.

The structures of two major phosphoglycolipids from the thermophilic bacteria Thermus oshimai NTU-063, Thermus thermophilus NTU-077, Meiothermus ruber NTU-124, and Meiothermus taiwanensis NTU-220 were determined using spectroscopic and chemical analyses to be 2'-O-(1,2-diacyl-sn-glycero-3-phospho) -3'-O-(alpha-N-acetyl-glucosaminyl)-N-glyceroyl alkylamine [PGL1 (1)] and the novel structure 2'-O-(2-acylalkyldio-1-O-phospho)-3'-O-(alpha-N-acetylglucosaminyl)-N-glyceroyl alkylamine [PGL2 (2)]. PGL2 (2) is the first phosphoglycolipid identified with a 2-acylalkyldio-1-O-phosphate moiety. The fatty acids of the phosphoglycolipids are mainly iso-C(15:0), -C(16:0), and -C(17:0) and anteiso-C(15:0) and -C(17:0). The ratios of PGL2 (2) to PGL1 (1) are significantly altered when grown at different temperatures for three strains, T. thermophilus NTU-077, M. ruber NTU-124, and M. taiwanensis NTU-220, but not for T. oshimai NTU-063. Accordingly, the ratios of iso- to anteiso-branched fatty acids increase when grown at the higher temperature.

[Characterization of lipopolysaccharides from Ralstonia solanacearum]. / Kharakteristika lipopolisakharidov Ralstonia solanacearum.

Lipopolysaccharides (LPSs) from four strains of Ralstonia solanacearum belonging to biovar I (ICMP 6524, 8115, 5712, and 8169) were isolated and investigated. The structural components of the LPS molecule, such as lipid A, the core oligosaccharide, and O-specific polysaccharide (O-PS), were obtained after mild acid hydrolysis of the LPS preparations. In lipid A from all the LPS samples studied, 3-hydroxyhexadecanoic, 2-hydroxyhexadecanoic, tetradecanoic, and hexadecanoic fatty acids prevailed. The dominant monosaccharides of the core oligosaccharides of all of the strains studied were rhamnose, glucose, glucosamine, 2-keto-3-deoxyoctulosonic acid, and heptose. However, individual strains varied in the content of galactose, ribose, xylose, and arabinose. Three types of the O-PS structure were established, which differed in their configuration (alpha or beta), as well as in the type of the bond between glucosamine and rhamnose residues (1-->2 or 1-->3).

Aequorivita gen. nov., a member of the family Flavobacteriaceae isolated from terrestrial and marine Antarctic habitats.

Several strains isolated from Antarctic winter sea water, sea-ice algal assemblages and quartz stone subliths were found to belong to a novel 16S rDNA sequence cluster within the family Flavobacteriaceae (Cytophaga-Flavobacterium-Bacteroides division). The strains were gram-negative, non-motile, psychrotolerant, strictly aerobic, chemoheterotrophic rod-shaped cells that contained orange or yellow carotenoid pigments and required yeast extract when grown in defined mineral-salts media. The requirement for sodium ions varied between strains. Results of DNA-DNA hybridization analysis were used to divide the strains into four distinct genospecies, which were differentiated by physiological and nutritional characteristics. The DNA G+C content of the strains was 33-39 mol%. The fatty acid profiles of representative strains were very similar, with major constituents including i15:1omega10c, a15:1omega10c, i15:0, a15:0, i16:1omega6c, i17:1omega5c and 3-OH i16:0. The novel genus Aequorivita gen. nov., which has widespread distribution in the Antarctic region, is proposed. The genus comprises four species: the type species Aequorivita antarctica sp. nov. (type strain SW49T = ACAM 640T = DSM 14231T), Aequorivita lipolytica sp. nov. (type strain Y10-2T = ACAM 641T = DSM 14236T), Aequorivita crocea sp. nov. (type strain Y12-2T = ACAM 642T = DSM 14239T) and Aequorivita sublithincola sp. nov. (type strain 9-3T= ACAM 643T = DSM 14238T).

Why are rod-shaped bacteria rod shaped?

Generally speaking, bacteria grow and divide indefinitely, and as long as the growth conditions are maintained they retain constant dimensions and shapes with little variation. How they do this is a question that I have been considering for three decades. Here, I discuss two hypothetical mechanisms, one for Gram-positive rods and the other for Gram-negative rods. These mechanisms are consistent with what is known, but make some unproven assumptions.

[The study of bacterial glycopolymers using laser spectroscopy]. / Issledovanie bakterial'nykh glikopolimerov metodom lazernoi spektroskopii.

A possibility has been demonstrated to use laser spectroscopy of bacterial glycopolymers by means of measurement of their water solutions fluorescence. Comparative investigations of native lipopolysaccharide (LPS) Ralstonia solanacearum and its structure components permits a supposition to be made that the LPS total spectrum is a result of superposition of the spectrum of O-specific polysaccharide and core oligosaccharide as well as core oligosaccharide and lipid A. The LPS spectrum maximum shift is determined by core oligosaccharide and lipid A luminescence contribution. A decrease as well as complete loss of serological activity as a result of 30 and 60 min UV irradiation of LPS has been established. It has been shown that LPS Rhizobium leguminosarum bv. viciae quenches luminescence of host-plant (pea) lectin depending on the extent of their affinity. Luminescence spectrum of glucan Sinorhizobium meliloti CXM1-188 and two its LPS-mutants differ between themselves both in luminescence intensity and in presence and expression degree of the site 2 with maximum 2.8 eV.

Classification of three airborne bacteria and proposal of Hymenobacter aerophilus sp. nov.

Three aerobic, gram-negative, rod-shaped, non-spore-forming, red-pigmented, airborne bacteria (I/26-Cor1T, I/32A-Cor1 and I/74-Cor2) collected in the Museo Correr (Venice, Italy) were investigated to determine their taxonomic status by analysing their biochemical, physiological and chemotaxonomic features and the G+C content of genomic DNA and by comparing their genomic fingerprints. Additionally, the almost complete 16S rRNA gene sequence of strain I/26-Cor1T was analysed. The three strains were nearly identical in their morphological, physiological, biochemical and chemotaxonomic properties. The strains contained a menaquinone system with the predominant menaquinone MK-7 and a fatty acid profile with C15:0 anteiso, C15:0 iso and C16:1 predominant. Phosphatidylethanolamine and several unidentified lipids were detected in the polar lipid profiles. The polyamine pattern consisted of sym-homospermidine as the major compound. meso-Diaminopimelic acid was found as the characteristic cell-wall diamino acid. The DNA base composition of the three strains ranged from 60 to 63 mol% G+C. Phylogenetically, strain I/26-Cor1T was most closely related to Hymenobacter actinosclerus (95.8% 16S rRNA gene sequence similarity). Physiological and genomic characteristics indicated that the two strains I/26-Cor1T and I/32A-Cor1 are representatives of the same species. The phylogenetic distance to any validly described taxon as indicated by 16S rRNA gene sequence similarities demonstrates that I/26-Cor1T and I/32A-Cor1 represent a novel species, for which the name Hymenobacter aerophilus sp. nov. is proposed, with the type strain I/26-Cor1T (= DSM 13606T = LMG 19657T). I/32A-Cor1 (= DSM 13607 = LMG 19658) is another strain of the species Hymenobacter aerophilus. Since the taxonomic status of strain I/74-Cor2 within the genus Hymenobacter was not determined unambiguously, it is designated Hymenobacter sp. I/74-Cor2 (= DSM 13611 = LMG 19659).

In vivo detection of the cyclic osmoregulated periplasmic glucan of Ralstonia solanacearum by high-resolution magic angle spinning NMR.

We investigate the mobility of the osmoregulated periplasmic glucans of Ralstonia solanacearum in the bacterial periplasm through the use of high-resolution (HR) NMR spectroscopy under static and magic angle spinning (MAS) conditions. Because the nature of periplasm is far from an isotropic aqueous solution, the molecules could be freely diffusing or rather associated to a periplasmic protein, a membrane protein, a lipid, or the peptidoglycan. HR MAS NMR spectroscopy leads to more reproducible results and allows the in vivo detection and characterization of the complex molecule.

Extremely thermostable elongation factor G from Aquifex aeolicus: cloning, expression, purification, and characterization in a heterologous translation system.

The fus gene of the translation factor G (EF-G) from the hyperthermophilic bacterium Aquifex aeolicus was cloned under control of a phage promoter and overexpressed in Escherichia coli with the T7 RNA polymerase system. A heat denaturation step at 95 degrees C was used to purify the protein from the cell extract. This approach simplified the chromatographic procedures and decreased the protein loss since most of Escherichia coli proteins were denatured and precipitated. Ten milligrams of the highly purified protein was isolated from 4 liters of induced culture. The overproduced EF-G was active in ribosome-dependent GTP hydrolysis and a poly(U)-directed polyphenylalanine translation system with E. coli 70S ribosomes. The method presented here might facilitate functional and structural studies of important components of the protein biosynthesis system.

Characterization and role of tbuX in utilization of toluene by Ralstonia pickettii PKO1.

The tbu regulon of Ralstonia pickettii PKO1 encodes enzymes involved in the catabolism of toluene, benzene, and related alkylaromatic hydrocarbons. The first operon in this regulon contains genes that encode the tbu pathway's initial catabolic enzyme, toluene-3-monooxygenase, as well as TbuT, the NtrC-like transcriptional activator for the entire regulon. It has been previously shown that the organization of tbuT, which is located immediately downstream of tbuA1UBVA2C, and the associated promoter (PtbuA1) is unique in that it results in a cascade type of up-regulation of tbuT in response to a variety of effector compounds. In our efforts to further characterize this unusual mode of gene regulation, we discovered another open reading frame, encoded on the strand opposite that of tbuT, 63 bp downstream of the tbuT stop codon. The 1,374-bp open reading frame, encoding a 458-amino-acid peptide, was designated tbuX. The predicted amino acid sequence of TbuX exhibited significant similarity to several putative outer membrane proteins from aromatic hydrocarbon-degrading bacteria, as well as to FadL, an outer membrane protein needed for uptake of long-chain fatty acids in Escherichia coli. Based on sequence analysis, transcriptional and expression studies, and deletion analysis, TbuX seems to play an important role in the catabolism of toluene in R. pickettii PKO1. In addition, the expression of tbuX appears to be regulated in a manner such that low levels of TbuX are always present within the cell, whereas upon toluene exposure these levels dramatically increase, even more than those of toluene-3-monooxygenase. This expression pattern may relate to the possible role of TbuX as a facilitator of toluene entry into the cell.

Characterization of a novel lipid A containing D-galacturonic acid that replaces phosphate residues. The structure of the lipid a of the lipopolysaccharide from the hyperthermophilic bacterium Aquifex pyrophilus.

According to the 16 S rRNA phylogenetic tree, the hyperthermophilic bacterium Aquifex pyrophilus represents the deepest and shortest branching species of the kingdom Bacteria. We show for the first time that an organism, which is phylogenetically ancient on the basis of its 16 S rRNA and that exists at extreme conditions, may contain lipopolysaccharide (LPS). The LPS was extracted from dried bacteria using a modified phenol/water method. SDS-polyacrylamide gel electrophoresis and silver stain displayed a ladder-like pattern, which is typical for smooth-form LPS (possessing an O-specific polysaccharide). The molecular masses of the LPS populations were determined by matrix-assisted laser-desorption ionization mass spectrometry. Lipid A was precipitated after mild acid hydrolysis of LPS. Its complete structure was determined by chemical analyses, combined gas-liquid chromatography-mass spectrometry, matrix-assisted laser-desorption ionization mass spectrometry, and one- and two-dimensional NMR spectroscopy. The lipid A consists of a beta-(1-->6)-linked 2,3-diamino-2,3-dideoxy-D-glucopyranose (DAG) disaccharide carrying two residues each of (R)-3-hydroxytetradecanoic acid and (R)-3-hydroxyhexadecanoic acid in amide linkage and one residue of octadecanoic acid in ester linkage. Each DAG moiety carries one residue of each 3-hydroxytetradecanoic and 3-hydroxyhexadecanoic acid. In the nonreducing DAG, the octadecanoic acid is attached to the 3-hydroxy group of 3-hydroxytetradecanoic acid. Each DAG is substituted by one D-galacturonic acid residue, which is linked to O-1 of the reducing and to O-4 of the nonreducing end. This structure represents a novel type of lipid A.

Septic arthritis caused by a gram-negative bacterium representing a new species related to the Bordetella-Alcaligenes complex.

A knee-joint exudate culture yielded on two occasions a gram-negative bacterium. Regular methods for speciation did not provide an identification. The infection was successfully treated with ciprofloxacin. The unknown isolate, CCUG 36768, was subjected to further investigation, including 16S rDNA sequencing, protein profiling, cellular fatty acid analysis, and various biochemical tests, in order to produce a species identification. The 1469 bp-long 16S rDNA sequence did not reveal identity with any known species sequence. CCUG 36768 clustered in a group of species, including Alcaligenes defragrans, Denitrobacter permanens, Taylorella equigenitalis, Alcaligenes faecalis, and four strains of Alcaligenes species without a specific species name. Bordetella species also showed a high degree of similarity with CCUG 36768. Protein profiling, cellular fatty acid analysis and computer-assisted analysis of biochemical profiles indicated similarity with Bordetella-Alcaligenes species, often close to B. holmesii and B. avium. API 20 NE indicated the profile of Moraxella species of poor identity. It is concluded that CCUG 36768 represents a new bacterial species of pathogenic potential in humans. It is related to the Bordetella-Alcaligenes group. Powerful new methods for speciation are available and it is recommended that unknown isolates from normally sterile sites be submitted for further analysis. Several isolates are required for the definition of new species.

Structures of a histone deacetylase homologue bound to the TSA and SAHA inhibitors.

Histone deacetylases (HDACs) mediate changes in nucleosome conformation and are important in the regulation of gene expression. HDACs are involved in cell-cycle progression and differentiation, and their deregulation is associated with several cancers. HDAC inhibitors, such as trichostatin A (TSA) and suberoylanilide hydroxamic acid (SAHA), have anti-tumour effects, as they can inhibit cell growth, induce terminal differentiation and prevent the formation of tumours in mice models, and they are effective in the treatment of promyelocytic leukemia. Here we describe the structure of the histone deacetylase catalytic core, as revealed by the crystal structure of a homologue from the hyperthermophilic bacterium Aquifex aeolicus, that shares 35.2% identity with human HDAC1 over 375 residues, deacetylates histones in vitro and is inhibited by TSA and SAHA. The deacetylase, deacetylase-TSA and deacetylase-SAHA structures reveal an active site consisting of a tubular pocket, a zinc-binding site and two Asp-His charge-relay systems, and establish the mechanism of HDAC inhibition. The residues that make up the active site and contact the inhibitors are conserved across the HDAC family. These structures also suggest a mechanism for the deacetylation reaction and provide a framework for the further development of HDAC inhibitors as antitumour agents.

A [2Fe-2S] protein from the hyperthermophilic bacterium Aquifex aeolicus.

Overexpression in Escherichia coli of the fdx4 gene from Aquifex aeolicus has allowed isolation and characterization of the first hyperthermophilic [2Fe-2S](Scys)(4) protein, a homodimer of M = 2 x 12.4 kDa with one [2Fe-2S] cluster per subunit. This protein is undamaged by heating to 100 degrees C for at least three hours. The primary structure, in particular the characteristic distribution of the four cysteine ligands of the metal site, and the spectroscopic properties of the A. aeolicus protein relate it to well characterized [2Fe-2S] proteins from Clostridium pasteurianum and Azotobacter vinelandii. These proteins are also homologous to subunits or domains of hydrogenases and NADH-ubiquinone oxidoreductase (Complex I) of respiratory chains. The A. aeolicus [2Fe-2S] protein is thus representative of a presumably novel protein fold involved in a variety of functions in very diverse cellular backgrounds.

An assessment of protein profiles from the marine oligotrophic ultramicrobacterium, Sphingomonas sp. strain RB2256.

The protein expression profile of a novel marine oligotrophic ultramicrobacterium, Sphingomonas sp. strain RB2256, was investigated by two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). Analytical reference maps were generated from mid-log phase batches and steady-state chemostat cultures with pH 4-8 immobilised pH gradients (IPGs) followed by sodium dodecyl sulphate-polyacrylamide gel electrophoresis. The resolved proteins were detected by two different methods: radioactive labeling and silver staining. Protein profiles generated from analytical 2-D PAGE gels were compared and differential analysis was performed using Melanie II software. Both methods (radioactive labeling and silver staining) resulted in reproducible, high resolution gels (up to 1600 protein spots). This approach is proving to be a powerful tool for investigating the molecular basis of the unique physiology of this model oligotrophic microorganism.

Reclassification of Pseudomonas echinoides Heumann 1962, 343AL, in the genus Sphingomonas as Sphingomonas echinoides comb. nov.

[Pseudomonas] echinoides DSM 1805T (= ATTC 14820T, DSM 50409T, ICBP 2835T, NCIB 9420T) has been reinvestigated to clarify its taxonomic position. 16S rDNA sequence comparisons demonstrated that this species clusters phylogenetically with species of the genus Sphingomonas. Investigation of fatty acid patterns, polar lipid profiles, polyamine patterns and quinone systems supported this delineation. Substrate utilization profiles and biochemical characteristics displayed no distinct overall similarity to any validly described species of the genus Sphingomonas. Therefore, the reclassification of [Pseudomonas] echinoides as Sphingomonas echinoides comb. nov. is proposed, based upon the estimated phylogenetic position derived from 16S rRNA gene sequence data, chemotaxonomic data and previously published genomic DNA G+C content data.