Eukaryotic picoplankton communities of the Mediterranean Sea in summer assessed by molecular approaches (DGGE, TTGE, QPCR)

The composition and abundance of eukaryotic picoplankton (defined here as cells smaller than 3 mum) was investigated in the Morocco upwelling and throughout the Mediterranean Sea in late summer using flow cytometry and molecular methods (gradient gel electrophoresis and quantitative PCR). The picoplankton displayed characteristics typical of oligotrophic oceanic areas with concentrations down to 1000 cells mL(-1) in the Eastern Basin. The most abundant eukaryotic sequences recovered by gradient gel electrophoresis were related to uncultivated marine groups: alveolates I (16%) and II (26%) and a newly discovered group (env Nansha, 17%) for which sequences have been recently obtained from the South China Sea and that could be related to Acantharians. Prasinophyceae (photosynthetic green algae) accounted for 10% of the sequences, whereas Cercozoa, Stramenopiles, Polycystinea, dinoflagellates and ciliates provided minor contributions. The use of quantitative PCR coupled with taxon-specific primers allowed us to estimate the relative abundance of several taxa belonging to the Prasinophyceae. Of the three genera assessed, Bathycoccus appeared as the most abundant, forming localized maxima at depth.     

Genetic diversity and paternal origin of domestic donkeys

Numerous studies have been conducted to investigate genetic diversity, origins and domestication of donkey using autosomal microsatellites and the mitochondrial genome, whereas the male‐specific region of the Y chromosome of modern donkeys is largely uncharacterized. In the current study, 14 published equine Y chromosome‐specific microsatellites (Y‐STR) were investigated in 395 male donkey samples from China, Egypt, Spain and Peru using fluorescent labeled microsatellite markers. The results showed that seven Y‐STRs—EcaYP9, EcaYM2, EcaYE2, EcaYE3, EcaYNO1, EcaYNO2 and EcaYNO4—were male specific and polymorphic, showing two to eight alleles in the donkeys studied. A total of 21 haplotypes corresponding to three haplogroups were identified, indicating three independent patrilines in domestic donkey. These markers are useful for the study the Y‐chromosome diversity and population genetics of donkeys in Africa, Europe, South America and China.     

Kinetic modulation of bacterial hydrolases by microbial community structure in coastal waters

In this study, we hypothesized that shifts in the kinetic parameters of extracellular hydrolytic enzymes may occur as a consequence of seasonal environmental disturbances and would reflect the level of adaptation of the bacterial community to the organic matter of the ecosystem. We measured the activities of enzymes that play a key role in the bacterial growth (leucine aminopeptidase, β- and α-glucosidases) in surface coastal waters of the Eastern Cantabrian Sea and determined their kinetic parameters by computing kinetic models of distinct complexity. Our results revealed the existence of two clearly distinct enzymatic systems operating at different substrate concentrations: a high-affinity system prevailing at low substrate concentrations and a low-affinity system characteristic of high substrate concentrations. These findings could be the result of distinct functional bacterial assemblages growing concurrently under sharp gradients of high-molecular-weight compounds. We constructed an ecological network based on contemporaneous and time-delayed correlations to explore the associations between the kinetic parameters and the environmental variables. The analysis revealed that the recurring phytoplankton blooms registered throughout the seasonal cycle trigger the wax and wane of those members of the bacterial community able to synthesize and secrete specific enzymes.     

The ability of natural tolerance to be applied to allogeneic tissue: determinants and limits

Background  

Transplant rejection has been considered to occur primarily because donor antigens are not present during the development of the recipient's immune system to induce tolerance. Thus, transplantation prior to recipient immune system development (pre-immunocompetence transplants) should induce natural tolerance to the donor. Surprisingly, tolerance was often not the outcome in such 'natural tolerance models'. We explored the ability of natural tolerance to prevent immune responses to alloantigens, and the reasons for the disparate outcomes of pre-immunocompetence transplants.     

Comparative analysis of bacterioplankton assemblages from maritime Antarctic freshwater lakes with contrasting trophic status

The bacterioplankton assemblages of eight maritime Antarctic lakes with a wide range of trophic status and geographic span (six lakes from Hope Bay, Antarctic Peninsula and two from Potter Peninsula, King George Island) were described using denaturing gradient gel electrophoresis and band sequencing during two consecutive austral summers (2003–2004). Analyses of the gels identified a total of 230 bands spread across 57 different positions. Among those bands, 14 were shared between lakes from Hope Bay and Potter Peninsula, 17 were observed only in particular lakes, and 17 were registered both years in the same lake. We successfully reamplified and sequenced 43 bands located in 36 different positions belonging to Bacteroidetes, Actinobacteria, Betaproteobacteria and Cyanobacteria. The closest matches for 63% of the sequenced bands were from Antarctic or from other cold environment clones and sequences already in the databases, suggesting the widespread dominance of microbial communities adapted to cold habitats. The results of the multivariate analyses (Cluster Analysis and CCA) indicated that the nutrient status of the lake influences the bacterioplankton assemblages. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Differential elimination of enteric bacteria by protists in a freshwater system

J. IRIBERRI, I. AZÚA, A. LABIRUA-ITURBURU, I. ARTOLOZAGA AND I. BARCINA. 1994. The short-term (1 h) and long-term (3 d) elimination of low and high densities of five enteric bacteria, Klebsiella pneumoniae, Aeromonas hydrophila, Escherichia coli, Enterococcus faecalis and Staphylococcus epidermidis, by flagellate and ciliate protists were measured in a freshwater system. In addition, the two processes, ingestion and digestion, which cause the disappearance of those enteric bacteria as time passes, were quantified.
The results showed that the elimination of these enteric bacteria by protists depends on their initial density, which confirms that the lower the bacterial density the more difficult is their elimination. On the other hand, the short-term and long-term elimination rates of each enteric bacteria were different, and moreover, the order of priority for elimination in the two cases was not the same. Escherichia coli showed the highest elimination rate in short-term experiments, while Aer. hydrophila disappeared at highest rates in long-term experiments. This different order of priority in the elimination rates and the different digestion rates on the five enteric bacteria by phagotrophic protists indicated that the elimination in time is very much influenced by the digestive capacity on each enteric bacteria of those protists. Thus, the low digestion rates of Ent. faecalis and Staph. epidermidis by flagellates and ciliates as well as their low disappearance percentages in the long-term experiments confirm that enteric Gram-positive bacteria are eliminated from the aquatic systems at lower rates, because their digestion is difficult.     

A structurally unique Fusobacterium nucleatum tannase provides detoxicant activity against gallotannins and pathogen resistance

Colorectal cancer pathogenesis and progression is associated with the presence of Fusobacterium nucleatum and the reduction of acetylated derivatives of spermidine, as well as dietary components such as tannin-rich foods. We show that a new tannase orthologue of F. nucleatum (TanBF_nn) has significant structural differences with its Lactobacillus plantarum counterpart affecting the flap covering the active site and the accessibility of substrates. Crystallographic and molecular dynamics analysis revealed binding of polyamines to a small cavity that connects the active site with the bulk solvent which interact with catalytically indispensable residues. As a result, spermidine and its derivatives, particularly N⁸-acetylated spermidine, inhibit the hydrolytic activity of TanBF_nn and increase the toxicity of gallotannins to F. nucleatum. Our results support a model in which the balance between the detoxicant activity of TanBF_nn and the presence of metabolic inhibitors can dictate either conducive or unfavourable conditions for the survival of F. nucleatum.     

Phylogenetic relationships and biogeography of Pseudoxiphophorus (Teleostei: Poeciliidae) based on mitochondrial and nuclear genes

Phylogenetic relationships of species of genus Pseudoxiphophorus have been only tackled in detail based on morphology so far. However, phylogenetic evidence based on molecular data is still lacking. In this study, we have used five molecular markers (mitochondrial cytb, 16S, atp6-8, and nuclear actB and S7) to reconstruct a robust, inclusive phylogeny of Pseudoxiphophorus. Our phylogenetic results strongly disagree with the main morphological hypothesis, and indicate different phylogenetic relationships among the recognized species of Pseudoxiphophorus. Pseudoxiphophorus jonesii is recovered as the sister group of all other Pseudoxiphophorus lineages, and this initial splitting may be associated to the extension of the Mexican Neovolcanic Plateau at the Punta del Morro site (event used to calibrate our dating analysis). The branch leading to all other Pseudoxiphophorus separated subsequently into two major groups, one comprising those lineages occurring in southern Mexico and Guatemala–Belize, and another with those lineages that extended further southwards to Honduras and Nicaragua. This event took place during the Pliocene, and is likely associated with periods of inundation of the Polochic–Motagua fault area. The Isthmus of Tehuantepec also appears to have been a strong biogeographic barrier triggering cladogenesis in Pseudoxiphophorus. Heterandria formosa (traditionally placed as sister to Pseudoxiphophorus) is not sharing the most recent common ancestor with Pseudoxiphophorus, and is recovered as more distantly related to them. Furthermore, Pseudoxiphophorus bimaculatus (the most cosmopolitan species) is also recovered as a polyphyletic assemblage that appears to comprise those Pseudoxiphophorus that have not been assigned to the other eight, more localized species. All this suggests that Pseudoxiphophorus needs a major taxonomic revision as a whole in order to incorporate all existing diversity.