Parasitic plant small RNA analyses unveil parasite-specific signatures of microRNA retention, loss, and gain

Parasitism is a successful life strategy that has evolved independently in several families of vascular plants. The genera Cuscuta and Orobanche represent examples of the two profoundly different groups of parasites: one parasitizing host shoots and the other infecting host roots. In this study, we sequenced and described the overall repertoire of small RNAs from Cuscuta campestris and Orobanche aegyptiaca. We showed that C. campestris contains a number of novel microRNAs (miRNAs) in addition to a conspicuous retention of miRNAs that are typically lacking in other Solanales, while several typically conserved miRNAs seem to have become obsolete in the parasite. One new miRNA appears to be derived from a horizontal gene transfer event. The exploratory analysis of the miRNA population (exploratory due to the absence of a full genomic sequence for reference) from the root parasitic O. aegyptiaca also revealed a loss of a number of miRNAs compared to photosynthetic species from the same order. In summary, our study shows partly similar evolutionary signatures in the RNA silencing machinery in both parasites. Our data bear proof for the dynamism of this regulatory mechanism in parasitic plants.MicroRNAs in parasitic plants reflect their lifestyle

Thermal acclimation of methanotrophs from the genus Methylobacter

Methanotrophs oxidize most of the methane (CH4) produced in natural and anthropogenic ecosystems. Often living close to soil surfaces, these microorganisms must frequently adjust to temperature change. While many environmental studies have addressed temperature effects on CH4 oxidation and methanotrophic communities, there is little knowledge about the physiological adjustments that underlie these effects. We have studied thermal acclimation in Methylobacter, a widespread, abundant, and environmentally important methanotrophic genus. Comparisons of growth and CH4 oxidation kinetics at different temperatures in three members of the genus demonstrate that temperature has a strong influence on how much CH4 is consumed to support growth at different CH4 concentrations. However, the temperature effect varies considerably between species, suggesting that how a methanotrophic community is composed influences the temperature effect on CH4 uptake. To understand thermal acclimation mechanisms widely we carried out a transcriptomics experiment with Methylobacter tundripaludum SV96T . We observed, at different temperatures, how varying abundances of transcripts for glycogen and protein biosynthesis relate to cellular glycogen and ribosome concentrations. Our data also demonstrated transcriptional adjustment of CH4 oxidation, oxidative phosphorylation, membrane fatty acid saturation, cell wall composition, and exopolysaccharides between temperatures. In addition, we observed differences in M. tundripaludum SV96T cell sizes at different temperatures. We conclude that thermal acclimation in Methylobacter results from transcriptional adjustment of central metabolism, protein biosynthesis, cell walls and storage. Acclimation leads to large shifts in CH4 consumption and growth efficiency, but with major differences between species. Thus, our study demonstrates that physiological adjustments to temperature change can substantially influence environmental CH4 uptake rates and that consideration of methanotroph physiology might be vital for accurate predictions of warming effects on CH4 emissions

Molecular biology and physiology of isolated chloroplasts from the algae Vaucheria

Sea slugs of the genus Elysia (e.g. E. chlorotica) are known for their ability to incorporate chloroplasts from the yellow-green alga Vaucheria litorea. These “kleptoplasts” stay active in the digestive tract of the sea slug for several months. Chloroplasts from Vaucheria litorea are also reported to be significantly more stable after in vitro isolation than chloroplasts of other algae or of higher plants. In organello assays with isolated chloroplasts are used in studies on photosynthetical and biochemical processes in these organelles, chloroplast-nucleus communication, plant development and plant responses to environmental changes. The major limiting factor of the chloroplast in organello systems is the rapid decline in function and intactness of the plastids. This study is investigating the stability and longevity of chloroplasts isolated from V. litorea and its relative V. bursata in comparison to an angiosperm Pisum sativum. The structural intactness of the chloroplasts was investigated by phase contrast microscopy and the overall transcriptional activities were analyzed by run-on transcription assays. The recently completed sequence of the plastid genome from V.litorea has made it possible to investigate also the specific changes in isolated chloroplasts on the transcriptional level. The expression patterns of chloroplast-encoded genes trnE, rrn23, rrn16, rbcL, psbD, psbA and psaA directly after isolation and 4 hours post-isolation time were analyzed using dot blot hybridization. The ability of isolated chloroplasts to incorporate 35S-methionine into de novo synthesized proteins at 0, 4 and 24 hours after isolation was tested by translational assays. The chloroplasts of Vaucheria litorea were both transcriptionally and translationally stable over an extended period of time. However, the culturing limitations and low plastid yields diminish the potential of this alga as a chloroplast donor for in organello assays. Chloroplasts of Pisum sativum, previously suspected to be more unstable, did not show a decline in transcription rate until 4 hours after isolation. The decrease in incorporation of 35S-methionine between time 0 and 4 hours after isolation was only minor, between 4 and 24 hours more significant but the radioactive signal was still readily detectable at 24 hours. Pisum sativum has simple growth requirements and offers high yields of isolated chloroplasts. Chloroplasts from this plant should therefore be in the centre of further investigations into their suitability to express foreign genes and their potential for in organello assays

Frenulate siboglinids at high Arctic methane seeps and insight into high latitude frenulate distribution

International audienceFrenulate species were identified from a high Arctic methane seep area on Vestnesa Ridge, western Svalbard margin (79°N, Fram Strait) based on mitochondrial cy-tochrome oxidase subunit I (mtCOI). Two species were found: Oligobrachia haakon-mosbiensis, and a new, distinct, and undescribed Oligobrachia species. The new species adds to the cryptic Oligobrachia species complex found at high latitude methane seeps in the north Atlantic and the Arctic. However, this species displays a curled tube morphology and light brown coloration that could serve to distinguish it from other members of the complex. A number of single tentacle individuals were recovered which were initially thought to be members of the only unitentaculate genus, Siboglinum. However, sequencing revealed them to be the new species and the single tentacle morphology, in addition to thin, colorless, and ringless tubes indicate that they are juveniles. This is the first known report of juveniles of northern Oligobrachia. Since the juveniles all appeared to be at about the same developmental stage, it is possible that reproduction is either synchronized within the species, or that despite continuous reproduction, settlement, and growth in the sediment only takes place at specific periods. The new find of the well-known species O. haakonmosbiensis extends its range from the Norwegian Sea to high latitudes of the Arctic in the Fram Strait. We suggest bottom currents serve as the main distribution mechanism for high latitude Oligobrachia species and that water depth constitutes a major dispersal barrier. This explains the lack of overlap between the distributions of northern Oligobrachia species despite exposure to similar current regimes. Our results point toward a single speciation event within the Oligobrachia clade, and we suggest that this occurred in the late Neogene, when topographical changes occurred and exchanges between Arctic and North Atlantic water masses and subsequent thermohaline circulation intensified

Old drug, new wrapping – A possible comeback for chloramphenicol?

The antimicrobial drug chloramphenicol (CAM) exhibits activity against resistant bacteria, such as methicillin-resistant Staphylococcus aureus (MRSA). However, its use has been limited due to its toxicity. As the threat of antibiotic resistance continues to grow, a promising approach might be to increase the use of historical antimicrobial agents that demonstrate clinical efficacy, but are hampered by toxicity. We therefore aimed to prepare a liposome-in-hydrogel system for dermal delivery of CAM. Chitosan (CS) was used as the hydrogel vehicle due to its antimicrobial activity and excellent biocompatibility. All critical preparation steps were carried out by dual centrifugation (DC). The DC-method proved to be fast and simple, and organic solvents were avoided in all processing steps. Liposomes with high drug entrapment (49–56%), low polydispersity and a size of approximately 120 nm were produced. Mixing of liposomes into CS-hydrogel by DC produced a homogenous liposomes-in-hydrogel system. Bioadhesive properties were good and comparable to plain CS-hydrogel formulations. Ex vivo permeation studies using pig skin indicated a sustained release of CAM and limited skin permeation. The in vitro antimicrobial activity of CAM in the new liposome-in-hydrogel formulation was similar or better as compared to CAM in solution. Thus, the new formulation was considered highly promising

Simultaneous Oxidation of Atmospheric Methane, Carbon Monoxide and Hydrogen for Bacterial Growth

The second largest sink for atmospheric methane (CH4) is atmospheric methane oxidizing-bacteria (atmMOB). How atmMOB are able to sustain life on the low CH4 concentrations in air is unknown. Here, we show that during growth, with air as its only source for energy and carbon, the recently isolated atmospheric methane-oxidizer Methylocapsa gorgona MG08 (USCα) oxidizes three atmospheric energy sources: CH4, carbon monoxide (CO), and hydrogen (H2) to support growth. The cell-specific CH4 oxidation rate of M. gorgona MG08 was estimated at ~0.7 × 10−18 mol cell−1 h−1, which, together with the oxidation of CO and H2, supplies 0.38 kJ Cmol−1 h−1 during growth in air. This is seven times lower than previously assumed necessary to support bacterial maintenance. We conclude that atmospheric methane-oxidation is supported by a metabolic flexibility that enables the simultaneous harvest of CH4, H2 and CO from air, but the key characteristic of atmospheric CH4 oxidizing bacteria might be very low energy requirements

Cuscuta campestris fine-tunes gene expression during haustoriogenesis as an adaptation to different hosts

The Cuscuta genus comprises obligate parasitic plants that have an unusually wide host range. Whether Cuscuta uses different infection strategies for different hosts or whether the infection strategy is mechanistically and enzymatically conserved remains unknown. To address this, we investigated molecular events during the interaction between field dodder (Cuscuta campestris) and two host species of the Solanum genus that are known to react differently to parasitic infection. We found that host gene induction, particularly of cell wall fortifying genes, coincided with a differential induction of genes for cell wall degradation in the parasite in the cultivated tomato (Solanum lycopersicum) but not in a wild relative (Solanum pennellii). This indicates that the parasite can adjust its gene expression in response to its host. This idea was supported by the increased expression of C. campestris genes encoding an endo-β-1,4-mannanase in response to exposure of the parasite to purified mono- and polysaccharides in a host-independent infection system. Our results suggest multiple key roles of the host cell wall in determining the outcome of an infection attempt

Draft Genome Sequence of Methylocapsa palsarum NE2T, an Obligate Methanotroph from Subarctic Soil.

Methylocapsa palsarum NE2T is an aerobic, mildly acidophilic, obligate methanotroph. Similar to other Methylocapsa species, it possesses only a particulate methane monooxygenase and is capable of atmospheric nitrogen fixation. The genome sequence of this typical inhabitant of subarctic wetlands and soils also contains genes indicative of aerobic anoxygenic photosynthesis