Microbial and nematode communities associated with potatoes genetically modified to express the antimicrobial peptide magainin and unmodified potato cultivars

The antimicrobial peptide magainin II has activity against a range of micro-organisms. Tubers harvested from potatoes genetically modified (GM) to express a synthetic magainin gene show improved resistance to the bacterial pathogen Erwinia carotovora. The microbial and nematode communities associated with three magainin-expressing potato lines, their near-isogenic, unmodified parental cultivar (Iwa) and an unrelated cultivar (Karaka) were investigated on field-grown plants. Heterotrophic plate counts were used to enumerate aerobic culturable bacterial and fungal populations, while cultivation-independent analysis of bacterial communities was based on denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments amplified from community DNA from phyllosphere, rhizosphere and geocaulosphere (tuber surface) samples. Small but statistically significant differences in the population sizes of culturable bacteria, fungi and yeast were detected among some GM magainin-expressing lines and the unmodified control. However, these differences were typically smaller than the differences between the unmodified parental line control (Iwa) and the unrelated cultivar control (Karaka). Similarly, the difference in the proportion of the nematode population belonging to the fungal feeding trophic group between Iwa and Karaka was greater than that amongst Iwa and its near-isogenic GM lines, and was significantly so for the genus Aphelenchus. The nematode channel ratio (NCR) indicated a more fungal-dominated decomposition channel in soil beneath Karaka compared to Iwa at harvest. In general, eubacterial phylloplane communities were similar for all lines, while the rhizosphere communities associated with two of the three GM lines differed from communities associated with their unmodified parental line control. When roots were senescent, there was no significant difference among potato lines in rhizosphere eubacterial communities or individual trophic groups of the nematode community. Greater diversity was found in geocaulosphere; α-proteobacteria and actinomycete communities of two of the three GM lines differed significantly from their unmodified parental line control and the unrelated cultivar control, while the communities associated with the third GM line were more similar to those of the two control lines. This highlights the importance of testing several GM lines when assessing non-target effects. Results suggest that there is little likelihood of any major sustained non-target effect of genetic modification using a magainin II transgene on plant-associated and soil microflora and function.     

Sampling the antibiotic resistome

Microbial resistance to antibiotics currently spans all known classes of natural and synthetic compounds. It has not only hindered our treatment of infections but also dramatically reshaped drug discovery, yet its origins have not been systematically studied. Soil-dwelling bacteria produce and encounter a myriad of antibiotics, evolving corresponding sensing and evading strategies. They are a reservoir of resistance determinants that can be mobilized into the microbial community. Study of this reservoir could provide an early warning system for future clinically relevant antibiotic resistance mechanisms.     

Isotopic criteria in the characterization of aromatic molecules. 2. Influence of the chemical elaboration process

Most valued natural aromatic molecules can be substituted by their low-cost chemical counterparts. Isotopic methods, which offer the most powerful tool to infer the origin of a molecule, are applied to the characterization of a large number of chemical aromatic species. Isotopic affiliation between precursors and products is investigated in several types of reactions: oxidation of benzyl chloride and benzyl alcohol and hydrolysis of benzylidene chloride and cinnamaldehyde. The isotopic parameters strongly depend not only on the type of process but, for a given process, on the experimental conditions of the reaction. Kinetic isotope effects occurring in several formylation reactions are estimated. It is shown that, in the drastic experimental conditions of many industrial processes, the benzenic hydrogen atoms may be affected by exchange phenomena. Consequently, the site-specific isotopic parameters of the ring fragment of chemical species are usually much less stable than those of the corresponding natural molecules biosynthesized in mild environments. The isotope ratios of substituents such as CH3, CH2Cl, and CHO are more resistant to exchange and provide useful criteria for characterizing both the raw materials and the process. It is shown in particular that radical hydrogen abstraction in toluene to produce benzyl chloride induces relatively moderate fractionation effects. In contrast, oxidation reactions frequently produce strong fractionation effects. In particular, industrial direct oxidation of toluene into benzaldehyde is characterized by deuterium enrichments at the formyl site, which may exceed 900 ppm. Taking into account the large magnitude and high variability of many fractionation effects occurring in chemical reactions, the isotopic fingerprint may provide unambiguous criteria, not only for excluding a natural origin and characterizing the type of process, but also for differentiating molecules synthesized by a given process in different industrial contexts. The isotopic fingerprint may therefore be used by manufacturers as a powerful label for characterizing their production batches.     

Isotopic criteria in the characterization of aromatic molecules. 1. Hydrogen affiliation in natural benzenoid/phenylpropanoid molecules

The site-specific isotope ratios of several families of aromatic molecules are analyzed in terms of hydrogen affiliation and discriminating potential. Among the aromatic molecules produced by plants, many are biosynthesized by the shikimate pathway, but the terpenic pathway also forms some compounds with a benzenic ring. In compounds of the phenylpropanoid family, specific hydrogen connections are determined with cinnamic acid, a key intermediate in the formation of a large number of aromatic molecules. Then affiliations through the phenylalanine precursor, back to the parent d-erythrose 4-phosphate and phosphoenolpyruvate molecules and finally to glucose, are considered. Typical isotopic profiles of the benzenic ring in natural, as compared to non-natural, molecules are defined. The dispersion observed in the (D/H)i ratios of the lateral chains is illustrative of diverse mechanistic responses and the role of exchange phenomena. The isotopic patterns of aromatic molecules pertaining to the terpenic family are drastically different from those of the shikimate descendants, and they exhibit much less variability. They enable the stereochemical affiliation of individual hydrogen atoms to be traced back first to the parent atoms in the common intermediate, geranyl diphosphate, then to the glyceraldehyde 3-phosphate and pyruvate couple involved in the DOXP pathway, and ultimately to the glucose precursor. The results illustrate the aptitude of the site-specific isotope ratios not only to authenticate natural with respect to chemical molecules but also to characterize different metabolic pathways and to reveal differences associated with the nature of the plant precursor.     

Absorption of anthocyanins from blueberry extracts by caco-2 human intestinal cell monolayers

Recent studies have shown that dietary polyphenols may contribute to the prevention of cardiovascular disease and cancer. Anthocyanins from different plant sources including blueberries have been shown to possess potential anticancer activities. One of the key factors needed to correctly relate the in vitro study results to human disease outcomes is information about bioavailability. The objectives of the current study were to evaluate the absorption of blueberry anthocyanin extracts using Caco-2 human intestinal cell monolayers and investigate the effects of different aglycones, sugar moieties, and chemical structure on bioavailability of different types of anthocyanins. The results of this study showed that anthocyanins from blueberries could be transported through the Caco-2 cell monolayers although the transport/absorption efficiency was relatively low compared to other aglycone polyphenols. The transport efficiency of anthocyanins averaged approximately 3-4% [less than 1% in delphinidin glucoside (Dp-glc)]. No significant difference in transport/absorption efficiency was observed among three blueberry cultivars. The observed trends among different anthocyanins generally agreed well with some published in vivo results. Dp-glc showed the lowest transport/absorption efficiency, and malvidin glucoside (Mv-glc) showed the highest transport/absorption efficiency. Our result indicates that more free hydroxyl groups and less OCH(3) groups can decrease the bioavailability of anthocyanins. In addition, cyanindin glucoside (Cy-glc) showed significantly higher transport efficiency than cyanidin galactoside (Cy-gal), and peonidin glucoside (Pn-glc) showed significantly higher transport efficiency than peonidin galactoside (Pn-gal), indicating that glucose-based anthocyanins have higher bioavailability than galactose-based anthocyanins.     

Effect of fishing effort on catch rate and catchability of largemouth bass in small impoundments

Largemouth bass Micropterus salmoides (Lacepède) catch rates decline with sustained fishing effort, even without harvest. It is unclear why declines in catch rate occur, and little research has been directed at how to improve catch rate. Learning has been proposed as a reason for declining catch rate, but has never been tested on largemouth bass. If catch rate declines because fish learn to avoid lures, periods of no fishing could be a management tool for increasing catch rate. In this study, six small impoundments with established fish populations were fished for two May to October fishing seasons to evaluate the effect of fishing effort on catch rate. Closed seasons were implemented to test whether a 2‐month period of no fishing improved catch rates and to determine whether conditioning from factors other than being captured reduced catch rate. Mixed‐model analysis indicated catch rate and catchability declined throughout the fishing season. Catch rate and catchability increased after a 2‐month closure but soon declined to the lowest levels of the fishing season. These changes in catch rate and catchability support the conclusion of learned angler avoidance, but sustained catchability of fish not previously caught does not support that associative or social learning affected catchability.     

Effects of food supply and stream physical characteristics on habitat use of a stream‐dwelling fish

Identifying the environmental factors that affect freshwater fish can be crucial for their conservation and management. Despite the widespread investigation of relationships between fish habitat use and environmental variables, there is a paucity of knowledge on how abiotic and biotic factors jointly influence stream fish habitat use. Three New Zealand South Island streams were selected to investigate the habitat preference of a stream‐dwelling galaxiid, banded kokopu (Galaxias fasciatus). Fish abundance in several permanent pools was determined by spotlighting at night once a month from June 2008 to May 2009. Drifting invertebrates and key physical features of each pool were measured at the time of fish sampling. An information‐theoretic approach (AIC) indicated that the most parsimonious candidate model to predict banded kokopu biomass was the one that included pool area, undercut banks, water velocity, overhanging vegetation, invertebrate drift density and an interaction term between invertebrate drift density and water velocity. Banded kokopu biomass was positively related to pool area, undercut banks, overhanging vegetation and invertebrate drift density. Our study suggests that fish resource use patterns need to be understood in the context of multiple interacting ecological factors, including prey abundance.     

Characterizing larval swordfish habitat in the western tropical North Atlantic

Swordfish Xiphias gladius (Linnaeus, 1758) are a circumglobal pelagic fish targeted by multiple lucrative fisheries. Determining the distribution of swordfish larvae is important for indicating reproductive activity and understanding the early life history of swordfish. We identify and characterize larval swordfish distributions during peak swordfish spawning throughout the Gulf of Mexico and western Caribbean Sea with generalized additive models (GAMs) using catches of swordfish larvae during ichthyoplankton surveys in April and May of 2010, 2011, and 2012. The best fit GAM, as determined by stepwise, backward Akaike Information Criterion selection, included both physiochemical (temperature at 5 m, sea surface height anomaly (SSHA), eddy kinetic energy (EKE)), temporal (lunar illumination, hour of sampling) and spatial (location) variables, while near surface chlorophyll a concentration residuals remained as a random effect. The highest probability of larval swordfish catch occurred at sub‐surface temperatures, SSHA, and EKE values indicative of boundary currents. Standard lengths of larvae were larger further downstream in the boundary currents, despite high variability in length with location due to multiple spawning locations of swordfish near these currents. Probability of larval swordfish catch also peaked during the crescent and gibbous moons, indicating a lunar periodicity to swordfish spawning. These results suggest that swordfish may spawn during select moon phases near boundary currents that transport their larvae to larval and juvenile habitat including the northern Gulf of Mexico and coastal waters of the southeast United States.     

Long-term P fertilisation of pasture soil did not increase soil organic matter stocks but increased microbial biomass and activity

The soil organic matter (OM) content of soils in a long-term fertiliser field trial (Winchmore, New Zealand) are similar (P > 0.05) despite >60 years application of different phosphorus (P) rates. As the net primary productivity increased with P addition, greater losses of carbon (C) occur concomitantly with increased P fertility. Several hypotheses have been proposed to explain the mechanisms, including C leaching, increased earthworm activity or elevated rates of microbial activity. In this study, we found support for both direct and secondary effects of soil P on soil C through impacts on the soil microbial community. Microbial biomass, inferred through quantification of hot water extractable C, increased with soil P status and decreased with C/P ratio (P < 0.001). However, the microbial biomass had no relationship with soil organic C content (P = 0.485). Mineralisation of C substrates added to soil also increased with soil P status (total P, R ² = 0.84; P < 0.001). These results indicated potential conditioning of the microbial community for rapid C cycling. Utilisation of different C compounds was clustered by cophenetic similarity; a distinct group of ten carbon compounds was identified for which rates of mineralisation were strongly associated with soil P status and microbial biomass. However, this alteration of microbial community size and activity was not reflected in abundances of selected oligotrophic and copiotrophic taxa. As such, the alteration may be due to changes in the abundances of all taxa, i.e. a general community response.