A two primers random amplified polymorphic DNA procedure to obtain polymerase chain reaction fingerprints of bacterial species

Stable, fluorescent markers for tracking synthetic communities and assembly dynamics

BACKGROUND

After two decades of extensive microbiome research, the current forefront of scientific exploration involves moving beyond description and classification to uncovering the intricate mechanisms underlying the coalescence of microbial communities. Deciphering microbiome assembly has been technically challenging due to their vast microbial diversity but establishing a synthetic community (SynCom) serves as a key strategy in unravelling this process. Achieving absolute quantification is crucial for establishing causality in assembly dynamics. However, existing approaches are primarily designed to differentiate a specific group of microorganisms within a particular SynCom.

RESULTS

To address this issue, we have developed the differential fluorescent marking (DFM) strategy, employing three distinguishable fluorescent proteins in single and double combinations. Building on the mini-Tn7 transposon, DFM capitalises on enhanced stability and broad applicability across diverse Proteobacteria species. The various DFM constructions are built using the pTn7-SCOUT plasmid family, enabling modular assembly, and facilitating the interchangeability of expression and antibiotic cassettes in a single reaction. DFM has no detrimental effects on fitness or community assembly dynamics, and through the application of flow cytometry, we successfully differentiated, quantified, and tracked a diverse six-member SynCom under various complex conditions like root rhizosphere showing a different colonisation assembly dynamic between pea and barley roots.

CONCLUSIONS

DFM represents a powerful resource that eliminates dependence on sequencing and/or culturing, thereby opening new avenues for studying microbiome assembly. Video Abstract.

Characterization of two new strains of Lactococcus lactis for their probiotic efficacy over commercial synbiotics consortia

Lactococcus spp. are industrially crucial lactic acid bacteria (LAB) used to manufacture lactic acid, pickled vegetables, buttermilk, cheese, and many kinds of delicious dairy foods and drinks. In addition to these, they are also being used as probiotics in specific formulations. However, their uses as probiotics are comparatively less than the other LAB genera. The present communication hypothesizes to validate the probiotic potentiality of two new Lactococcus lactis subsp. lactis strains for their future uses. These native food fermenting strains were characterized for in vitro acid tolerance, tolerance to simulated gastric and pancreatic juices, autoaggregation and co-aggregation, hydrophobicity, haemolytic activity, bile salt deconjugation, cholesterol removal, antimicrobial spectrum, and antibiotic sensitivity. The in vivo live bacterial feeding of these strains for 30 days was done in Swiss albino mice either singly or in combination with prebiotic inulin and evaluated for hypocholesterolemic activity, immune enhancement, and gut colonization efficiency and compared with the commercial probiotic consortia. The study revealed that the strains could survive in human gut bile concentration, gastric pH conditions at pH 2.0, 3.0, and 8.0 for 6 h, had a broad antibacterial spectrum, and cholesterol binding efficacy. The strains could survive with higher colony-forming units (CFU/mL) when amended with sodium caseinate. The strains had autoaggregation ranges from 15 to 25% over 24 h and had a significant co-aggregation with both lactic acid and Gram-positive and Gram-negative bacterial strains related to human illness. The strains also showed solvent and media-specific hydrophobicity against n-hexane and xylene. The live bacterial feeding either singly or in combination with prebiotic inulin resulted in a significant reduction of LDL (low-density lipoprotein), VLDL (very low-density lipoprotein) cholesterol and triglyceride (TG), and a significant increase in HDL (high-density lipoprotein) cholesterol level, and improved gut colonization and gut immunomodulation. The results prove that these non-haemolytic, non-toxic strains had significant health benefits than the commercial probiotics consortium with the recommended prebiotics mix. Thus, these new Lactococcus lactis subsp. lactis strains could be trialled as a new probiotic combination for human and animal feeds.

Genomic Diversity of Pigeon Pea (Cajanus cajan L. Millsp.) Endosymbionts in India and Selection of Potential Strains for Use as Agricultural Inoculants

Pigeon pea (Cajanus cajan L. Millsp. ) is a legume crop resilient to climate change due to its tolerance to drought. It is grown by millions of resource-poor farmers in semiarid and tropical subregions of Asia and Africa and is a major contributor to their nutritional food security. Pigeon pea is the sixth most important legume in the world, with India contributing more than 70% of the total production and harbouring a wide variety of cultivars. Nevertheless, the low yield of pigeon pea grown under dry land conditions and its yield instability need to be improved. This may be done by enhancing crop nodulation and, hence, biological nitrogen fixation (BNF) by supplying effective symbiotic rhizobia through the application of "elite" inoculants. Therefore, the main aim in this study was the isolation and genomic analysis of effective rhizobial strains potentially adapted to drought conditions. Accordingly, pigeon pea endosymbionts were isolated from different soil types in Southern, Central, and Northern India. After functional characterisation of the isolated strains in terms of their ability to nodulate and promote the growth of pigeon pea, 19 were selected for full genome sequencing, along with eight commercial inoculant strains obtained from the ICRISAT culture collection. The phylogenomic analysis [Average nucleotide identity MUMmer (ANIm)] revealed that the pigeon pea endosymbionts were members of the genera Bradyrhizobium and Ensifer. Based on nodC phylogeny and nod cluster synteny, Bradyrhizobium yuanmingense was revealed as the most common endosymbiont, harbouring nod genes similar to those of Bradyrhizobium cajani and Bradyrhizobium zhanjiangense. This symbiont type (e.g., strain BRP05 from Madhya Pradesh) also outperformed all other strains tested on pigeon pea, with the notable exception of an Ensifer alkalisoli strain from North India (NBAIM29). The results provide the basis for the development of pigeon pea inoculants to increase the yield of this legume through the use of effective nitrogen-fixing rhizobia, tailored for the different agroclimatic regions of India.

Biodegradation and Kinetic Analysis of Acetaminophen with Co-culture of Bacterial Strains Isolated from Sewage Wastewater

Acetaminophen (paracetamol, APAP) is one of the fastest growing pharmaceutical pollutants in the environment and has been classified under among the emerging organic pollutants (EOPs). The increasing concentration of it in our environment is not only harmful to the ecosystem, but also to the humans as well. In this study, the microscopy, biochemical test and 16S rRNA sequencing the characterization of APAP as the sole degrading stains viz. Staphylococcus sciuri strain DPP1 (MN744326), Bacillus subtilis strain DPP3 (MN744327), Bacillus paralicheniformis strain DKP1 (MN744324), Enterococcus faecium strain DKP2 (MN744325) and DDP2 (MT705211) were performed. Haldane's growth kinetic model was used to identify specific growth rate and observed for DPP1 (485 mg/L), DPP3 (593 mg/L), DKP1 (477 mg/L), DKP2 (702 mg/L) and DDP2 (685 mg/L). The maximum specific growth rate was reported for the stains viz. DPP1, DPP3, DKP1, DKP2, and DDP2, was in order of 0.076, 0.223, 0.259, 0.179, and 0.141, respectively. The Box-Behnken Design (BBD) was used to identify the effect of physical parameters on degradation using mathematical modeling. The analysis of variance (ANOVA) showed that the strains DPP1, DPP3, DKP1, DKP2, and DDP2 had significant F-value and regression coefficient (R²) value of 0.01%, 0.06%, 0.37%, and 0.18%, respectively. The co-culture of the five strains has utilized 1200 mg/L of APAP within 70 h while individual strains took 10 days. The intermediate metabolites like 4-aminophenol, benzamide, (R)-2-methylpentanoic acid, methylene-3-vinyl cyclohexane, and 1,5-hexadiene were identified by GC-MS. The degradation metabolic pathway was predicted by the intermediates by GC-MS, and PathPred based analysis.

Evaluation of random amplified polymorphic DNA and multiple-locus variable number tandem repeat analyses for Mycoplasma cynos

Mycoplasma spp. can cause diseases of the respiratory system as well as urogenital infections, infertility, and anemia. The members of this genus have a low G + C content compared to other bacteria. Because primers used in the random amplified polymorphic DNA (RAPD) technique are only 10 bp long and have high GC content, this method can be inadequate for genotyping Mycoplasma spp. isolates. The aim of this study was to develop and evaluate multiple-locus variable number tandem repeat analysis (MLVA) and two-primer RAPD (TP-RAPD) procedures for subtyping Mycoplasma cynos isolates. A total of 55 M. cynos isolates obtained from 162 bronchoalveolar lavage fluid samples from shelter and pet dogs were used in this study. Seventy-four tandem repeat regions were detected in the M. cynos genome, and two of these loci were determined to be suitable and used for development of the MLVA scheme. The results of variable number tandem repeat (VNTR) analysis and TP-RAPD-PCR were compared with RAPD-PCR. The discriminatory power of TP-RAPD-PCR (Hunter-Gaston diversity index [HGDI] = 0.84) was higher than those of RAPD-PCR (HGDI = 0.727), VNTR1 (HGDI = 0.8), and VNTR3 (HGDI = 0.757). We observed that the TP-RAPD-PCR and MLVA methods provide clearer data and are more successful in determining genetic diversity, in contrast to the RAPD-PCR method for this species.

Efficiency of pilot-scale horizontal subsurface flow constructed wetlands and microbial community composition operating under tropical conditions

This study assesses the microbial diversity of Thalia geniculate (L.) and Cyperus articulates (L.) in the rhizosphere in planted and unplanted systems with respect to removal efficiency in an experimental horizontal sub-surface constructed wetland pilot plant. The pilot-scale units consisted of six (6) cells of concrete of 0.94 × 0.6 × 0.4 m arranged in a parallel configuration. 29 L d^-1 were distributed to the cells by gravity. The hydraulic retention time was 3 days and influent and effluent measurements of COD and nutrients were monitored with standard methodology. Bacteria samples were isolated from the roots of plants and gravel in selective media and incubated at 37 °C. Isolates were biochemically characterized and genotyped with group-specific primers. Results showed that systems planted with T. geniculata removed greater proportions of COD (82%), NH₄⁺-N (83%) and PO₄²-P (83%) than C. articulatus (85, 74 and 72%, respectively) and unplanted wetland systems (80, 72 and 66%, respectively). Bacterial typing revealed several phyla were most abundant, α-Proteobacteria followed by β-Proteobacteria and there was a significant difference (p < 0.05) in CFU between planted and unplanted treatments. The bacterial community varied with respect to plant species or unplanted and demonstrated significant effects to contaminants removal efficiency.

Improvement of the Uranium Sequestration Ability of a Chlamydomonas sp. (ChlSP Strain) Isolated From Extreme Uranium Mine Tailings Through Selection for Potential Bioremediation Application

The extraction and processing of uranium (U) have polluted large areas worldwide, rendering anthropogenic extreme environments inhospitable to most species. Noticeably, these sites are of great interest for taxonomical and applied bioprospection of extremotolerant species successfully adapted to U tailings contamination. As an example, in this work we have studied a microalgae species that inhabits extreme U tailings ponds at the Saelices mining site (Salamanca, Spain), characterized as acidic (pH between 3 and 4), radioactive (around 4 μSv h⁻¹) and contaminated with metals, mainly U (from 25 to 48 mg L⁻¹) and zinc (from 17 to 87 mg L⁻¹). After isolation of the extremotolerant ChlSP strain, morphological characterization and internal transcribed spacer (ITS)-5.8S gene sequences placed it in the Chlamydomonadaceae, but BLAST analyses identity values, against the nucleotide datasets at the NCBI database, were very low (<92%). We subjected the ChlSP strain to an artificial selection protocol to increase the U uptake and investigated its response to selection. The ancestral strain ChlSP showed a U-uptake capacity of ≈4.30 mg U g⁻¹ of dry biomass (DB). However, the artificially selected strain ChlSG was able to take up a total of ≈6.34 mg U g⁻¹ DB, close to the theoretical maximum response (≈7.9 mg U g⁻¹ DB). The selected ChlSG strain showed two possible U-uptake mechanisms: the greatest proportion by biosorption onto cell walls (ca. 90%), and only a very small quantity, ~0.46 mg g⁻¹ DB, irreversibly bound by bioaccumulation. Additionally, the kinetics of the U-uptake process were characterized during a microalgae growth curve; ChlSG cells removed close to 4 mg L⁻¹ of U in 24 days. These findings open up promising prospects for sustainable management of U tailings waters based on newly evolved extremotolerants and outline the potential of artificial selection in the improvement of desired features in microalgae by experimental adaptation and selection.

Mesorhizobium bacterial strains isolated from the legume Lotus corniculatus are an alternative source for the production of polyhydroxyalkanoates (PHAs) to obtain bioplastics

Polyhydroxyalkanoic acids (PHAs) are natural polyesters that can be used to produce bioplastics which are biodegradable. Numerous microorganisms accumulate PHAs as energy reserves. Combinations of different PHAs monomers lead to the production of bioplastics with very different properties. In the present work, we show the capability of strains belonging to various phylogenetic lineages within the genus Mesorhizobium, isolated from Lotus corniculatus nodules, to produce different PHA monomers. Among our strains, we found the production of 3-hydroxybutyrate, 3-hydroxyvalerate, 3-hydroxydodecanoate, and 3-hydroxyhexadecanoate. Most of the PHA-positive strains were phylogenetically related to the species M. jarvisii. However, our findings suggest that the ability to produce different monomers forming PHAs is strain-dependent.

Culturable bacterial diversity from the chestnut (Castanea sativa Mill.) phyllosphere and antagonism against the fungi causing the chestnut blight and ink diseases

The phyllosphere supports a large and complex bacterial community that varies both across plant species and geographical locations. Phyllosphere bacteria can have important effects on plant health. The sweet chestnut (Castanea sativa Mill.) is an economically important tree species affected worldwide by the fungal pathogens Cryphonectria parasitica and Phytophthora cinnamomi. We examined the culturable phyllosphere bacterial community of the sweet chestnut at two nearby locations in Central Spain in order to know its geographical variability and to explore its potential as source of biological control agents against these two pathogenic fungi. The bacterial diversity at strain level was high but it varied significantly between locations; however, phylotype richness and diversity were more comparable. The isolates were affiliated with the phyla Actinobacteria, Firmicutes and Proteobacteria. Most of them were members of recognized bacterial species, with a notable proportion of representative of the genera Dietzia and Lonsdalea, but a small fraction of the strains revealed the existence of several potential novel species or even genera. Antagonism tests showed the occurrence in the chestnut phyllosphere of bacterial strains potentially useful as biological control agents against the two pathogenic fungi, some of which belong to species never before described as fungal antagonists. Chestnut phyllosphere, therefore, contains a great diversity of culturable bacteria and may represent an untapped source of potential biocontrol agents against the fungi causing blight and ink diseases of this tree species.

The Symbiotic Performance of Chickpea Rhizobia Can Be Improved by Additional Copies of the clpB Chaperone Gene

The ClpB chaperone is known to be involved in bacterial stress response. Moreover, recent studies suggest that this protein has also a role in the chickpea-rhizobia symbiosis. In order to improve both stress tolerance and symbiotic performance of a chickpea microsymbiont, the Mesorhizobium mediterraneum UPM-Ca36^T strain was genetically transformed with pPHU231 containing an extra-copy of the clpB gene. To investigate if the clpB-transformed strain displays an improved stress tolerance, bacterial growth was evaluated under heat and acid stress conditions. In addition, the effect of the extra-copies of the clpB gene in the symbiotic performance was evaluated using plant growth assays (hydroponic and pot trials). The clpB-transformed strain is more tolerant to heat shock than the strain transformed with pPHU231, supporting the involvement of ClpB in rhizobia heat shock tolerance. Both plant growth assays showed that ClpB has an important role in chickpea-rhizobia symbiosis. The nodulation kinetics analysis showed a higher rate of nodule appearance with the clpB-transformed strain. This strain also induced a greater number of nodules and, more notably, its symbiotic effectiveness increased ~60% at pH5 and 83% at pH7, compared to the wild-type strain. Furthermore, a higher frequency of root hair curling was also observed in plants inoculated with the clpB-transformed strain, compared to the wild-type strain. The superior root hair curling induction, nodulation ability and symbiotic effectiveness of the clpB-transformed strain may be explained by an increased expression of symbiosis genes. Indeed, higher transcript levels of the nodulation genes nodA and nodC (~3 folds) were detected in the clpB-transformed strain. The improvement of rhizobia by addition of extra-copies of the clpB gene may be a promising strategy to obtain strains with enhanced stress tolerance and symbiotic effectiveness, thus contributing to their success as crop inoculants, particularly under environmental stresses. This is the first report on the successful improvement of a rhizobium with a chaperone gene.

Role of Rhizobium endoglucanase CelC2 in cellulose biosynthesis and biofilm formation on plant roots and abiotic surfaces

Background

The synthesis of cellulose is among the most important but poorly understood biochemical processes, especially in bacteria, due to its complexity and high degree of regulation. In this study, we analyzed both the production of cellulose by all known members of the Rhizobiaceae and the diversity of Rhizobium celABC operon predicted to be involved in cellulose biosynthesis. We also investigated the involvement in cellulose production and biofilm formation of celC gene encoding an endoglucanase (CelC2) that is required for canonical symbiotic root hair infection by Rhizobium leguminosarum bv. trifolii.

Results

ANU843 celC mutants lacking (ANU843ΔC2) or overproducing cellulase (ANU843C2⁺) produced greatly increased or reduced amounts of external cellulose micro fibrils, respectively. Calcofluor-stained cellulose micro fibrils were considerably longer when formed by ANU843ΔC2 bacteria rather than by the wild-type strain, in correlation with a significant increase in their flocculation in batch culture. In contrast, neither calcofluor-stained extracellular micro fibrils nor flocculation was detectable in ANU843C2⁺ cells. To clarify the role of cellulose synthesis in Rhizobium cell aggregation and attachment, we analyzed the ability of these mutants to produce biofilms on different surfaces. Alteration of wild-type CelC2 levels resulted in a reduced ability of bacteria to form biofilms both in abiotic surfaces and in planta.

Conclusions

Our results support a key role of the CelC2 cellulase in cellulose biosynthesis by modulating the length of the cellulose fibrils that mediate firm adhesion among Rhizobium bacteria leading to biofilm formation. Rhizobium cellulose is an essential component of the biofilm polysaccharidic matrix architecture and either an excess or a defect of this “building material” seem to collapse the biofilm structure. These results position cellulose hydrolytic enzymes as excellent anti-biofilm candidates.

Successful culture techniques for Helicobacter species: verification of Helicobacter identity using 16S rRNA gene sequence analysis

This chapter describes protocols for the verification of putative Helicobacter species' identities using 16S rRNA gene sequence analysis.

Diversity and community structure of culturable arsenic-resistant bacteria across a soil arsenic gradient at an abandoned tungsten-tin mining area

We studied the bacterial diversity at a single location (the Terrubias mine; Salamanca province, Spain) with a gradient of soil As contamination to test if increasing levels of As would (1) change the preponderant groups of arsenic-resistant bacteria and (2) increase the tolerance thresholds to arsenite [As(III)] and arsenate [As(V)] of such bacteria. We studied the genetic and taxonomic diversity of culturable arsenic-resistant bacteria by PCR fingerprinting techniques and 16S rRNA gene sequencing. Then, the tolerance thresholds to As(III) and As(V) were determined for representative strains and mathematically analyzed to determine relationships between tolerances to As(III) and As(V), as well as these tolerances with the soil contamination level. The diversity of the bacterial community was, as expected, inversely related to the soil As content. The overall preponderant arsenic-resistant bacteria were Firmicutes (mainly Bacillus spp.) followed by γ-Proteobacteria (mainly Pseudomonas spp.), with increasing relative frequencies of the former as the soil arsenic concentration increased. Moreover, a strain of the species Rahnella aquatilis (γ-Proteobacteria class) exhibited strong endurance to arsenic, being described for the first time in literature such a phenotype within this bacterial species. Tolerances of the isolates to As(III) and As(V) were correlated but not with their origin (soil contamination level). Most of the strains (64%) showed relatively low tolerances to As(III) and As(V), but the second most numerous group of isolates (19%) showed increased tolerance to As(III) rather than to As(V), even though the As(V) anion is the prevalent arsenic species in soil solution at this location. To our knowledge, this is the first study to report a shift towards preponderance of Gram-positive bacteria (Firmicutes) related to high concentrations of soil arsenic. It was also shown that, under aerobic conditions, strains with relatively enhanced tolerance to As(III) predominated over the most As(V)-tolerant ones.

Novel associations between rhizobial populations and legume species within the genera Lathyrus and O xytropis grown in the temperate region of China

Fifty rhizobial isolates of Lathyrus and Oxytropis collected from northern regions of China were studied in their genotypic characterization based upon analyses of ARDRA, 16S-23S IGS PCR-RFLP, TP-RAPD, MLEE, sequences of 16S rDNA gene and housekeeping genes of atpD, recA and glnII. The results demonstrated that most of the Lathyrus rhizobia belonged to Rhizobium and most of the Oxytropis rhizobia belonged to Sinorhizobium. A novel group of Rhizobium sp. I and S. meliloti were identified as the main microsymbionts respectively associated with Lathyrus and Oxytropis species in the collection area, which were new associations between rhizobia and the mentioned hosts. This study also provides new evidence for biogeography of rhizobia.

dnaJ is a useful phylogenetic marker for alphaproteobacteria

In the past, bacterial phylogeny relied almost exclusively on 16S rRNA gene sequence analysis. More recently, multilocus sequence analysis has been used to infer organismal phylogenies. In this study, the dnaJ chaperone gene was investigated as a marker for phylogeny studies in alphaproteobacteria. Preliminary analysis of G+C contents and G+C3s contents (the G+C content of the synonymous third codon position) showed no clear evidence of horizontal transfer of this gene in proteobacteria. dnaJ-based phylogenies were then analysed at three taxonomic levels: the Proteobacteria, the Alphaproteobacteria and the genus Mesorhizobium. Dendrograms based on DnaJ and 16S rRNA gene sequences revealed the same topology described previously for the Proteobacteria. These results indicate that the DnaJ phylogenetic signal is able to reproduce the accepted relationships among the five classes of the Proteobacteria. At a lower taxonomic level, using 20 alphaproteobacteria, the 16S rRNA gene-based phylogeny is distinct from the one based on DnaJ sequence analysis. Although the same clusters are generated, only the topology of the DnaJ tree is consistent with broader phylogenies from recent studies based on concatenated alignments of multiple core genes. For example, the DnaJ tree shows the two clusters within the Rhizobiales as closely related, as expected, while the 16S rRNA gene-based phylogeny shows them as distantly related. In order to evaluate the phylogenetic performance of dnaJ at the genus level, a multilocus analysis based on five housekeeping genes (atpD, gapA, gyrB, recA and rplB) was performed for ten Mesorhizobium species. In contrast to the 16S rRNA gene, the DnaJ sequence analysis generated a tree similar to the multilocus dendrogram. For identification of chickpea mesorhizobium isolates, a dnaJ nucleotide sequence-based tree was used. Despite different topologies, 16S rRNA gene- and dnaJ-based trees led to the same species identification. This study suggests that the dnaJ gene is a good phylogenetic marker, particularly for the class Alphaproteobacteria, since its phylogeny is consistent with phylogenies based on multilocus approaches.

Cohnella phaseoli sp. nov., isolated from root nodules of Phaseolus coccineus in Spain, and emended description of the genus Cohnella

A bacterial strain designated GSPC1 T was isolated from root nodules of Phaseolus coccineus in Segovia (Spain). The 16S rRNA gene sequence of this strain showed 95.9 and 94.7 % sequence similarity, respectively, with those of the type strains of Cohnella hongkongensis and Cohnella thermotolerans. Strain GSPC1 T presented phenotypic, chemotaxonomic and molecular differences with respect to Cohnella species which indicated that it belonged to a different species. The isolate was a Gram-positive, aerobic, sporulated rod, motile by means of peritrichous flagella. The strain was catalase-positive and showed weak oxidase activity. It grew in the presence of 2 % NaCl. MK-7 was the predominant menaquinone. anteiso-C15:0, iso-C15:0, iso-C16: 0 and C16:0 were the major fatty acids. Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The G+C content was 60.3 mol%. The results of this study suggest that isolate GSPC1 T should be classified within a novel Cohnella species, for which the name Cohnella phaseoli sp. nov. is proposed, with strain GSPC1T (=LMG 24086T =DSM 19269T) as the type strain.

Shinella kummerowiae sp. nov., a symbiotic bacterium isolated from root nodules of the herbal legume Kummerowia stipulacea

Bacterial strain CCBAU 25048(T) was isolated from root nodules of Kummerowia stipulacea grown in Shandong province of China. Cells of the strain were Gram-negative, strictly aerobic, non-spore-forming, motile short rods. Phylogeny of 16S rRNA gene sequences revealed that the strain belonged to the genus Shinella, a member of family Rhizobiaceae. Its closest phylogenetic relatives were Shinella granuli Ch06(T) and Shinella zoogloeoides IAM 12669(T), respectively showing 98.3 and 98.9 % 16S rRNA gene sequence similarity. Strain CCBAU 25048(T) had DNA-DNA relatedness of 43.5 and 34.8 %, respectively, with S. zoogloeoides JCM 20728(T) and S. granuli JCM 13254(T). In addition, in TP-RAPD analysis, different patterns were obtained for these three strains and some rhizobial strains. The nifH, nodC and nodD sequences of CCBAU 25048(T) were identical or very similar to those of bean-nodulating Rhizobium tropici strains. Several phenotypic characteristics, including the use of citrate and d-ribose as carbon sources and growth at pH 11.0, as well as the fatty acid composition, could differentiate CCBAU 25048(T) from the two defined Shinella species. Therefore, a novel species Shinella kummerowiae sp. nov. is proposed, with strain CCBAU 25048(T) (=JCM 14778(T) =LMG 24136(T)) as the type strain.

Genetic diversity of endophytic bacteria which could be find in the apoplastic sap of the medullary parenchym of the stem of healthy sugarcane plants

The genetic diversity of 29 endophytic bacterial strains isolated from apoplastic sap of the medullary parenchym of the stem of healthy sugarcane plants grown in Cuba was analysed by Two Primers-Ramdom Amplified Polymorphic DNA fingerprinting (TP-RAPD) and 16S rRNA gene sequencing. The strains were distributed into 17 groups on the basis of their TP-RAPD patterns, and a representative strain from each group was subjected to 16S rRNA gene sequencing. Analysis of these sequences showed that the isolates belong to a wide variety of phylogenetic groups being closely related to species of genera Bacillus and Staphylococcus from Firmicutes, Microbacterium, Micrococcus and Kokuria from Actinobacteria, Rhizobium and Gluconacetobacter from alpha -Proteobacteria, Comamonas and Xanthomonas from beta-Proteobacteria, and Acinetobacter and Pantoea from gamma-Proteobacteria. These results show the complexity of the bacterial populations present in inner tissues of sugarcane, and indicate the interest and relevance of the studies on microbial diversity to improve our knowledge on the plant endophytic bacterial communities.

Rhizobium cellulase CelC2 is essential for primary symbiotic infection of legume host roots

The rhizobia-legume, root-nodule symbiosis provides the most efficient source of biologically fixed ammonia fertilizer for agricultural crops. Its development involves pathways of specificity, infectivity, and effectivity resulting from expressed traits of the bacterium and host plant. A key event of the infection process required for development of this root-nodule symbiosis is a highly localized, complete erosion of the plant cell wall through which the bacterial symbiont penetrates to establish a nitrogen-fixing, intracellular endosymbiotic state within the host. This process of wall degradation must be delicately balanced to avoid lysis and destruction of the host cell. Here, we describe the purification, biochemical characterization, molecular genetic analysis, biological activity, and symbiotic function of a cell-bound bacterial cellulase (CelC2) enzyme from Rhizobium leguminosarum bv. trifolii, the clover-nodulating endosymbiont. The purified enzyme can erode the noncrystalline tip of the white clover host root hair wall, making a localized hole of sufficient size to allow wild-type microsymbiont penetration. This CelC2 enzyme is not active on root hairs of the nonhost legume alfalfa. Microscopy analysis of the symbiotic phenotypes of the ANU843 wild type and CelC2 knockout mutant derivative revealed that this enzyme fulfils an essential role in the primary infection process required for development of the canonical nitrogen-fixing R. leguminosarum bv. trifolii-white clover symbiosis.

Ochrobactrum cytisi sp. nov., isolated from nodules of Cytisus scoparius in Spain

Two strains named ESC1(T) and ESC5 were isolated from nodules of Cytisus scoparius growing in a Spanish soil. Phylogenetic analysis of the 16S rRNA gene showed that these strains belong to the genus Ochrobactrum, their closest relatives being Ochrobactrum anthropi and Ochrobactrum lupini, with 100 and 99.9 % similarity to the respective type strains. Despite this high similarity, the results of DNA-DNA hybridization, phenotypic tests and fatty acid analyses showed that these strains represent a novel species of genus Ochrobactrum. The DNA-DNA hybridization values were respectively 70, 66 and 55 % with respect to O. lupini LUP21(T), O. anthropi DSM 6882(T) and Ochrobactrum tritici DSM 13340(T). The predominant fatty acids were C(18 : 1)omega7c and C(18 : 1) 2-OH. Strains ESC1(T) and ESC5 were strictly aerobic and were able to reduce nitrate and to hydrolyse aesculin. They produced beta-galactosidase and beta-glucosidase and did not produce urease after 48 h incubation. The G+C content of strain ESC1(T) was 56.4 mol%. Both strains ESC1(T) and ESC5 contained nodD and nifH genes on megaplasmids that were related phylogenetically to those of rhizobial strains nodulating Phaseolus, Leucaena, Trifolium and Lupinus. From the results of this work, we propose that the strains isolated in this study be included in a novel species named Ochrobactrum cytisi sp. nov. The type strain is ESC1(T) (=LMG 22713(T)=CECT 7172(T)).

Alcanivorax balearicus sp. nov., isolated from Lake Martel

A bacterial strain designated MACL04(T) was isolated from Lake Martel, a subterraneous saline lake in Mallorca (Spain). The complete 16S rRNA gene sequence of this strain showed nearly 100 % similarity to that of Alcanivorax dieselolei B-5(T). Despite this high similarity, strain MACL04(T) showed phenotypic, chemotaxonomic and molecular differences with respect to A. dieselolei, indicating that strain MACL04(T) represents a separate species. Cells of strain MACL04(T) were motile by means of a single polar or subpolar flagellum and colonies formed on media containing 1 % (v/v) Tween 20 were opaque and mucoid, with blue-green iridescence. The generation time of strain MACL04(T) in this medium was approximately half that of A. dieselolei B-5(T) and strain MACL04(T) did not produce lipases after incubation for 5 days. Strain MACL04(T) did not require NaCl for growth and grew in the presence of up to 15 % (w/v) NaCl. The strain was able to use alkanes as a sole carbon source; however, glucose could also be used, albeit weakly, as a carbon source. Several amino acids and organic acids were used as carbon sources. Strain MACL04(T) produced acid in media containing pyruvate as the sole carbon source. The major fatty acids were C(19 : 0) cyclo omega8c and C(16 : 0). The fatty acid C(16 : 1)omega8c, present in strain MACL04(T), was not detected in the recognized Alcanivorax species. The sequences of the large and short 16S-23S intergenic spacer regions showed similarities of 97.2 and 98.8 % (ungapped) with respect to A. dieselolei B-5(T). Partial sequences of gyrB and alkb genes showed 94.0 % similarity between strain MACL04(T) and A. dieselolei B-5(T). The G+C content of strain MACL04(T) was 62.8 mol%. The data from this polyphasic study indicate that strain MACL04(T) represents a novel species of the genus Alcanivorax, for which the name Alcanivorax balearicus sp. nov. is proposed. The type strain is MACL04(T) (=LMG 22508(T)=CECT 5683(T)).

High-speed gel microelectrophoresis, a new and easy approach for detection of PCR-amplified microbial DNA from environmental and clinical samples in microgels using conventional equipment

AIMS

Microelectrophoresis allows the detection of DNA bands using minimal amounts of sample in a short time, but commonly requires the use of special equipment which is not available in all laboratories. This fact has limited the application of this technique in microbiology despite its advantages. In this work, we describe a new approach to perform gel microelectrophoresis, named high-speed gel microelectrophoresis (HSGME), and its application for rapid detection of bacteria, protozoa and viruses in clinical, vegetal and environmental samples.

METHODS AND RESULTS

Aliquots of 0.4-1 microl of PCR product were loaded in 2 cm 1% agarose microgels and electrophoresed at high voltage (125 V cm(-1)) in conventional submarine horizontal mini-slabs. By using HSGME, single-DNA bands obtained after specific-PCR useful in diagnosis of different diseases caused by micro-organisms were detected in 5 min.

CONCLUSIONS

HSGME is a rapid and easy procedure applicable to detection of microbial genes, which is carried out using conventional equipment and thus can be performed in any research and diagnostic laboratory.

SIGNIFICANCE AND IMPACT OF THE STUDY

The performance of HSGME saves up to 90% time, material and energy costs, as well as laboratory hazardous wastes including carcinogenic agents used for visualizing DNA bands.

Rhizobium cellulosilyticum sp. nov., isolated from sawdust of Populus alba

During a study of polysaccharide-hydrolysing bacteria present in different plant sources, two strains were isolated from pulverized decaying wood of Populus alba and classified in the genus Rhizobium on basis of their almost complete 16S rRNA gene sequences. Their closest phylogenetic relatives were Rhizobium galegae USDA 4128T and Rhizobium huautlense S02T, with 98.2 and 98.1 % 16S rRNA gene sequence similarity, respectively. recA and atpD sequence analysis showed that these species have less than 88 and 92 % similarity, respectively, to the novel strains. In contrast to their closest phylogenetic relatives, the two strains showed strong cellulase activity on plates containing CM-cellulose as a carbon source. They were also distinguishable from these species on the basis of other phenotypic characteristics. The strains were able to induce ineffective nodules on Medicago sativa and the sequence of their nodD gene was phylogenetically close to that of Ensifer meliloti 1021 (99.6 % similarity). DNA–DNA hybridization values ranged from 10 to 22 % with respect to R. galegae USDA 4128T and 14 to 25 % with respect to R. huautlense S02T, showing that the strains from this study belong to a novel species, for which the name Rhizobium cellulosilyticum sp. nov. is proposed. The type strain is ALA10B2T (=LMG 23642T=DSM 18291T=CECT 7176T).

Paenibacillus cellulosilyticus sp. nov., a cellulolytic and xylanolytic bacterium isolated from the bract phyllosphere of Phoenix dactylifera

A bacterial strain designated PALXIL08(T) was isolated from the phyllosphere of Phoenix dactylifera bracts. A phylogenetic analysis based on the 16S rRNA gene sequence placed the isolate within the genus Paenibacillus in the same subgroup as Paenibacillus kobensis and Paenibacillus curdlanolyticus (98.9 and 97.9 % sequence similarity, respectively). The DNA hybridization values between the isolate and the type strains of Paenibacillus kobensis and Paenibacillus curdlanolyticus were found to be 27.4 and 17.6 %, respectively. The isolate comprised Gram-variable, facultatively anaerobic, motile, sporulating rods. Catalase and oxidase were produced and cellulose, xylan, starch and aesculin were hydrolysed. Many carbohydrates served as carbon sources for growth. MK-7 was the predominant menaquinone, and anteiso-C(15 : 0) and iso-C(16 : 0) were the major fatty acids. The DNA G+C content was 51 mol%. DNA relatedness data and the results of phylogenetic and phenotypic analyses showed that strain PALXIL08(T) should be considered as the type strain of a novel species of the genus Paenibacillus, for which the name Paenibacillus cellulosilyticus sp. nov. is proposed. The type strain is PALXIL08(T) (=LMG 22232(T)=CECT 5696(T)).

Rhizobium lusitanum sp. nov. a bacterium that nodulates Phaseolus vulgaris

The species Phaseolus vulgaris is a promiscuous legume nodulated by several species of the family Rhizobiaceae. During a study of rhizobia nodulating this legume in Portugal, we isolated several strains that nodulate P. vulgaris effectively and also Macroptilium atropurpureum and Leucaena leucocephala, but they form ineffective nodules in Medicago sativa. According to phylogenetic analysis of the 16S rRNA gene sequence, the strains from this study belong to the genus Rhizobium, with Rhizobium rhizogenes and Rhizobium tropici as the closest related species, with 99.9 and 99.2 % similarity, respectively, between the type strains of these species and strain P1-7T. The nodD and nifH genes carried by strain P1-7T are phylogenetically related to those of other species nodulating Phaseolus. This strain does not carry virulence genes present in the type strain of R. rhizogenes, ATCC 11325T. Analysis of the recA and atpD genes confirms this phylogenetic arrangement, showing low similarity with respect to those of R. rhizogenes ATCC 11325T (91.9 and 94.1 % similarity, respectively) and R. tropici IIB CIAT 899T (90.6 % and 91.8 % similarity, respectively). The intergenic spacer (ITS) of the strains from this study is phylogenetically divergent from those of R. rhizogenes ATCC 11235T and R. tropici CIAT 899T, with 85.9 and 82.8 % similarity, respectively, with respect to strain P1-7T. The tRNA profile and two-primer random amplified polymorphic DNA pattern of strain P1-7T are also different from those of R. rhizogenes ATCC 11235T and R. tropici CIAT 899T. The strains isolated in this study can be also differentiated from R. rhizogenes and R. tropici by several phenotypic characteristics. The results of DNA–DNA hybridization showed means of 28 and 25 % similarity between strain P1-7T and R. rhizogenes ATCC 11235T and R. tropici CIAT 899T, respectively. All these data showed that the strains isolated in this study belong to a novel species of the genus Rhizobium, for which we propose the name Rhizobium lusitanum sp. nov.; the type strain is P1-7T (=LMG 22705T=CECT 7016T).

Burkholderia ferrariae sp. nov., isolated from an iron ore in Brazil

A Gram-negative, non-spore-forming bacterial strain with the ability to solubilize highly insoluble phosphatic minerals was isolated from a high-phosphorous iron ore from Minas Gerais State, Brazil. This strain, designated FeGl01T, was subjected to a polyphasic taxonomic investigation. Comparative 16S rRNA gene sequence analysis indicated that it formed a distinct phylogenetic lineage within the genus Burkholderia together with several other species of the genus, e.g. Burkholderia sacchari, Burkholderia tropica and Burkholderia unamae. Partial nucleotide sequencing and analysis of the recA gene roughly corroborated the phylogenetic position of strain FeGl01T within the genus Burkholderia. The chemotaxonomic properties of strain FeGl01T, such as ubiquinone Q-8 as the predominant quinone system and C16 : 0, C17 : 0 cyclo, C18 : 1 ω7c and C19 : 0 ω8c cyclo as the major fatty acids, were also consistent with its classification within the genus Burkholderia. DNA–DNA hybridization experiments between strain FeGl01T and the type strains of B. unamae, B. sacchari and B. tropica yielded reassociation values of 40 % or lower, which, together with qualitative and quantitative differences in fatty acid composition and with differences in several phenotypic traits, support the separation of the new isolate from the phylogenetically most closely related species. Therefore, it is suggested that strain FeGl01T represents a novel species of the genus Burkholderia, for which the name Burkholderia ferrariae sp. nov. is proposed. The type strain is FeGl01T (=LMG 23612T=CECT 7171T=DSM 18251T).

Ultrastructural and chemotaxonomic analysis of a xylanolytic strain of Cryptococcus adeliensis isolated from sheep droppings in Spain

Cryptococcus adeliensis was initially described as a psycrophilic species containing a single strain CBS 8351(T) isolated from decayed algae in Terre Adelie (Antartida). Later, a second strain of this species was isolated from an immunosuppressed patient affected by leukaemia in Germany and recently several strains from this species have been found in human patients and pigeon droppings of the same country. In this study, we isolated from sheep droppings in Spain a xylanolytic strain named LEVX01 that was phenotypically related to the strain CBS 8351(T) and showed a 100% similarity in the D1/D2 domain and 5.8S-ITS region sequences with respect to the remaining described strains of C. adeliensis. These findings suggest that this species has a wide geographical distribution and that the animal faeces are a common habitat for C. adeliensis. The chemotaxonomic analyses showed the absence of detectable amounts of xylose in the cell walls of the strains LEVX01 and CBS8351(T) in contrast to other Cryptococcus species. Interestingly, the ultrastructural study showed the presence of fimbriae in these two strains that could be involved in the attachment to the host cells and, as occurs in Candida albicans, they could also be a pathogenicity factor for the man.

Terrabacter terrae sp. nov., a novel actinomycete isolated from soil in Spain

A Gram-positive, aerobic, long-rod-shaped, non-spore-forming bacterium (strain PPLB(T)) was isolated from soil mixed with Iberian pig hair. This actinomycete showed keratinase activity in vitro when chicken feathers were added to the culture medium. Strain PPLB(T) was oxidase-negative and catalase-positive and produced lipase and esterase lipase. This actinomycete grew at 40 degrees C on nutrient agar and in the same medium containing 5 % (w/v) NaCl. Growth was observed with many different carbohydrates as the sole carbon source. On the basis of 16S rRNA gene sequence similarity, strain PPLB(T) was shown to belong to the genus Terrabacter of the family Intrasporangiaceae. Strain PPLB(T) showed 98.8 % 16S rRNA gene sequence similarity to Terrabacter tumescens. Chemotaxonomic data, such as the main ubiquinone (MK-8), the main polar lipids (phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylinositol) and the main fatty acids (i-C(15 : 0), ai-C(15 : 0), i-C(16 : 0) and ai-C(17 : 0)) supported the affiliation of strain PPLB(T) to the genus Terrabacter. The G+C content of the DNA was 71 mol%. The results of DNA-DNA hybridization (36.6 % relatedness between Terrabacter tumescens and strain PPLB(T)) and physiological and biochemical tests suggested that strain PPLB(T) belongs to a novel species of the genus Terrabacter, for which the name Terrabacter terrae sp. nov. is proposed. The type strain is PPLB(T) (=CECT 3379T=LMG 22921T).

Application of horizontal staircase electrophoresis in agarose minigels to the random intergenic spacer analysis of clinical samples

The random intergenic spacer analysis is a recently developed technique for the study of microbial populations. The bacterial intergenic spacer (ITS) is located between 16S rRNA and 23S rRNA genes and presents different length and sequence among bacterial species. Therefore, the amplicons can be separated by electrophoresis commonly performed at low voltage during several hours. Although this technique is especially useful for unculturable microorganisms, it has not been applied before to clinical sample analysis. As these samples have a limited number of bacterial species, the size of the gels may be reduced to facilitate their handling and to reduce the running time. To obtain maximum separation among the ITS bands, we analysed in this work different electrophoretical conditions including staircase electrophoresis, a technique based on the application of several voltage steps. The results obtained showed a different behaviour of the electrical resistance during the performance of submarine horizontal and vertical staircase electrophoresis. In the first case the resistance decreased during most of the running time whereas in the second case it increased. Here, we show that the performance of horizontal staircase electrophoresis reduces the running time more than 80% with respect to conventional electrophoresis at low voltages. This procedure was applied to the separation of ITS bands from bacterial DNA present in a tissue from a vocal cord biopsy. The sequencing of these bands allowed their identification. This new procedure may be very useful in the rapid diagnosis of bacteria present in human, animal and plant tissues.

The coexistence of symbiosis and pathogenicity-determining genes in Rhizobium rhizogenes strains enables them to induce nodules and tumors or hairy roots in plants

Bacteria belonging to the family Rhizobiaceae may establish beneficial or harmful relationships with plants. The legume endosymbionts contain nod and nif genes responsible for nodule formation and nitrogen fixation, respectively, whereas the pathogenic strains carry vir genes responsible for the formation of tumors or hairy roots. The symbiotic and pathogenic strains currently belong to different species of the genus Rhizobium and, until now, no strains able to establish symbiosis with legumes and also to induce tumors or hairy roots in plants have been reported. Here, we report for the first time the occurrence of two rhizobial strains (163C and ATCC11325T) belonging to Rhizobium rhizogenes able to induce hairy roots or tumors in plants and also to nodulate Phaseolus vulgaris under natural environmental conditions. Symbiotic plasmids (pSym) containing nod and nif genes and pTi- or pRi-type plasmids containing vir genes were found in these strains. The nodD and nifH genes of the strains from this study are phylogenetically related to those of Sinorhizobium strains nodulating P. vulgaris. The virA and virB4 genes from strain 163C are phylogenetically related to those of R. tumefaciens C58, whereas the same genes from strain ATCC 11325T are related to those of hairy root-inducing strains. These findings may be of high relevance for the better understanding of plant-microbe interactions and knowledge of rhizobial phylogenetic history.

Martelella mediterranea gen. nov., sp. nov., a novel alpha-proteobacterium isolated from a subterranean saline lake

A bacterial strain was isolated from the water of Lake Martel in Mallorca (Spain). The isolate, designated MACL11(T), was halotolerant and strictly aerobic. The cells were non-motile, non-spore-forming, Gram-negative short rods. Comparative 16S rRNA gene sequence analysis revealed that MACL11(T) represents a separate line of descent within the order 'Rhizobiales' of the class 'Alphaproteobacteria'. Strain MACL11(T) was most closely related to the genera Rhizobium (93.3 % sequence similarity to Rhizobium rhizogenes), Aurantimonas (90.3 % sequence similarity to Aurantimonas coralicida) and Fulvimarina (90.3 % sequence similarity to Fulvimarina pelagi). Chemotaxonomically, strain MACL11(T) was characterized by the presence of Q-10 as the major respiratory lipoquinone. The major fatty acids detected were C(19 : 0) cycloomega8c, C(18 : 1)omega7c, C(16 : 0) and 11-methyl C(18 : 1)omega7c. The G+C content of the DNA was 57.4 mol%. Oxidase and catalase activities were present. Growth with many different carbohydrates as the sole carbon source was observed. The data from this polyphasic study suggest that this bacterium belongs to a novel genus of the order 'Rhizobiales' and is not associated with any of the known families of this order. It is proposed that isolate MACL11(T) should be classified in a novel genus and species, Martelella mediterranea gen. nov., sp. nov., with MACL11(T) (=LMG 22193(T)=CECT 5861(T)) as the type strain.

Sphingomonas phyllosphaerae sp. nov., from the phyllosphere of Acacia caven in Argentina

Two bacterial strains (FA1 and FA2(T)) were isolated from the phyllosphere of a leguminous tree, Acacia caven, in central Argentina. The strains were Gram-negative, strictly aerobic, rod-shaped, motile and formed yellow-pigmented colonies on nutrient agar. The two-primer RAPD patterns of the two strains were identical, suggesting that they belong to the same species. The complete 16S rRNA gene sequences of the two strains were obtained and comparisons demonstrated that they cluster phylogenetically with the species of the genus Sphingomonas sensu stricto. Strain FA2(T) was most closely related (97.6 %) to Sphingomonas adhaesiva. 16S rRNA gene sequence similarities to all other established Sphingomonas species ranged from 94.4 % (to Sphingomonas echinoides) to 97.6 % (to S. adhaesiva). Strains FA1 and FA2(T) were catalase-positive and oxidase-negative. Aesculin was hydrolysed, gelatin and urea were not. beta-Galactosidase was produced. From 51 compounds tested 21 were used as single sources of carbon. The major respiratory lipoquinone was ubiquinone-10. The predominant cellular fatty acids were 16 : 0, 18 : 1omega7c and 16 : 1omega7c (from summed feature 3). Hydroxy fatty acids 14 : 0 2-OH and 15 : 0 iso 2-OH were present as well (from summed feature 4). The polar lipids detected in strain FA2(T) were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid and two unidentified phospholipids. The DNA G+C content of strain FA2(T) was 61 mol%. DNA-DNA hybridization experiments showed 27.6 % relatedness between strain FA2(T) and S. adhaesiva DSM 7418(T). Based upon phenotypic and molecular evidence, a novel species of the genus Sphingomonas is proposed, Sphingomonas phyllosphaerae sp. nov., with strain FA2(T) (=LMG 21958(T)=CECT 5832(T)) as the type strain.

Nodulation of Lupinus albus by strains of Ochrobactrum lupini sp. nov

The nodulation of legumes has for more than a century been considered an exclusive capacity of a group of microorganisms commonly known as rhizobia and belonging to the alpha-Proteobacteria. However, in the last 3 years four nonrhizobial species, belonging to alpha and beta subclasses of the Proteobacteria, have been described as legume-nodulating bacteria. In the present study, two fast-growing strains, LUP21 and LUP23, were isolated from nodules of Lupinus honoratus. The phylogenetic analysis based on the 16S and 23S rRNA gene sequences showed that the isolates belong to the genus Ochrobactrum. The strains were able to reinfect Lupinus plants. A plasmid profile analysis showed the presence of three plasmids. The nodD and nifH genes were located on these plasmids, and their sequences were obtained. These sequences showed a close resemblance to the nodD and nifH genes of rhizobial species, suggesting that the nodD and nifH genes carried by strain LUP21T were acquired by horizontal gene transfer. A polyphasic study including phenotypic, chemotaxonomic, and molecular features of the strains isolated in this study showed that they belong to a new species of the genus Ochrobactrum for which we propose the name Ochrobactrum lupini sp. nov. Strain LUP21T (LMG 20667T) is the type strain.

Paenibacillus phyllosphaerae sp. nov., a xylanolytic bacterium isolated from the phyllosphere of Phoenix dactylifera

A bacterial strain, designated PALXIL04T, was isolated from the phyllosphere of Phoenix dactylifera. Phylogenetic analysis placed the isolate within the genus Paenibacillus with the closest relatives being Paenibacillus curdlanolyticus and Paenibacillus kobensis. DNA–DNA hybridization measurements showed low DNA relatedness (15–20 %) between the isolate and its closest relatives. Cells were Gram-variable, facultatively anaerobic, motile, sporulating rods. Catalase and oxidase were produced by the organism. Cellulose, starch, aesculin and xylan were hydrolysed. Growth was supported by many carbohydrates as the carbon source. MK-7 was the predominant menaquinone and anteiso-C15 : 0 the major fatty acid. The G+C content of the DNA was 50·7 mol%. Phylogenetic, DNA–DNA relatedness and phenotypic analyses indicated that strain PALXIL04T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus phyllosphaerae sp. nov. is proposed. The type strain is PALXIL04T (=LMG 22192T=CECT 5862T).

Bradyrhizobium betae sp. nov., isolated from roots of Beta vulgaris affected by tumour-like deformations

Some varieties of sugar beet, Beta vulgaris, cultivated in northern Spain have large deformations that resemble the tumours produced by Agrobacterium species. In an attempt to isolate the agent responsible for these deformations, several endophytic slow-growing bacterial strains were isolated, the macroscopic morphology of which resembled that of Bradyrhizobium species. These strains were not able to produce tumours in Nicotiana tabacum plants and, based on phylogenetic analysis of their 16S rRNA, they are closely related to the genus Bradyrhizobium. Phenotypic and molecular characteristics of these strains revealed that they represent a species different from all Bradyrhizobium species previously described. Sequence analysis of the 16S-23S rDNA intergenic spacer region indicated that these novel strains form a homogeneous group, related to Bradyrhizobium japonicum, Bradyrhizobium liaoningense and Bradyrhizobium yuanmingense. DNA-DNA hybridization confirmed that these strains represent a novel species of the genus Bradyrhizobium, for which the name Bradyrhizobium betae sp. nov. is proposed. The type strain is PL7HG1T (=LMG 21987T=CECT 5829T).

Phenotypic and Genotypic Characterization of Rhizobia from Diverse Geographical Origin that Nodulate Pachyrhizus species

Legumes from the genus Pachyrhizus, commonly known as yam bean, are cultivated in several countries from the American continent and constitute an alternative source for sustainable starch, oil and protein production. The endosymbionts of these legumes have been poorly studied although it is known that this legume is nodulated by fast and slow growing rhizobia. In this study we have analyzed a collection of strains isolated in several countries using different phenotypic and molecular methods. The results obtained by SDS-PAGE analysis, LPS profiling and TP-RAPD fingerprinting showed the high diversity of the strains analyzed, although all of them presented slow growth in yeast mannitol agar (YMA) medium. These results were confirmed using 16S-23S internal transcribed spacer (ITS) region and complete sequencing of the 16S rRNA gene, showing that most strains analyzed belong to different species of genus Bradyrhizobium. Three strains were closely related to B. elkanii and the rest of the strains were related to the phylogenetic group constituted by B. japonicum, B. liaoningense, B. yuanmingense and B. betae. These results support that the study of rhizobia nodulating unexplored legumes in different geographical locations will allow the discovery of new species able to establish legume symbioses.

Mycobacterium psychrotolerans sp. nov., isolated from pond water near a uranium mine

An acid-fast, rapidly growing, psychrotolerant short rod was isolated from pond water near a uranium mine. Phylogenetic analysis of the 16S rRNA gene sequence grouped this strain with the rapidly growing mycobacteria. The 16S rRNA gene sequence of isolate WA101T showed highest similarity to that of Mycobacterium sphagni DSM 44076T; however, DNA–DNA relatedness between the two strains was less than 30 %. Chemotaxonomic analyses, which included fatty acid and mycolic acid patterns, confirmed the classification of strain WA101T in the genus Mycobacterium. Physiological data, including antibiotic resistance, NaCl tolerance, carbon sources, temperature growth range and enzyme activities, were also determined. Based on the genotypic and phenotypic results it is proposed that isolate WA101T represents a novel Mycobacterium species. The name Mycobacterium psychrotolerans sp. nov. is proposed, with type strain WA101T (=DSM 44697T=LMG 21953T).

Pseudomonas lutea sp. nov., a novel phosphate-solubilizing bacterium isolated from the rhizosphere of grasses

A phosphate-solubilizing bacterial strain designated OK2T was isolated from rhizospheric soil of grasses growing spontaneously in a soil from Spain. Cells of the strain were Gram-negative, strictly aerobic, rod-shaped and motile. Phylogenetic analysis of the 16S rRNA gene indicated that this bacterium belongs to the γ-subclass of Proteobacteria within the genus Pseudomonas and that the closest related species is Pseudomonas graminis. The strain produced catalase but not oxidase. Cellulose, casein, starch, gelatin and urea were not hydrolysed. Aesculin was hydrolysed. Growth was observed with many carbohydrates as carbon sources. The main non-polar fatty acids detected were hexadecenoic acid (16 : 1), hexadecanoic acid (16 : 0) and octadecenoic acid (18 : 1). The hydroxy fatty acids detected were 3-hydroxydecanoic acid (3-OH 10 : 0), 3-hydroxydodecanoic acid (3-OH 12 : 0) and 2-hydroxydodecanoic acid (2-OH 12 : 0). The G+C DNA content determined was 59·3 mol%. DNA–DNA hybridization showed 48·7 % relatedness between strain OK2T and P. graminis DSM 11363T and 26·2 % with respect to Pseudomonas rhizosphaerae LMG 21640T. Therefore, these results indicate that strain OK2T (=LMG 21974T=CECT 5822T) belongs to a novel species of the genus Pseudomonas, and the name Pseudomonas lutea sp. nov. is proposed.

Identification of microorganisms by PCR amplification and sequencing of a universal amplified ribosomal region present in both prokaryotes and eukaryotes

The small ribosomal subunit contains 16S rRNA in prokaryotes and 18S rRNA in eukaryotes. Even though it has been known that some small ribosomal sequences are conserved in 16S rRNA and 18S rRNA molecules, they have been used separately for taxonomic and phylogenetic studies. Here, we report the existence of two highly conserved ribosomal sequences in all organisms that allow the amplification of a zone containing approximately 495 bp in prokaryotes and 508 bp in eukaryotes which we have named the "Universal Amplified Ribosomal Region" (UARR). Amplification and sequencing of this zone is possible using the same two universal primers (U1F and U1R) designed on the basis of two highly conserved ribosomal sequences. The UARR encompasses the V6, V7 and V8 domains from SSU rRNA in both prokaryotes and eukaryotes. The internal sequence of this zone in prokaryotes and eukaryotes is variable and the differences become less marked on descent from phyla to species. Nevertheless, UARR sequence allows species from the same genus to be differentiated. Thus, by UARR sequence analysis the construction of universal phylogenetic trees is possible, including species of prokaryotic and eukaryotic microorganisms together. Single isolates of prokaryotic and eukaryotic microorganisms from different sources can be identified by amplification and sequencing of UARR using the same pair of primers and the same PCR and sequencing conditions.

Cellulomonas xylanilytica sp. nov., a cellulolytic and xylanolytic bacterium isolated from a decayed elm tree

A Gram-positive, aerobic, non-motile bacterium was isolated from a decayed elm tree. Phylogenetic analysis based on 16S rDNA sequences revealed 99·0 % similarity to Cellulomonas humilata. Chemotaxonomic data that were determined for this isolate included cell-wall composition, fatty acid profiles and polar lipids; the results supported the placement of strain XIL11T in the genus Cellulomonas. The DNA G+C content was 73 mol%. The results of DNA–DNA hybridization with C. humilata ATCC 25174T, in combination with chemotaxonomic and physiological data, demonstrated that isolate XIL11T should be classified as a novel Cellulomonas species. The name Cellulomonas xylanilytica sp. nov. is proposed, with strain XIL11T (=LMG 21723T=CECT 5729T) as the type strain.

Paenibacillus favisporus sp. nov., a xylanolytic bacterium isolated from cow faeces

During a search for xylan-degrading micro-organisms, a sporulated bacterium was recovered from recent and old cow dung and rectal samples. The isolates were identified as members of a novel species of the genus Paenibacillus, based on 16S rRNA gene sequences. According to the results of phylogenetic analysis, the most closely related species was Paenibacillus azoreducens. Phenotypic and chemotaxonomic analyses and DNA–DNA hybridization experiments also showed that the isolates belonged to a novel species of the genus Paenibacillus. The novel species is a facultatively anaerobic, motile, Gram-variable, sporulated rod. The spores of this rod-shaped micro-organism occur in slightly swollen sporangia and are honeycomb-shaped. The main fatty acid is anteiso-branched C15 : 0. Growth was observed with many carbohydrates, including xylan, as the only carbon source and gas production was not observed from glucose. The novel species produces a wide variety of hydrolytic enzymes, such as xylanases, cellulases, amylases, gelatinase, urease and β-galactosidase. On the contrary, it does not produce caseinase, phenylalanine deaminase or lysine decarboxylase. According to the data obtained in this work, the strains belong to a novel species, for which the name Paenibacillus favisporus sp. nov. is proposed (type strain, GMP01T=LMG 20987T=CECT 5760T).

Description of Devosia neptuniae sp. nov. that nodulates and fixes nitrogen in symbiosis with Neptunia natans, an aquatic legume from India

Neptunia natans is a unique aquatic legume indigenous to tropical and sub-tropical regions and is nodulated symbiotically by rhizobia using an unusual infection process unlike any previously described. Previously, isolates of neptunia-nodulating rhizobia from Senegal were characterized as Allorhizobium undicola. Here we report on a different group of neptunia-nodulating rhizobia isolated from India. Sequencing of the 16S rDNA gene from two of these Indian isolates (strains J1T and J2) show that they belong in the genus Devosia rather than Allorhizobium. Currently, the only described Devosia species is D. riboflavina (family Hyphomicrobiaceae, order Rhizobiales). The complete 16S rDNA sequences of strains J1T and J2 are 95.9% homologous to the type strain, D. riboflavina LMG 2277T, suggesting that these neptunia-nodulating strains from India belong to a new Devosia species. This hypothesis was confirmed by further studies of polyphasic taxonomy (DNA-DNA hybridisation, TP-RAPD patterns, SDS-PAGE of cellular proteins, 16S rDNA RFLP patterns, carbon source utilisation, cellular fatty acid analysis and other phenotypic characterisations), all of which support the proposal that these neptunia-nodulating strains constitute a new Devosia species, which we name Devosia neptuniae sp. nov. These gram negative, strictly aerobic short rods are motile by a subpolar flagellum, positive for catalase, oxidase, urease and beta-galactosidase, can utilise several carbohydrates (but not organic acids) as carbon sources and contain C18:0 3-OH, cis-7 C18:1 11-methyl and cis-7 C18:1 as their major cellular fatty acids. Unlike D. riboflavina, the longer-chain C24:1 3-OH and C26:1 3-OH hydroxy fatty acids are not detected. The type strain of D. neptuniae is LMG 21357T (CECT 5650T). Assignment of this new taxon represents the fourth example in the literature of a non-rhizobial genus of bacteria capable of forming a bonafide dinitrogen-fixing root-nodule symbiosis with legume plants.

Xylanimonas cellulosilytica gen. nov., sp. nov., a xylanolytic bacterium isolated from a decayed tree (Ulmus nigra)

A bacterial strain, designated XIL07T, isolated from a decayed tree, Ulmus nigra, in Salamanca (Spain) produced abundant cellulases and xylanases. The micro-organism was Gram-positive, aerobic, coccoid and non-motile. Growth was observed on many carbohydrates, including cellulose and xylan as the sole carbon sources. No growth was observed with acetate, citrate, gluconate, inositol, malate or mannitol as carbon sources. The strain showed very weak catalase activity. HPLC analysis of menaquinones revealed two peaks: the main peak corresponded with MK-9(H4) and the smaller one with MK-8(H4). The major fatty acid found was anteiso-C15:0 (12-methyl tetradecanoic acid). Mycolic acids were absent. The polar lipids detected were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. Peptidoglycan type was A4alpha, L-Lys-D-Asp. The cell-wall sugars detected were galactose and rhamnose. The complete 16S rDNA sequence of strain XIL07T was obtained and phylogenetic analysis based on the neighbour-joining method indicated that this bacterium belongs to the high-G + C-content Gram-positive bacteria and that the closest related genera are Promicromonospora and Cellulosimicrobium. The DNA G + C content was 73 mol%. According to the data obtained in this work, this bacterium belongs to a new genus in the family Promicromonosporaceae and the name Xylanimonas cellulosilytica gen. nov., sp. nov. is proposed; the type strain is strain XIL07T (=LMG 20990T =CECT 5975T).

A new species of Devosia that forms a unique nitrogen-fixing root-nodule symbiosis with the aquatic legume Neptunia natans (L.f.) druce

Rhizobia are the common bacterial symbionts that form nitrogen-fixing root nodules in legumes. However, recently other bacteria have been shown to nodulate and fix nitrogen symbiotically with these plants. Neptunia natans is an aquatic legume indigenous to tropical and subtropical regions and in African soils is nodulated by Allorhizobium undicola. This legume develops an unusual root-nodule symbiosis on floating stems in aquatic environments through a unique infection process. Here, we analyzed the low-molecular-weight RNA and 16S ribosomal DNA (rDNA) sequence of the same fast-growing isolates from India that were previously used to define the developmental morphology of the unique infection process in this symbiosis with N. natans and found that they are phylogenetically located in the genus Devosia, not Allorhizobium or RHIZOBIUM: The 16S rDNA sequences of these two Neptunia-nodulating Devosia strains differ from the only species currently described in that genus, Devosia riboflavina. From the same isolated colonies, we also located their nodD and nifH genes involved in nodulation and nitrogen fixation on a plasmid of approximately 170 kb. Sequence analysis showed that their nodD and nifH genes are most closely related to nodD and nifH of Rhizobium tropici, suggesting that this newly described Neptunia-nodulating Devosia species may have acquired these symbiotic genes by horizontal transfer.

Tandem oligonucleotide synthesis on solid-phase supports for the production of multiple oligonucleotides

More than one oligonucleotide can be synthesized at a time by linking multiple oligonucleotides end-to-end in a tandem manner on the surface of a solid-phase support. The 5'-terminal hydroxyl position of one oligonucleotide serves as the starting point for the next oligonucleotide synthesis. The two oligonucleotides are linked via a cleavable 3'-O-hydroquinone-O,O'-diacetic acid linker arm (Q-linker). The Q-linker is rapidly and efficiently coupled to the 5'-OH position of immobilized oligonucleotides using HATU, HBTU, or HCTU in the presence of 1 equiv of DMAP. This protocol avoids introduction of phosphate linkages on either the 3'- or 5'-end of oligonucleotides. A single NH(4)OH cleavage step can simultaneously release the products from the surface of the support and each other to produce free 5'- and 3'-hydroxyl termini. Selective cleavage of one oligonucleotide out of two sequences has also been accomplished via a combination of succinyl and Q-linker linker arms. Tandem synthesis of multiple oligonucleotides is useful for producing sets of primers for PCR, DNA sequencing, and other diagnostic applications as well as double-stranded oligonucleotides. Tandem synthesis of the same sequence multiple times increases the yield of material from any single synthesis column for maximum economy in large-scale synthesis. This method can also be combined with reusable solid-phase supports to further reduce the cost of oligonucleotide production.