Draft genome of Pseudomonas stutzeri strain ZoBell (CCUG 16156), a marine isolate and model organism for denitrification studies

Pseudomonas stutzeri strain ZoBell, formerly a strain of Pseudomonas perfectomarina (CCUG 16156 = ATCC 14405), is a model organism for denitrification. It was isolated by ZoBell in 1944 from a marine sample, and here we report the first genome draft of a strain assigned to genomovar 2 of the species P. stutzeri.     

Pseudomonas putida KT2440 metabolism undergoes sequential modifications during exponential growth in a complete medium as compounds are gradually consumed

Pseudomonas putida is a soil bacterium with a versatile and robust metabolism. When confronted with mixtures of carbon sources, it prioritizes the utilization of the preferred compounds, optimizing metabolism and growth. This response is particularly strong when growing in a complex medium such as LB. This work examines the changes occurring in P. putida KT2440 metabolic fluxes, while it grows exponentially in LB medium and sequentially consumes the compounds available. Integrating the uptake rates for each compound at three different moments during the exponential growth with the changes observed in the proteome, and with the metabolic fluxes predicted by the iJN1411 metabolic model for this strain, allowed the metabolic rearrangements that occurred to be determined. The results indicate that the bacterium changes significantly the configuration of its metabolism during the early, mid and late exponential phases of growth. Sugars served as an energy source during the early phase and later as energy and carbon source. The configuration of the tricarboxylic acids cycle varied during growth, providing no energy in the early phase, and turning to a reductive mode in the mid phase and to an oxidative mode later on. This work highlights the dynamism and flexibility of P. putida metabolism.     

Simulated ungulate herbivory affects differently two herbivorous arthropod guilds in bilberry

Dense ungulate populations, both domestic and wild, accompanied by high grazing intensities, are known to have effects on the abundance and diversity of the community of arthropods hosted by plants. However, research combining ungulate herbivory with nutrient addition effects is scarce. By means of a nitrogen (N) addition and clipping experiment, we investigated the effects of both factors on the diversity, abundance and trophic structure of the arthropod community hosted by the bilberry, Vaccinium myrtillus, focusing on the response of herbivorous arthropods by considering leaf-chewers and sap-feeders separately. In addition, we assessed altitudinal variation on the arthropod community and also specifically on herbivores. Neither of the variables estimated for the arthropod community (total abundance, richness and biomass) were affected by simulated ungulate herbivory. However, clipping reduced the abundance of sap-feeders although had no significant effect on leaf-chewer insects. We therefore suggest that ungulates can compete with sap-feeders by reducing suitable food resources, or via changing plant nutritional state. Moreover, the lack of response on leaf-chewers could correspond with the absence of chemical defence in bilberry after repeated damage. Despite this effect on sap-feeder abundance, clipping did not cause a cascade effect on the trophic structure of the arthropod community associated with bilberry, at least in the short term. In turn, N fertilization at levels close to atmospheric N deposition did not cause any significant effect on the invertebrate community. Finally, the number of arthropod morphospecies and biomass decreased with altitude.     

ExpR is not required for swarming but promotes sliding in Sinorhizobium meliloti

Swarming is a mode of translocation dependent on flagellar activity that allows bacteria to move rapidly across surfaces. In several bacteria, swarming is a phenotype regulated by quorum sensing. It has been reported that the swarming ability of the soil bacterium Sinorhizobium meliloti Rm2011 requires a functional ExpR/Sin quorum-sensing system. However, our previous published results demonstrate that strains Rm1021 and Rm2011, both known to have a disrupted copy of expR, are able to swarm on semisolid minimal medium. In order to clarify these contradictory results, the role played by the LuxR-type regulator ExpR has been reexamined. Results obtained in this work revealed that S. meliloti can move over semisolid surfaces using at least two different types of motility. One type is flagellum-independent surface spreading or sliding, which is positively influenced by a functional expR gene mainly through the production of exopolysaccharide II (EPS II). To a lesser extent, EPS II-deficient strains can also slide on surfaces by a mechanism that is at least dependent on the siderophore rhizobactin 1021. The second type of surface translocation shown by S. meliloti is swarming, which is greatly dependent on flagella and rhizobactin 1021 but does not require ExpR. We have extended our study to demonstrate that the production of normal amounts of succinoglycan (EPS I) does not play a relevant role in surface translocation but that its overproduction facilitates both swarming and sliding motilities.     

Microtubule structure at 8 A resolution

We have obtained a 3D reconstruction of intact microtubules, using cryoelectron microscopy and image processing, at a resolution of about 8 A, sufficient to resolve much of the secondary structure. The level of detail in the map allows docking of the tubulin structure previously determined by electron crystallography, with very strong constraints, providing several important insights not previously available through docking tubulin into lower-resolution maps. This work provides an improved picture of the interactions between adjacent protofilaments, which are responsible for microtubule stability, and also suggests that some structural features are different in microtubules from those in the zinc sheets with which the tubulin structure was determined.     

A revised nomenclature for the human and rodent alpha-tubulin gene family

An essential component of microtubules, alpha-tubulin is also a multigene family in many species. An orthology-based nomenclature for this gene family has previously been difficult to assign due to incomplete genome builds and the high degree of sequence similarity between members of this family. Using the current genome builds, sequence analysis of human, mouse, and rat alpha-tubulin genes has enabled an updated nomenclature to be generated. This revised nomenclature provides a unified language for the discussion of these genes in mammalian species; it has been approved by the gene nomenclature committees of the three species and is supported by researchers in the field.     

Differential seed dispersal systems of endemic junipers in two oceanic Macaronesian archipelagos: the influence of biogeographic and biological characteristics

This article evaluates the seed dispersal systems of two congeneric and endemic fleshy-fruited plants in the context of two relatively close oceanic archipelagos. For this purpose, representative populations of the endangered junipers Juniperus cedrus in the Canary Islands and Madeira, and Juniperus brevifolia in the Azores were studied. Despite both species sharing the same biogeographic region, we set out to test whether different conditions of the islands and biological characteristics of each juniper species determine the distinctive guilds of seed dispersers involved. We assessed the quantitative and qualitative role of the potential frugivores, showing that the wintering Turdus torquatus and the native Turdus merula were the main seed dispersers for J. cedrus and J. brevifolia, respectively (Frequency of occurrence: 74.9%, 80.2%; germination increase with respect to controls: 11.6%, 15.5%; for J. cedrus and J. brevifolia, respectively). The endemic lizard Gallotia galloti was quantitatively outstanding as seed disperser of J. cedrus, although its qualitative effect does not appear to be beneficial. The introduced rabbit Oryctolagus cuniculus acts as a disruptor in both natural seed dispersal systems, as inferred from the high percentage of damaged seeds found in their droppings. Our results indicate that J. cedrus and J. brevifolia are primarily adapted to ornithochory processes, T. torquatus and T. merula being their respective legitimate long-distance dispersers. Although these birds should be playing a key role in the connectivity of fragmented populations, the dependence of J. cedrus on a migrant bird involves a notable fragility of the system.