Field evaluation of PGP Bacillus sp. strain D5 native to Crocus sativus, in traditional and non traditional areas, and mining of PGP genes from its genome.

Native Bacillus sp. strain D5 coded as (Bar D5) has been isolated from the saffron corm that showed plant growth promotion (PGP) properties and also inhibits the growth of corm rot causing Fusarium oxysporum R1 (Fox R1) in-vitro. Bar D5 was more efficient PGP bacterium in comparison to earlier reported native bio-formulations by our group.

Root Nodule Rhizobia From Undomesticated Shrubs of the Dry Woodlands of Southern Africa Can Nodulate Angolan Teak , an Important Source of Timber.

, a leguminous tree native to the dry woodlands of Southern Africa, provides valuable timber, but is threatened by land conversion and overharvesting while showing limited natural regeneration. Nitrogen-fixing root nodule symbionts that could improve establishment of young seedlings have not yet been described. Therefore, we investigated the ability of to form nodules with a diverse range of rhizobia.

Complete Genomes of the Anaerobic Degradation Specialists Aromatoleum petrolei ToN1T and Aromatoleum bremense PbN1T.

The betaproteobacterial genus Aromatoleum comprises facultative denitrifiers specialized in the anaerobic degradation of recalcitrant organic compounds (aromatic and terpenoid). This study reports on the complete and manually annotated genomes of Ar. petrolei ToN1T (5.

Novel cultivated endophytic Verrucomicrobia reveal deep-rooting traits of bacteria to associate with plants.

Despite the relevance of complex root microbial communities for plant health, growth and productivity, the molecular basis of these plant-microbe interactions is not well understood. Verrucomicrobia are cosmopolitans in the rhizosphere, nevertheless their adaptations and functions are enigmatic since the proportion of cultured members is low. Here we report four cultivated Verrucomicrobia isolated from rice, putatively representing four novel species, and a novel subdivision.

Dual coding potential of a 2',5'-branched ribonucleotide in DNA.

Branchpoints in RNA templates are highly mutagenic, but it is not known yet whether this also applies to branchpoints in DNA templates. Here, we report how nucleic acid polymerases replicate a 2',5'-branched DNA (bDNA) molecule. We constructed long-chained bDNA templates containing a branch guanosine and T7 promoters at both arms by splinted ligation.

Arm-specific cleavage and mutation during reverse transcription of 2΄,5΄-branched RNA by Moloney murine leukemia virus reverse transcriptase.

Branchpoint nucleotides of intron lariats induce pausing of DNA synthesis by reverse transcriptases (RTs), but it is not known yet how they direct RT RNase H activity on branched RNA (bRNA). Here, we report the effects of the two arms of bRNA on branchpoint-directed RNA cleavage and mutation produced by Moloney murine leukemia virus (M-MLV) RT during DNA polymerization. We constructed a long-chained bRNA template by splinted-ligation.

Bradyrhizobium vignae sp. nov., a nitrogen-fixing symbiont isolated from effective nodules of Vigna and Arachis.

Twenty one strains of symbiotic bacteria from root nodules of local races of cowpea (Vigna unguiculata), Bambara groundnut (Vigna subterranea) and peanuts (Arachis hypogaea) grown on subsistence farmers' fields in the Kavango region of Namibia, were previously characterized as a novel group within the genus Bradyrhizobium. To verify their taxonomic position, the strains were further analysed using a polyphasic approach. 16S rRNA gene sequences were most similar to Bradyrhizobium manausense BR 3351T, with Bradyrhizobium ganzhouense RITF806T being the most closely related type strain in the phylogenetic analysis, and Bradyrhizobium yuanmingense CCBAU 10071T in the ITS sequence analysis.

Bradyrhizobium kavangense sp. nov., a symbiotic nitrogen-fixing bacterium from root nodules of traditional Namibian pulses.

Eight strains of symbiotic bacteria from root nodules of local races of cowpea (Vigna unguiculata) and Bambara groundnut (Vigna subterranea) grown on subsistence farmers' fields in the Kavango region, Namibia, were previously characterized and identified as a novel group within the genus Bradyrhizobium. To clarify their taxonomic status, these strains were further characterized using a polyphasic approach. In phylogenetic analysis of the 16S rRNA gene sequence the novel group was most closely related to Bradyrhizobium iriomotense EK05T and Bradyrhizobium ingae BR 10250T, and to 'Bradyrhizobium arachidis' CCBAU 051107 in the ITS sequence analysis.

Roots shaping their microbiome: global hotspots for microbial activity.

Land plants interact with microbes primarily at roots. Despite the importance of root microbial communities for health and nutrient uptake, the current understanding of the complex plant-microbe interactions in the rhizosphere is still in its infancy. Roots provide different microhabitats at the soil-root interface: rhizosphere soil, rhizoplane, and endorhizosphere.

Microbial community structure and functional diversity of nitrogen-fixing bacteria associated with Colophospermum mopane.

Colophospermum mopane is an indigenous legume tree that grows in Southern Africa and is one of the predominant trees of the woodland vegetation. In order to increase knowledge about its ecology, especially how C. mopane thrives in the nitrogen-poor soils of the region, we analyzed the root-associated bacteria to assess the active diazotrophic diversity and total microbial diversity by culture-dependent and independent techniques.

Rhizobia Indigenous to the Okavango Region in Sub-Saharan Africa: Diversity, Adaptations, and Host Specificity.

The rhizobial community indigenous to the Okavango region has not yet been characterized. The isolation of indigenous rhizobia can provide a basis for the formulation of a rhizobial inoculant. Moreover, their identification and characterization contribute to the general understanding of species distribution and ecology.

Lamins of the sea lamprey (Petromyzon marinus) and the evolution of the vertebrate lamin protein family.

Lamin proteins are found in all metazoans. Most non-vertebrate genomes including those of the closest relatives of vertebrates, the cephalochordates and tunicates, encode only a single lamin. In teleosts and tetrapods the number of lamin genes has quadrupled.

Bias in topoisomerase (TOPO)-cloning of multitemplate PCR products using locked nucleic acid (LNA)-substituted primers.

Locked nucleic acid (LNA) modifications help to improve nucleic acid recognition in molecular biology applications. We report that LNA-substituted primers in PCR reactions may cause considerable cloning bias when the widely used topoisomerase-based ligation is used for cloning of multitemplate PCR products.

A novel regulatory role of the Rnf complex of Azoarcus sp. strain BH72.

The superfamily of P(II) proteins contains the most widely distributed signalling proteins in nature. Remarkable is the variety of targets whose activity is affected by protein-protein interactions. Here we identified as novel partner for interaction with GlnK an Rnf complex, known to couple the energy of ion transport to reduce ferredoxins.

Functional characteristics of an endophyte community colonizing rice roots as revealed by metagenomic analysis.

Roots are the primary site of interaction between plants and microorganisms. To meet food demands in changing climates, improved yields and stress resistance are increasingly important, stimulating efforts to identify factors that affect plant productivity. The role of bacterial endophytes that reside inside plants remains largely unexplored, because analysis of their specific functions is impeded by difficulties in cultivating most prokaryotes.

Predominant nifH transcript phylotypes related to Rhizobium rosettiformans in field-grown sugarcane plants and in Norway spruce.

Although some sugarcane cultivars may benefit substantially from biological nitrogen fixation (BNF), the responsible bacteria have been not identified yet. Here, we examined the active diazotrophic bacterial community in sugarcane roots from Africa and America by reverse transcription (RT)-PCR using broad-range nifH-specific primers. Denaturing gradient gel electrophoresis (DGGE) profiles obtained from sugarcane showed a low diversity at all sample locations with one phylotype amounting up to 100% of the nifH transcripts.

Living inside plants: bacterial endophytes.

As current research activities have focused on symbiotic or parasitic plant-microbe interactions, other types of associations between plants and microorganisms are often overlooked. Endophytic bacteria colonize inner host tissues, sometimes in high numbers, without damaging the host or eliciting strong defense responses. Unlike endosymbionts they are not residing in living plant cells or surrounded by a membrane compartment.

Global characterization of the root transcriptome of a wild species of rice, Oryza longistaminata, by deep sequencing.

Background: Oryza longistaminata, an AA genome type (2 n = 24), originates from Africa and is closely related to Asian cultivated rice (O. sativa L.).

LNA-substituted degenerate primers improve detection of nitrogenase gene transcription in environmental samples.

In order to study the active diazotrophic bacterial community and to capture the majority of its individuals in environmental samples, strategies improving gene detection by increasing sensitivity and efficiency of PCR reactions are highly desirable. Since LNA (locked nucleic acids) modifications might alleviate a low sensitivity and specificity often limiting PCR reactions utilizing degenerate primers, the effect of LNA substituted primers on the detection of nifH transcripts in roots of rice and sugar cane by direct reverse transcription polymerase chain reaction (RT-PCR) was studied. The LNA substitution of the RT primer increased the sensitivity of the RT-PCR up to 26-fold, whereas LNA substitution of the PCR primers decreased specificity.

Evaluation of PCR primers for universal nifH gene targeting and for assessment of transcribed nifH pools in roots of Oryza longistaminata with and without low nitrogen input.

The bias of widely used degenerate nifH-specific primer sets was first tested using denaturing gradient gel electrophoresis (DGGE), and their application for profiling of complex communities assessed for roots of Oryza longistaminata. When primers (P) with mismatches at nondegenerate positions were used on genomic DNA of Azotobacter vinelandii, which harbors three single divergent nifH genes, template-to-product ratios were highly skewed. In contrast, we obtained no evidence for a large PCR bias when we used highly degenerate primers with no mismatches (Z).

Twitching motility is essential for endophytic rice colonization by the N2-fixing endophyte Azoarcus sp. strain BH72.

Azoarcus sp. strain BH72, as an endophyte of grasses, depends on successful host colonization. Type IV pili are essential for mediating the initial interaction with rice roots.

A nifH-based oligonucleotide microarray for functional diagnostics of nitrogen-fixing microorganisms.

Nitrogen fixation is an important process in biogeochemical cycles exclusively carried out by prokaryotes, mostly by an evolutionarily conserved nitrogenase protein complex, of which one of the structural genes (nifH) is highly valuable for phylogenetic and diversity analyses. We developed a nifH-based short oligonucleotide microarray (nifH diagnostic microarray) as a rapid tool to effectively monitor nitrogen-fixing diazotrophic populations in a wide range of environments. Taking account of the overwhelming predominance of environmental nifH fragments from uncultivated microorganisms in public databases, our nifH microarray is mainly based on nifH sequences from as yet unidentified prokaryotes.

Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72.

Azoarcus sp. strain BH72, a mutualistic endophyte of rice and other grasses, is of agrobiotechnological interest because it supplies biologically fixed nitrogen to its host and colonizes plants in remarkably high numbers without eliciting disease symptoms. The complete genome sequence is 4,376,040-bp long and contains 3,992 predicted protein-coding sequences.

Characterization of culturable bacterial populations associating with Pinus sylvestris--Suillus bovinus mycorrhizospheres.

Bacterial isolations were carried out on Pinus sylvestris--Suillus bovinus mycorrhizospheres obtained directly from boreal pine forest. When samples were taken during dry weather, the numbers of bacterial colony-forming units were significantly higher in uncolonized short roots and external mycelia than in mycorrhizal roots and soil outside the mycorrhizosphere. In contrast, the colony-forming unit counts were similar in all hypogeous samples after rainy weather.