Focusing on the nuclear and subnuclear dynamics of light and circadian signalling

Circadian clocks provide organisms the ability to synchronise theirinternal physiological responses with the external environment. Thisprocess, termed entrainment, occurs through the perception of internaland external stimuli. As with other organisms, in plants the perception oflight is a critical for the entrainment and sustainment of circadianrhythms. Red, blue, far-red and UV-B light is perceived by the oscillatorthrough the activity of photoreceptors. Four classes of photoreceptorssignal to the oscillator: phytochromes, cryptochromes, UVR8 and LOV-KELCH domain proteins. In most cases, these photoreceptors localise tothe nucleus in response to light and can associate to subnuclearstructures to initiate downstream signalling. In this review, we willhighlight the recent advances made in understanding the mechanismsfacilitating the nuclear and subnuclear localisation of photoreceptors andthe role these subnuclear bodies have in photoreceptor signalling,including to the oscillator. We will also highlight recent progress that hasbeen made in understanding the regulation of the nuclear andsubnuclear localisation of components of the plant circadian clock

Bacterial diversity of biofilm samples from deep mines in South Africa

The Au, Pt and diamond mines of South Africa provide access to microorganism bearing fluids emanating from fractures at depths ranging from 0.7 to 3.2 km. Due to the unique characteristic of mine environment as demonstrated by extreme pH, pressure, temperatureand/or salinity, it is anticipated that it could hold the promise for novel gene sequences and hence gene products of industrial and pharmaceutical importance. To provide insight into themicrobial diversity of mines in South Africa, biofilm samples were collected from Goldfield and diamond mines and their bacterial diversity determined using molecular approaches. 16S rRNA genes were amplified from DNA extracted from these samples using polymerase chain reaction with universal bacterial primers 27F (5’- AGA GTT TGA TCM TGG CTC AG-3’) and 1492R (5’- GGT TAC CTT GTT ACG ACT T-3’). Metagenomic clone libraries were constructed and restriction fragment length polymorphism (RFLP) analysis of >100 derivedclones resulted in four major restriction patterns from which 40 clones were chosen for sequencing. More than half (53%) of the sequences were affiliated with the bacterial phylum Proteobacteria, forty-one percent (41%) of the sequences with yet uncultured bacteria andthe phyla Firmicutes and Planctomycetes were accounted for by 4% and 2% of the sequences respectively. DGGE analysis of PCR-amplified 16S rRNA genes showed characteristic fingerprints for each sample. The differences in community structure observed account for the uniqueness of each of the mines with respect to its microbial diversity

Sequence of the hyperplastic genome of the naturally competent Thermus scotoductus SA-01

<p>Abstract</p> <p>Background</p> <p>Many strains of <it>Thermus </it>have been isolated from hot environments around the world. <it>Thermus scotoductus </it>SA-01 was isolated from fissure water collected 3.2 km below surface in a South African gold mine. The isolate is capable of dissimilatory iron reduction, growth with oxygen and nitrate as terminal electron acceptors and the ability to reduce a variety of metal ions, including gold, chromate and uranium, was demonstrated. The genomes from two different <it>Thermus thermophilus </it>strains have been completed. This paper represents the completed genome from a second <it>Thermus </it>species - <it>T. scotoductus</it>.</p> <p>Results</p> <p>The genome of <it>Thermus scotoductus </it>SA-01 consists of a chromosome of 2,346,803 bp and a small plasmid which, together are about 11% larger than the <it>Thermus thermophilus </it>genomes. The <it>T. thermophilus </it>megaplasmid genes are part of the <it>T. scotoductus </it>chromosome and extensive rearrangement, deletion of nonessential genes and acquisition of gene islands have occurred, leading to a loss of synteny between the chromosomes of <it>T. scotoductus and T. thermophilus</it>. At least nine large inserts of which seven were identified as alien, were found, the most remarkable being a denitrification cluster and two operons relating to the metabolism of phenolics which appear to have been acquired from <it>Meiothermus ruber</it>. The majority of acquired genes are from closely related species of the Deinococcus-Thermus group, and many of the remaining genes are from microorganisms with a thermophilic or hyperthermophilic lifestyle. The natural competence of <it>Thermus scotoductus </it>was confirmed experimentally as expected as most of the proteins of the natural transformation system of <it>Thermus thermophilus </it>are present. Analysis of the metabolic capabilities revealed an extensive energy metabolism with many aerobic and anaerobic respiratory options. An abundance of sensor histidine kinases, response regulators and transporters for a wide variety of compounds are indicative of an oligotrophic lifestyle.</p> <p>Conclusions</p> <p>The genome of <it>Thermus scotoductus </it>SA-01 shows remarkable plasticity with the loss, acquisition and rearrangement of large portions of its genome compared to <it>Thermus thermophilus</it>. Its ability to naturally take up foreign DNA has helped it adapt rapidly to a subsurface lifestyle in the presence of a dense and diverse population which acted as source of nutrients. The genome of <it>Thermus scotoductus </it>illustrates how rapid adaptation can be achieved by a highly dynamic and plastic genome.</p

Effects of four soil-originated Bacillus spp. on the great spruce bark beetle, Dendroctonus micans (Kugelann) (Coleoptera: Curculionidae, Scolytinae)

WOS: 000443093100001fifty bacterial cultures were isolated from 156 soil samples. In order to identify six bacteria in both systems, a fatty acid methyl ester (FAMEs) analysis was conducted, and carbon utilization profiles were assessed, using microbial identification, Biolog Microplac Systems, and the VITEK bacterial identification systems (bioMerieux, Prod. No. 21341 and 21342). Results showed that four species of Bacillus ssp., isolated from soil, were safe and efficient biological control agent for plant pests in Ordu, Turkey. These bacteria were Bacillus mycoides, B. cereus, B. thuringiensis, Paenibacillus validus, B. atrophaeus, and Arthrobacter globiformis. Laboratory tests were conducted to assess the potential of the isolates against the great spruce bark beetle, Dendroctonus micans (Kugelann) (Coleoptera: Curculionidae, Scolytinae) (Curculionidae, Scolytinae). Mortality rates of larvae and adults were 60 and 50%, 40 and 30%, and 80 and 70% when using B. mycoides, B. cereus, and B. thuringiensis, respectively. P. valid us, B. atrophaeus, and A. globiformis showed insufficient rates of mortality, 30 and 20% on the larvae and adults of D. micans, respectively. Also, these isolates had no antimicrobial effect on pathogen microorganisms. They have, however, a lethal effect on some insect groups that are agriculture and forest pests. The results indicated that the Bacillus isolates in question can be used as one of the biological control agent

Nematoda from the terrestrial deep subsurface of South Africa

Since its discovery over two decades ago, the deep subsurface biosphere has been considered to be the realm of single-cell organisms, extending over three kilometres into the Earth’s crust and comprising a significant fraction of the global biosphere1–4. The constraints of temperature, energy, dioxygen and space seemed to preclude the possibility of more-complex, multicellular organisms from surviving at these depths. Here we report species of the phylumNematoda that have been detected in or recovered from 0.9–3.6-kilometredeep fracture water in the deep mines of South Africa but have not been detected in the mining water. These subsurfacenematodes, including a new species, Halicephalobus mephisto, tolerate high temperature, reproduce asexually and preferentially feed upon subsurface bacteria. Carbon-14 data indicate that the fracture water in which the nematodes reside is 3,000–12,000-year-old palaeometeoric water. Our data suggest that nematodes should be found in other deep hypoxic settings where temperature permits, and that theymay control themicrobial population density by grazing on fracture surface biofilm patches. Our results expand the known metazoan biosphere and demonstrate that deep ecosystems are more complex than previously accepted. The discovery of multicellular life in the deep subsurface of the Earth also has important implications for the search for subsurface life on other planets in our Solar System