Spatial patterns of plant diversity below-ground as revealed by DNA barcoding

Our understanding of the spatial organization of root diversity in plant communities and of the mechanisms of community assembly has been limited by our ability to identify plants based on root tissue, especially in diverse communities. Here, we test the effectiveness of the plastid gene rbcL, a core plant DNA barcoding marker, for investigating spatial patterns of root diversity, and relate observed patterns to above-ground community structure. We collected 3800 root fragments from four randomly positioned, 1-m-deep soil profiles (two vertical transects per plot), located in an old-field community in southern Ontario, Canada, and extracted and sequenced DNA from 1531 subsampled fragments. We identified species by comparing sequences with a DNA barcode reference library developed previously for the local flora. Nearly 85% of sampled root fragments were successfully sequenced and identified as belonging to 29 plant species or species groups. Root abundance and species richness varied in horizontal space and were negatively correlated with soil depth. The relative abundance of taxa below-ground was correlated with their frequency above-ground (r = 0.73, P = 0.0001), but several species detected in root tissue were not observed in above-ground quadrats. Multivariate analyses indicated that diversity was highly structured below-ground, and associated with depth, root morphology, soil chemistry and soil texture, whereas little structure was evident above-ground. Furthermore, analyses of species co-occurrence indicates strong species segregation overall but random co-occurrence among confamilials. Our results provide insights into the role of environmental filtering and competitive interactions in the organization of plant diversity below-ground, and also demonstrate the utility of barcoding for the identification of plant roots.     

Root-Zone-Specific Oxygen Tolerance of Azospirillum spp. and Diazotrophic Rods Closely Associated with Kallar Grass

The effect of oxygen on N₂-dependent growth of two Azospirillum strains and two diazotrophic rods closely associated with roots of Kallar grass (Leptochloa fusca) was studied. To enable precise comparison, bacteria were grown in dissolved-oxygen-controlled batch and continuous cultures. Steady states were obtained from about 1 to 30 μM O₂, some of them being carbon limited. All strains needed a minimum amount of oxygen for N₂-dependent growth. Nitrogen contents between 10 and 13% of cell dry weight were observed. The response of steady-state cultures to increasing O₂ concentrations suggested that carbon limitation shifted to internal nitrogen limitation when N₂ fixation became so low that the bacteria could no longer meet their requirements for fixed nitrogen. For Azospirillum lipoferum Rp5, increase of the dilution rate resulted in decreased N₂ fixation in steady-state cultures with internal nitrogen limitation. Oxygen tolerance was found to be strain specific in A. lipoferum with strain Sp59b as a reference organism. Oxygen tolerance of strains from Kallar grass was found to be root zone specific. A. halopraeferens Au 4 and A. lipoferum Rp5, predominating on the rhizoplane of Kallar grass, and strains H6a2 and BH72, predominating in the endorhizosphere, differed in their oxygen tolerance profiles. Strains H6a2 and BH72 still grew and fixed nitrogen in steady-state cultures at O₂ concentrations exceeding those which absolutely inhibited nitrogen fixation of both Azospirillum strains. It is proposed that root-zone-specific oxygen tolerance reflects an adaptation of the isolates to the microenvironments provided by the host plant.     

Lack of PPARγ in myeloid cells confers resistance to Listeria monocytogenes infection

The peroxisomal proliferator-activated receptor γ (PPARγ) is a nuclear receptor that controls inflammation and immunity. Innate immune defense against bacterial infection appears to be compromised by PPARγ. The relevance of PPARγ in myeloid cells, that organize anti-bacterial immunity, for the outcome of immune responses against intracellular bacteria such as Listeria monocytogenes in vivo is unknown. We found that Listeria monocytogenes infection of macrophages rapidly led to increased expression of PPARγ. This prompted us to investigate whether PPARγ in myeloid cells influences innate immunity against Listeria monocytogenes infection by using transgenic mice with myeloid-cell specific ablation of PPARγ (LysMCre×PPARγ(flox/flox)). Loss of PPARγ in myeloid cells results in enhanced innate immune defense against Listeria monocytogenes infection both, in vitro and in vivo. This increased resistance against infection was characterized by augmented levels of bactericidal factors and inflammatory cytokines: ROS, NO, IFNγ TNF IL-6 and IL-12. Moreover, myeloid cell-specific loss of PPARγ enhanced chemokine and adhesion molecule expression leading to improved recruitment of inflammatory Ly6C(hi) monocytes to sites of infection. Importantly, increased resistance against Listeria infection in the absence of PPARγ was not accompanied by enhanced immunopathology. Our results elucidate a yet unknown regulatory network in myeloid cells that is governed by PPARγ and restrains both listeriocidal activity and recruitment of inflammatory monocytes during Listeria infection, which may contribute to bacterial immune escape. Pharmacological interference with PPARγ activity in myeloid cells might represent a novel strategy to overcome intracellular bacterial infection.     

Subtracted restriction fingerprinting--a tool for bacterial genome typing

Reproducible, discriminative, high-throughput methods are required for the identification of bacterial strains and isolates in a clinical environment. A new molecular typing method for bacteria was developed and tested on Salmonella and E. coli species. The technique is called subtracted restriction fingerprinting and is based on double restriction enzyme digestion of genomic DNA followed by end labeling. The "detection" enzyme produces TTAA overhangs that are filled in with digoxigenated nucleotides for subsequent detection, while the "subtraction" enzyme produces GCGC overhangs that are filled in with biotinylated nucleotides that permit the removal of this subset of fragments with either streptavidin-coated magnetic particles or AffiniTip streptavidin columns. The two restriction enzymes are selected to produce a fragment size profile suitable for a specific analytical system. In this demonstration of the principle of subtracted restriction fingerprinting, analysis of Salmonella enterica subsp. enterica serovar Dublin and E. coli on a 30-cm 1.2% agarose gel revealed up to 50 sharp evenly spaced bands, which were sufficient for the discrimination between various isolates and substrains. The restriction enzyme combinations suitable for the analysis of Salmonella and E. coli are presented. The method requires fewer enzymatic steps than amplified fragment length polymorphism, does not need the specialized DNA preparation essential for pulsed field gel electrophoresis, and has a higher reproducibility than PCR-based methods.     

Synthesis of 3-phenylsulfonylmethyl cyclohexylaminobenzamide-derived antagonists of CC chemokine receptor 2 (CCR2)

We report the synthesis of 3-phenylsulfonylmethyl cyclohexylaminobenzamides (4) as CCR2 inhibitors for the potential treatment of inflammatory diseases. Several of the compounds display nanomolar binding affinity for CCR2. The in vitro structure-activity relationships of 4 are described, and are also reconciled with those from the related 2-phenylsulfonylmethyl series.     

Seasonal changes in organic composition and caloric content of an Arctic marine amphipod, Onisimus (= Boeckosimus) affinis H.J. Hansen

Protein, lipid, carbohydrate, chitin, ash, and caloric energy contents of the Arctic marine benthic amphipod Onisimus (= Boeckosimus) affinis H.J. Hansen were determined at intervals over two and one half years. The lipid content exhibited the most pronounced seasonal change, from a minimum of about 14–17% of dry wt to a maximum of 25–27% of dry wt. An increase in lipid content in the spring coincided with the reproductive period of the species. Lipid and caloric content decreased during the summer to levels that were maintained through the winter, indicating that the animals do not store significant nutritional reserves for use during the winter. The dry weight proportions of other components were: protein 27.7–38.3%; carbohydrate 1.8–4.0%; chitin 7.8–8.2%; ash 21.3–27.2%. Caloric content varied between 3.29 and 4.18 cal/mg dry wt.     

Use of autonomous audio recordings for the rapid inventory of birds in the white‐sand forests of the Peruvian Amazon

White‐sand forests are patchily distributed ecosystems covering just 5% of Amazonia that host many specialist species of birds not found elsewhere, and these forests are threatened due to their small size and human exploitation of sand for construction projects. As a result, many species of birds that are white‐sand specialists are at risk of extinction, and immediate conservation action is paramount for their survival. Our objective was to evaluate current survey methods and determine the relative effect of the size of patches of these forests on the presence or absence of white‐sand specialists. Using point counts and autonomous recorders, we surveyed avian assemblages occupying patches of white‐sand forest in the Peruvian Amazon in April 2018. Overall, we detected 126 species, including 21 white‐sand forest specialists. We detected significantly more species of birds per survey point with autonomous recorders than point counts. We also found a negative relationship between avian species richness and distance from the edge of patches of white‐sand forest, but a significant, positive relationship when only counting white‐sand specialists. Although we detected more species with autonomous recorders, point counts were more effective for detecting canopy‐dwelling passerines. Therefore, we recommend that investigators conducting surveys for rare and patchily distributed species in the tropics use a mixed‐method approach that incorporates both autonomous recorders and visual observation. Finally, our results suggest that conserving large, continuous patches of white‐sand forest may increase the likelihood of survival of species of birds that are white‐sand specialists.     

Increase of circulating beta-endorphin-like immunoreactivity correlates with the change in feeling of pleasantness after running

Twenty-one male regular long distance runners participated in two 10 km runs one week apart. Their beta-endorphin-like immunoreactivity (beta-EIR) was assayed in plasma before and immediately after running. Mood was monitored by an adjective check list (Eigenschaftsw?rterliste, EWL) pre- and post-run. beta-EIR was significantly elevated post-run. Self-reliance and good mood scored higher after running. Both mood elevation and plasma beta-EIR increase showed a considerable individual variability but there was a significant correlation in the mean values of the two runs between individual beta-EIR increases (delta beta-EIR) and the changes of ratings in feeling of pleasantness (delta FP). High delta beta-EIR corresponded to positive mood change post-run.     

Ecological physiology of arctic marine invertebrates. Temperature and salinity relationships of the amphipod Onisimus affinis H. J. Hansen

Effects of temperature and salinity upon the survival, locomotion and metabolism of the Arctic marine amphipod Onisimus affinis H. J. Hansen have been investigated. The LD₅₀ for temperature is ≈ 18.7 °C. The metabolic rate-temperature curve shows a distinct plateau of relative temperature insensitivity the position of which varies seasonally to include a lower temperature range in winter than in summer. Similar shifts in the plateau can be induced in the laboratory by acclimating the animals at summer- and winter-like temperatures.Optimal locomotory activity was between 5° and 8 °C and included a combination of swimming and crawling. Above 12 °C the swimming component was increasingly inhibited.Onisimus is euryhaline and appears to be most successful in brackish water habitats. It tolerates elevated salinities better at low temperatures. The metabolic rate varies inversely with salinity during short-term exposures, but, if the animals are pre-adapted to the experimental salinities for 10 days, the metabolic rate is essentially independent of salinity between 10%. and 25%.The significance of these physiological responses in relation to the general ecology of the species is discussed.