Bacterial Endophytes from Vitis vinifera L. - Metabolomics Characterization of Plant-Endophyte Crosstalk.

Bacterial endophytes are known to protect Vitis vinifera L. against various harmful effects of the environment and support its growth. However, for the most part, biochemical responses of such co-existence have not yet been fully elucidated. In this work, we aimed to characterize the activities of endophytic consortia in a plant-endophyte extract by measuring five indicators of colonization (overall endophyte metabolic activity, microbial ACC deaminase activity, ability to solubilize phosphorus, ability to convert atmospheric nitrogen to ammonia ions, and ability to produce growth promoting indole acetic acid), and find relationships between these activities and metabolome. The V. vinifera canes for the metabolomics fingerprinting were extracted successively with water and methanol, and analysed by ultra-high performance liquid chromatography coupled with high resolution mass spectrometry. For data processing, the MS-DIAL - MS-CleanR - MS-FINDER software platform was used, and the data matrix was processed by PCA and PLS-DA multivariate statistical methods. The metabolites that were upregulated with the heavy endophyte colonization were mainly chlorins, phenolics, flavonoid and terpenoid glycosides, tannins, dihydropyranones, sesquiterpene lactones, and long-chain unsaturated fatty acids.

Classification of a Violacein-Producing Psychrophilic Group of Isolates Associated with Freshwater in Antarctica and Description of Rugamonas violacea sp. nov.

A group of 11 bacterial strains was isolated from streams and lakes located in a deglaciated northern part of James Ross Island, Antarctica. They were rod-shaped, Gram-stain-negative, motile, and catalase-positive and produced blue-violet-pigmented colonies on R2A agar. A polyphasic taxonomic approach based on 16S rRNA gene sequencing, whole-genome sequencing, automated ribotyping, repetitive element sequence-based PCR (rep-PCR), MALDI-TOF MS, fatty acid profile, chemotaxonomy analyses, and extensive biotyping was applied in order to clarify the taxonomic position of these isolates. Phylogenetic analysis based on the 16S rRNA gene indicated that all the isolates constituted a coherent group belonging to the genus Rugamonas. The closest relatives to the representative isolate P5900T were Rugamonas rubra CCM 3730T, Rugamonas rivuli FT103WT, and Rugamonas aquatica FT29WT, exhibiting 99.2%, 99.1%, and 98.6% 16S rRNA pairwise similarity, respectively. The average nucleotide identity and digital DNA-DNA hybridization values calculated from the whole-genome sequencing data clearly proved that P5900T represents a distinct Rugamonas species. The G+C content of genomic DNAs was 66.1 mol%. The major components in fatty acid profiles were summed feature 3 (C16:1ω7c/C16:1ω6c), C 16:0, and C12:0. The cellular quinone content contained exclusively ubiquinone Q-8. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. The polyamine pattern was composed of putrescine, 2-hydroxputrescine, and spermidine. IMPORTANCE Our polyphasic approach provides a new understanding of the taxonomy of novel pigmented Rugamonas species isolated from freshwater samples in Antarctica. The isolates showed considerable extracellular bactericidal secretions. The antagonistic activity of studied isolates against selected pathogens was proved by this study and implied the importance of such compounds' production among aquatic bacteria. The psychrophilic and violacein-producing species Roseomonas violacea may play a role in the diverse consortium among pigmented bacteria in the Antarctic water environment. Based on all the obtained results, we propose a novel species for which the name Rugamonas violacea sp. nov. is suggested, with the type strain P5900T (CCM 8940T; LMG 32105T). Isolates of R. violacea were obtained from different aquatic localities, and they represent the autochthonous part of the water microbiome in Antarctica.

FERONIA restricts Pseudomonas in the rhizosphere microbiome via regulation of reactive oxygen species.

Maintaining microbiome structure is critical for the health of both plants and animals. By re-screening a collection of Arabidopsis mutants affecting root immunity and hormone crosstalk, we identified a FERONIA (FER) receptor kinase mutant (fer-8) with a rhizosphere microbiome enriched in Pseudomonas fluorescens without phylum-level dysbiosis. Using microbiome transplant experiments, we found that the fer-8 microbiome was beneficial. The effect of FER on rhizosphere pseudomonads was largely independent of its immune scaffold function, role in development and jasmonic acid autoimmunity. We found that the fer-8 mutant has reduced basal levels of reactive oxygen species (ROS) in roots and that mutants deficient in NADPH oxidase showed elevated rhizosphere pseudomonads. The addition of RALF23 peptides, a FER ligand, was sufficient to enrich P. fluorescens. This work shows that FER-mediated ROS production regulates levels of beneficial pseudomonads in the rhizosphere microbiome.

An overview of siderophore biosynthesis among fluorescent Pseudomonads and new insights into their complex cellular organization.

Siderophores are iron-chelating molecules produced by bacteria to access iron, a key nutrient. These compounds have highly diverse chemical structures, with various chelating groups. They are released by bacteria into their environment to scavenge iron and bring it back into the cells. The biosynthesis of siderophores requires complex enzymatic processes and expression of the enzymes involved is very finely regulated by iron availability and diverse transcriptional regulators. Recent data have also highlighted the organization of the enzymes involved in siderophore biosynthesis into siderosomes, multi-enzymatic complexes involved in siderophore synthesis. An understanding of siderophore biosynthesis is of great importance, as these compounds have many potential biotechnological applications because of their metal-chelating properties and their key role in bacterial growth and virulence. This review focuses on the biosynthesis of siderophores produced by fluorescent Pseudomonads, bacteria capable of colonizing a large variety of ecological niches. They are characterized by the production of chromopeptide siderophores, called pyoverdines, which give the typical green colour characteristic of fluorescent pseudomonad cultures. Secondary siderophores are also produced by these strains and can have highly diverse structures (such as pyochelins, pseudomonine, yersiniabactin, corrugatin, achromobactin and quinolobactin).

Structure, properties, and biological functions of nonribosomal lipopeptides from pseudomonads.

Bacteria of the genus Pseudomonas are ubiquitous in nature. Pseudomonads display a fascinating metabolic diversity, which correlates with their ability to colonize an extremely wide range of ecological niches. As a result, these bacteria are a prolific source of natural products. Biosynthesis of the latter is often orchestrated by arrays of chemical signals arising from intraspecies communication or interspecies relationships with bacteria, fungi, amoebae, plants, and insects. Especially nonribosomal lipopeptides, which have diverse biological activities, play important roles in the lifestyle of pseudomonads. In this review, we will focus on the molecular structures, properties, biosynthetic pathways, and biological functions of pseudomonal lipopeptides. This review is not only addressed to bio/chemists rather it serves as a comprehensive guide for all researchers (micro/biologists, ecologists, and environmental scientists) working in this multidisciplinary field.

Pseudomonad reverse carbon catabolite repression, interspecies metabolite exchange, and consortial division of labor.

Microorganisms acquire energy and nutrients from dynamic environments, where substrates vary in both type and abundance. The regulatory system responsible for prioritizing preferred substrates is known as carbon catabolite repression (CCR). Two broad classes of CCR have been documented in the literature. The best described CCR strategy, referred to here as classic CCR (cCCR), has been experimentally and theoretically studied using model organisms such as Escherichia coli. cCCR phenotypes are often used to generalize universal strategies for fitness, sometimes incorrectly. For instance, extremely competitive microorganisms, such as Pseudomonads, which arguably have broader global distributions than E. coli, have achieved their success using metabolic strategies that are nearly opposite of cCCR. These organisms utilize a CCR strategy termed 'reverse CCR' (rCCR), because the order of preferred substrates is nearly reverse that of cCCR. rCCR phenotypes prefer organic acids over glucose, may or may not select preferred substrates to optimize growth rates, and do not allocate intracellular resources in a manner that produces an overflow metabolism. cCCR and rCCR have traditionally been interpreted from the perspective of monocultures, even though most microorganisms live in consortia. Here, we review the basic tenets of the two CCR strategies and consider these phenotypes from the perspective of resource acquisition in consortia, a scenario that surely influenced the evolution of cCCR and rCCR. For instance, cCCR and rCCR metabolism are near mirror images of each other; when considered from a consortium basis, the complementary properties of the two strategies can mitigate direct competition for energy and nutrients and instead establish cooperative division of labor.

Hopanoids, like sterols, modulate dynamics, compaction, phase segregation and permeability of membranes.

In recent years, hopanoids, a group of pentacyclic compounds found in bacterial membranes, are in the spotlight since it was proposed that they induce order in lipid membranes in a similar way cholesterol do in eukaryotes, despite their structural differences. We studied here whether diplopterol (an abundant hopanoid) promoted similar effects on model membranes as sterols do. We analyzed the compaction, dynamics, phase segregation, permeability and compressibility of model membranes containing diplopterol, and compared with those containing sterols from animals, plants and fungi. We also tested the effect that the incubation with diplopterol had on hopanoid-lacking bacteria. Our results show that diplopterol induces phase segregation, increases lipid compaction, and decreases permeability on phospholipid membranes, while retaining membrane fluidity and compressibility. Furthermore, the exposition to this hopanoid decreases the permeability of the opportunistic pathogen Pseudomonas aeruginosa and increases the resistance to antibiotics. All effects promoted by diplopterol were similar to those generated by the sterols. Our observations add information on the functional significance of hopanoids as molecules that play an important role in membrane organization and dynamics in model membranes and in a bacterial system.

New insight into poly (3-hydroxybutyrate) production by Azomonas macrocytogenes isolate KC685000: large scale production, kinetic modeling, recovery and characterization.

About 24 h incubation of Azomonas (A.) macrocytogenes isolate KC685000 in 14L fermenter produced 22% poly (3-hydroxybutyrate) (PHB) per cell dry weight (CDW) biopolymer using 1 vvm aeration, 10% inoculum size, and initial pH of 7.2. To control the fermentation process, Logistic and Leudeking-Piret models were used to describe the cell growth and PHB production, respectively. These two models were in good agreement with the experimental data confirming the growth associated nature of PHB production. The best method for recovery of PHB was chemical digestion using sodium hypochlorite alone. The characterization of the produced polymer was carried out using FT-IR, 1HNMR spectroscopy, gel permeation chromatography and transmission electron microscope. The analysis of the nucleotide sequences of PHA synthase enzyme revealed class III identity. The putative tertiary structure of PHA synthase enzyme was analyzed using Modular Approach to Structural class prediction software, Tied Mixture Hidden Markov Model server, and Swiss model software. It was deduced that PHA synthases' structural class was multidomain protein (α/ß) containing a conserved cysteine residue and lipase box as characteristic features of α/ß hydrolase super family. Taken together, all the results of molecular characterization and transmission electron microscope images supported that the PHB formation was attained by the micelle model. To the best of our knowledge, this is the first report on production of growth associated PHB polymer using A. macrocytogenes isolate KC685000, and its class III PHA synthase.

Comparative evaluation of spoilage-related bacterial diversity and metabolite profiles in chilled beef stored under air and vacuum packaging.

Microbial spoilage is a complex event to which different bacterial populations and metabolites can contribute depending on the storage conditions. This study explored the evolution of spoilage and related volatile organic compounds (VOCs) in chilled beef under air and vacuum packaging (VP). The results suggested that different storage conditions affected changes in bacterial communities and metabolites in beef and consequently affected the odor properties of the stored beef, thereby leading to spoilage. Bacterial species belonging to Pseudomonadaceae (Pseudomonas spp.) and lactic acid bacteria (Lactobacillus sp.) dominated the bacterial communities in beef stored under air and VP, respectively, with several VOCs associated with off-odors of the stored beef and most likely produced by both bacteria. Our results suggested several microbial VOCs that could be used as potential spoilage indicators, including acetic acid, butanoic acid, and 2-butanone in VP-stored beef and 3-methylbutan-1-ol, ethyl acetate, acetoin, 2-butanone, and diacetyl in air-stored beef. These findings might provide valuable information regarding the quality monitoring of beef during storage.

Enhanced drought tolerance in seedlings of Neotropical tree species inoculated with plant growth-promoting bacteria.

The inoculation of tree species with plant growth-promoting bacteria (PGPB) has emerged as an important strategy for the acclimation of seedlings by improving plant tolerance to biotic and abiotic stresses. This study aimed to evaluate the effects of inoculation with bacterial species (Azospirillum brasilense - Ab-V5, Bacillus sp., Azomonas sp. and Azorhizophillus sp.) on the growth and physiology of the Neotropical tree species Trema micrantha and Cariniana estrellensis under drought conditions. When associated with Ab-V5 and Azomonas sp., T. micrantha showed increased protein in the leaves, starch in the leaves and roots, photosynthesis, instantaneous carboxylation efficiency and root and shoot dry mass. Moreover, there were reductions in hydrogen peroxide, lipid peroxidation, water potential and proline. In C. estrellensis associated with Ab-V5, higher values of photosynthesis and instantaneous carboxylation efficiency were observed, in addition to higher starch content in the leaves and roots and higher protein content in the leaves; lower hydrogen peroxide and lipid peroxidation contents were also observed. The associations of T. micrantha with Ab-V5 and Azomonas sp. and C. estrellensis with Ab-V5 favored the activation of metabolic processes under drought, leading to greater drought tolerance. This work demonstrates the effects of compatible associations of Neotropical tree and PGPB species and suggests that the identification of compatible PGPB strains can result in tree seedlings with increased tolerance to abiotic stresses, such as drought.

Analysis of bacterial FAMEs using gas chromatography - vacuum ultraviolet spectroscopy for the identification and discrimination of bacteria.

The identification of microorganisms is very important in different fields and alternative methods are necessary for a rapid and simple identification. The use of fatty acids for bacterial identification is gaining attention as phenotypic characteristics are reflective of the genotype and are more easily analyzed. In this work, gas chromatography-vacuum ultraviolet spectroscopy (GC-VUV) was used to determine bacteria fatty acid methyl esters (FAMEs), to identify and discriminate different environmental bacteria based on their fatty acid profile. Microorganisms were grown in agar and their fatty acids extracted, saponified, and esterified before analysis. Unique FAME profiles were obtained for each microorganism mainly composed of branched, cyclopropane, hydroxy, saturated, and unsaturated fatty acid methyl esters. S. maltophilia showed a higher diversity of fatty acids while Bacillus species showed higher complexity in terms of branched-chain FAMEs, with several iso and anteiso forms. 12 different bacteria genera and 15 species were successfully differentiated based on their fatty acid profiles after performing PCA and cluster analysis. Some difficult to differentiate species, such as Bacillus sp., which are genetically very similar, were differentiated with the developed method.

Effects of organic loading rate on hydrogen and volatile fatty acid production and microbial community during acidogenic hydrogenesis in a continuous stirred tank reactor using molasses wastewater.

AIMS: Microbial community associated with hydrogen production and volatile fatty acids (VFAs) accumulation was characterized in acidogenic hydrogenesis using molasses wastewater as a feedstock. METHODS AND RESULTS: Hydrogen and VFAs production were measured under an organic loading rate (OLR) from 19 to 35 g-COD l-1  day-1 . The active microbial community was analysed using RNA-based massively parallel sequencing technique, and their correlation patterns were analysed using networking analysis. The continuous stirred tank reactor achieved stable hydrogen production at different OLR conditions, and the maximum hydrogen production rate (HPR) was 1·02 L-H2  l-1  day-1 at 31·0 g-COD l-1  day-1 . Butyrate (50%) and acetate (38%) positively increased with increase in OLR. Total VFA production stayed around 7135 mg l-1 during the operation period. Although Clostridiales and Lactobacillales were relatively abundant, the HPR was positively associated with Pseudomonadaceae and Micrococcineae. Total VFA and acetate, butyrate and propionate concentrations were positively correlated with lactic acid bacteria (LAB) such as Bacillales, Sporolactobacillus and Lactobacillus. CONCLUSIONS: The close relationship between Pseudomonadaceae and Micrococcineae, and LAB play important roles for stable hydrogen and VFA production from molasses wastewater. SIGNIFICANCE AND IMPACT OF THE STUDY: Microbial information on hydrogen and VFA production can be useful to design and operate for acidogenic hydrogenesis using high strength molasses wastewater.

Metagenomic analysis of denitrifying wastewater enrichment cultures able to transform the explosive, 3-nitro-1,2,4-triazol-5-one (NTO).

Removal of 3-nitro-1,2,4-triazol-5-one (NTO) was investigated in conjunction with heterotrophic and autotrophic denitrifying growth conditions by a microbial consortium from a wastewater treatment plant. Microcosms were supplemented with molasses, methanol, or thiosulfate. Cultures were passaged twice by transferring 10 % of the culture volume to fresh media on days 11 and 21. Rates of NTO removal were 18.71 ± 0.65, 9.04 ± 2.61, and 4.34 ± 2.72 mg/L/day while rates of nitrate removal were 20.08 ± 1.13, 21.58 ± 1.20, and 24.84 ± 1.26 mg/L/day, respectively, for molasses, methanol, or thiosulfate. Metagenomic analysis showed that Proteobacteria and Firmicutes were the major phyla in the microbial communities. In molasses supplemented cultures, the community profile at the family level changed over time with Pseudomonadaceae the most abundant (67.4 %) at day 11, Clostridiaceae (65.7 %) at day 21, and Sporolactobacillaceae (35.4 %) and Clostridiaceae (41.0 %) at day 29. Pseudomonadaceae was the dominant family in methanol and thiosulfate supplemented cultures from day 21 to 29 with 76.6 and 81.6 % relative abundance, respectively.

Distribution and diversity of biosurfactant-producing bacteria in a wastewater treatment plant.

The distribution and diversity of culturable biosurfactant-producing bacteria were investigated in a wastewater treatment plant (WWTP) using the Shannon and Simpson's indices. Twenty wastewater samples were analysed, and from 667 isolates obtained, 32 were classified as biosurfactant producers as they reduced the surface tension of the culture medium (71.1 mN/m), with the lowest value of 32.1 mN/m observed. Certain isolates also formed stable emulsions with diesel, kerosene and mineral oils. The 16S ribosomal RNA (rRNA) analysis classified the biosurfactant producers into the Aeromonadaceae, Bacillaceae, Enterobacteriaceae, Gordoniaceae and the Pseudomonadaceae families. In addition, numerous isolates carried the surfactin 4'-phosphopantetheinyl transferase (sfp), rhamnosyltransferase subunit B (rhlB) and bacillomycin C (bamC) genes involved in the biosynthesis of surfactin, rhamnolipid and bacillomycin, respectively. While, biosurfactant-producing bacteria were found at all sampling points in the WWTP, the Simpson's diversity (1 - D) and the Shannon-Weaver (H) indices revealed an increase in bacterial diversity in the influent samples (0.8356 and 2.08), followed by the effluent (0.8 and 1.6094) and then the biological trickling filter (0.7901 and 1.6770) samples. Numerous biosurfactant-producing bacteria belonging to diverse genera are thus present throughout a WWTP.

Microbial degradation of N-methyl-2-pyrrolidone in surface water and bacteria responsible for the process.

Due to widespread utilization in many industrial spheres and agrochemicals, N-methyl-2-pyrrolidone (NMP) is a potential contaminant of different surface water ecosystems. Hence, investigation was made into its aerobic microbial degradability in samples of water from a river, wetland area and spring. The results showed that the compound was degradable in all water types, and that the fastest NMP removal occurred in 4 days in river water, while in the wetland and spring samples the process was relatively slow, requiring several months to complete. Key bacterial degraders were successfully isolated in all cases, and their identification proved that pseudomonads played a major role in NMP degradation in river water, while the genera Rhodococcus and Patulibacter fulfilled a similar task in the wetland sample. Regarding spring water, degrading members of the Mesorhizobium and Rhizobium genera were found.

Microbiome response to controlled shifts in ammonium and LCFA levels in co-digestion systems.

Anaerobic co-digestion using protein-rich and lipid-rich co-substrates is limited by the accumulation of ammonia and long chain fatty acids (LCFAs), which are important inhibitors of the anaerobic microorganisms. This work aimed to study the microbial community dynamics during gradual and abrupt increase in ammonium and LCFAs concentrations by applying several molecular techniques, as well as during gradual decrease. For this purpose, two anaerobic reactors co-digesting three agro-industrial wastes underwent abrupt and gradual changes of ammonium and LCFAs concentrations. Both variations provoked volatile fatty acids (VFAs) accumulation, mainly acetic acid up to 4.5gL(-1). High ammonium levels were correlated to an increase in Pseudomonadaceae, Carnobacteriaceae and Clostridiadaceae families and to a drop in Syntrophomonadaceae. However, high LCFA levels provoked an increase in the Anaerobaculaceae and Peptococcaceae families. Both perturbations resulted in greater variations in the archaeal domain, going from Methanosaeta dominance in steady state to hydrogenotrophic pathway during the disturbance periods. During the abrupt changes, Bacteria domain experienced a minimal change, which indicates the adaptation bacterial populations to high ammonium and LCFAs levels. Species belonging to Porphyromonadaceae and Tissierellaceae families linked to VFAs consumption rose their presence during the recovery period. This study identifies a subset of microbial communities linked to high ammonia and LCFA concentrations, useful for optimizing the high-rate co-digestion processes dealing with lipid and protein-rich co-substrates.

[Enrichment and Characterization of A Denitrifying Bacteria Consortium from Lihe River's Sediment].

A denitrifying bacteria consortium was enriched from LiHe River's sediment, the dynamics of total nitrogen (TN), nitrate (NO3- -N), nitrite (NO2- -N), ammonium (NH4+ -N) and COD at different enrichment cultivation stages were studied, and the total volume, the releasing rates and the composition of gas released during the denitrification process were analyzed. The full-length 16S rDNA clone library was constructed, enclosing the diversity of the denitrifying bacteria consortium. The results showed, in the enrichment phase 4, under the load of TN 330 mg x L(-1), the best nitrogen removal effect was obtained, which the TN and NO3- -N removal rates reached 90.9% and 100% within 9 hours, respectively. The accumulation amounts of NO2- -N and NH4+ -N were merely 3.39 mg x L(-1) and 16.64 mg x L(-1). And the COD removal rate was 85%. The process released 260 mL of the compound gas, in which the main ingredient was N2 associated with a small quantity of CH4 and CO2. The denitrifying bacteria consortium consisted of the family Pseudomonadaceae and the family Rhodocyclaceae, belonging to Proteobacteria phylum, in which the OUT abundances were 57.8% and 31.6%, respectively. The family Pseudomonadaceae was the predominant group.

A lithotrophic microbial fuel cell operated with pseudomonads-dominated iron-oxidizing bacteria enriched at the anode.

In this study, we attempted to enrich neutrophilic iron bacteria in a microbial fuel cell (MFC)-type reactor in order to develop a lithotrophic MFC system that can utilize ferrous iron as an inorganic electron donor and operate at neutral pHs. Electrical currents were steadily generated at an average level of 0.6 mA (or 0.024 mA cm(-2) of membrane area) in reactors initially inoculated with microbial sources and operated with 20 mM Fe(2+) as the sole electron donor and 10 ohm external resistance; whereas in an uninoculated reactor (the control), the average current level only reached 0.2 mA (or 0.008 mA cm(-2) of membrane area). In an inoculated MFC, the generation of electrical currents was correlated with increases in cell density of bacteria in the anode suspension and coupled with the oxidation of ferrous iron. Cultivation-based and denaturing gradient gel electrophoresis analyses both show the dominance of some Pseudomonas species in the anode communities of the MFCs. Fluorescent in-situ hybridization results revealed significant increases of neutrophilic iron-oxidizing bacteria in the anode community of an inoculated MFC. The results, altogether, prove the successful development of a lithotrophic MFC system with iron bacteria enriched at its anode and suggest a chemolithotrophic anode reaction involving some Pseudomonas species as key players in such a system. The system potentially offers unique applications, such as accelerated bioremediation or on-site biodetection of iron and/or manganese in water samples.

Whole genome sequencing and analysis of plant growth promoting bacteria isolated from the rhizosphere of plantation crops coconut, cocoa and arecanut.

Coconut, cocoa and arecanut are commercial plantation crops that play a vital role in the Indian economy while sustaining the livelihood of more than 10 million Indians. According to 2012 Food and Agricultural organization's report, India is the third largest producer of coconut and it dominates the production of arecanut worldwide. In this study, three Plant Growth Promoting Rhizobacteria (PGPR) from coconut (CPCRI-1), cocoa (CPCRI-2) and arecanut (CPCRI-3) characterized for the PGP activities have been sequenced. The draft genome sizes were 4.7 Mb (56% GC), 5.9 Mb (63.6% GC) and 5.1 Mb (54.8% GB) for CPCRI-1, CPCRI-2, CPCRI-3, respectively. These genomes encoded 4056 (CPCRI-1), 4637 (CPCRI-2) and 4286 (CPCRI-3) protein-coding genes. Phylogenetic analysis revealed that both CPCRI-1 and CPCRI-3 belonged to Enterobacteriaceae family, while, CPCRI-2 was a Pseudomonadaceae family member. Functional annotation of the genes predicted that all three bacteria encoded genes needed for mineral phosphate solubilization, siderophores, acetoin, butanediol, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, chitinase, phenazine, 4-hydroxybenzoate, trehalose and quorum sensing molecules supportive of the plant growth promoting traits observed in the course of their isolation and characterization. Additionally, in all the three CPCRI PGPRs, we identified genes involved in synthesis of hydrogen sulfide (H2S), which recently has been proposed to aid plant growth. The PGPRs also carried genes for central carbohydrate metabolism indicating that the bacteria can efficiently utilize the root exudates and other organic materials as energy source. Genes for production of peroxidases, catalases and superoxide dismutases that confer resistance to oxidative stresses in plants were identified. Besides these, genes for heat shock tolerance, cold shock tolerance and glycine-betaine production that enable bacteria to survive abiotic stress were also identified.

Rhizobacter gummiphilus sp. nov., a rubber-degrading bacterium isolated from the soil of a botanical garden in Japan.

A rubber-degrading bacterium, the strain NS21, that was isolated from a soil sample in a botanical garden in Japan (Imai et al., 2011) was examined by phenotypic, phylogenetic and chemotaxonomic approaches to determine its taxonomic position. The strain NS21 was motile, possessing a single polar flagellum and a facultatively anaerobic straight rod. Analysis of the 16S rRNA and gyrB gene sequences of NS21 revealed a close relationship to the genus Rhizobacter. The predominant quinone type was Q-8. The G+C content of the NS21 genomic DNA was 70.8 mol%. The major fatty acids were C16:0, C17:0 cyclo, C18:1ω7c and C16:1ω7c and/or iso-C15:0 2-OH. C12:0 2-OH was present. The DNA-DNA hybridization experiments indicated that the DNA relatedness values of the strain NS21 to R. dauci H6(T) and R. fulvus Gsoil 322(T) were lower than 24%. The phenotypic characteristics showed obvious dissimilarities when compared to closely related species. On the basis of these taxonomic properties, a novel species is proposed as Rhizobacter gummiphilus sp. nov., with the strain NS21(T) (NBRC 109400(T), BCC 58006(T)) as the type strain. The emended description of the genus Rhizobacter was also presented.