Taxonomic and Functional Metagenomic Profiling of the Microbial Community in the Anoxic Sediment of a Sub-saline Shallow Lake (Laguna de Carrizo, Central Spain)

The phylogenetic and functional structure of the microbial community residing in a Ca(2+)-rich anoxic sediment of a sub-saline shallow lake (Laguna de Carrizo, initially operated as a gypsum (CaSO(4)?×?2 H(2)O) mine) was estimated by analyzing the diversity of 16S rRNA amplicons and a 3.1?Mb of consensus metagenome sequence. The lake has about half the salinity of seawater and possesses an unusual relative concentration of ions, with Ca(2+) and SO (4) (2-) being dominant. The 16S rRNA sequences revealed a diverse community with about 22% of the bacterial rRNAs being less than 94.5% similar to any rRNA currently deposited in GenBank. In addition to this, about 79% of the archaeal rRNA genes were mostly related to uncultured Euryarchaeota of the CCA47 group, which are often associated with marine and oxygen-depleted sites. Sequence analysis of assembled genes revealed that 23% of the open reading frames of the metagenome library had no hits in the database. Among annotated genes, functions related to (thio) sulfate and (thio) sulfonate-reduction and iron-oxidation, sulfur-oxidation, denitrification, synthrophism, and phototrophic sulfur metabolism were found as predominant. Phylogenetic and biochemical analyses indicate that the inherent physical-chemical characteristics of this habitat coupled with adaptation to anthropogenic activities have resulted in a highly efficient community for the assimilation of polysulfides, sulfoxides, and organosulfonates together with nitro-, nitrile-, and cyanide-substituted compounds. We discuss that the relevant microbial composition and metabolic capacities at Laguna de Carrizo, likely developed as an adaptation to thrive in the presence of moderate salinity conditions and potential toxic bio-molecules, in contrast with the properties of previously known anoxic sediments of shallow lakes.     

Effects of topography and crown-exposure on olive tree phenology

The importance of the olive tree phenology from agricultural and ecological point of view justifies the need to carry out phenological studies at local and regional scales. Furthermore, flowering phenology in the olive tree (Olea europaea L.) is an important indicator of climatic change in the Mediterranean region. In this paper, we study the effects of altitude and the exposure of crown-flowering branches on the flowering phenology of the olive tree. The study was carried out from 2009 to 2012 at eight sites of Cornicabra olive cultivar in central Spain (Toledo province, Castilla-La Mancha region), at altitudes between 440 and 875 m above sea level, since most olive groves in central Spain are to be found in this altitude range. Flowering phenology was also compared in two olive groves located at the same site and elevation; one in a flat area and the other on a north-facing hillside. Results revealed a significant correlation between altitude and flowering start-date: for each 100 m increase in altitude, flowering started 2.5 days later. Analysis of individual flowering branches of the same tree showed that preflowering and flowering started several days later on north-facing compared to south-facing branches. Olive trees growing on a north-facing hillside started the preflowering stage with some delay with respect to those growing in flat areas. Finally, taking onset of flowering as the variable, a hierarchical cluster analysis enabled olive-groves to be classified by flowering sequence across an altitudinal gradient.     

Solanesyl Diphosphate Synthase,an Enzyme of the Ubiquinone Synthetic Pathway,Is Required throughout the Life Cycle of Trypanosoma brucei

Ubiquinone 9 (UQ9), the expected product of the long-chain solanesyl diphosphate synthase of Trypanosoma brucei (TbSPPS), has a central role in reoxidation of reducing equivalents in the mitochondrion of T. brucei. The ablation of TbSPPS gene expression by RNA interference increased the generation of reactive oxygen species and reduced cell growth and oxygen consumption. The addition of glycerol to the culture medium exacerbated the phenotype by blocking its endogenous generation and excretion. The participation of TbSPPS in UQ synthesis was further confirmed by growth rescue using UQ with 10 isoprenyl subunits (UQ10). Furthermore, the survival of infected mice was prolonged upon the downregulation of TbSPPS and/or the addition of glycerol to drinking water. TbSPPS is inhibited by 1-[(n-oct-1-ylamino)ethyl] 1,1-bisphosphonic acid, and treatment with this compound was lethal for the cells. The findings that both UQ9 and ATP pools were severely depleted by the drug and that exogenous UQ10 was able to fully rescue growth of the inhibited parasites strongly suggest that TbSPPS and UQ synthesis are the main targets of the drug. These two strategies highlight the importance of TbSPPS for T. brucei, justifying further efforts to validate it as a new drug target.     

Lack of pattern among phytoplankton assemblages. Or,what does the exception to the rule mean?

In Science we cannot say that `the exception proves the rule'. We have been looking to define patterns in phytoplankton occurrence across trophic spectra where conspicuous covariations between algae and trophic states have been reported. We consider quite different phytoplankton communities observed under similar trophic conditions: we illustrate this point by considering five different phytoplankton communities living in five water bodies in the same wetland, along a TP gradient and over a period of 2 years. This system showed a remarkable dissimilarity of species representation, implying communities of uncorrelated species vary considerably over time. Despite the presence of some characteristic species, communities were not related to a given trophic state. However, coarser community attributes, such as clusters of taxonomic classes, appeared to be more useful in identifying patterns and assembly rules related to trophic spectra. Some ecological concepts can be related to this lack of pattern, e.g., nonconvergence, trajectories far from equilibrium and assembly rules of communities.     

Spatial, seasonal and long-term variability of phytoplankton photosynthesis in lakes

A cross-system, worldwide approach has been used to ascertainthe spatial, seasonal and long-term variability of areal phytoplanktonphotosynthesis (PP) in lakes using published data sets. Also,the average fraction of annual PP occurring under ice is calculated.The lakes considered embrace a range of properties (depth, mixing,flushing rate, latitude and trophic status). The overall yearlyPP distribution is skewed to the left, suggesting the dominanceof low PP rates in the data set. When comparing lake types,no differences in average PP have been found among them. Inparticular, there are no clear areal PP differences among lakesof different trophic status on yearly, averaged basis, suggestingthat environmental limitations to PP also exist in lakes ofhigher trophic status. Volumetric-based PP can be better usedto outline PP-based trophic differences, but some degree ofoverlap is also apparent. Across all lake types (except in tropicallakes), the PP seasonal course experiences only one peak inthe year, but its timing is clearly different for each laketype. The seasonal variability of PP is lower in tropical lakes,as previously reported, but the variability of the other laketypes is roughly the same. Therefore, the effects of depth,mixing regime, flushing rate and nutrient status on PP seasonalityare difficult to ascertain since they appear to be counterbalancedby other more pervasive, local effects. Particularly, thereis no increase in temporal variability with the trophic statusof lakes, suggesting that PP seasonal control by physical variablesoverrides that of nutrients. Also, no significant relationshipbetween average PP and latitude has been found. Seasonal variabilityincreases as the yearly PP increases. On a relative basis, thereis a spatial gradient of seasonal variability of PP, which isweaker when seasonal variability of PP is considered in interyearcomparisons. Long-term (i.e. interannual) variability of PPis clearly related to increasing yearly averaged PP. Specifically,in temperate, stratifying lakes the seasonal time course ofPP is clearly different from that of phytoplankton biomass,suggesting an uncoupling of both variables as a result of differingP_max and losses throughout the year. On an average basis, environmentalvariables are poor predictors of areal daily PP, thereby implyingthat the interplay of factors is complex and changing throughoutthe year. PP under ice averages 10% of yearly PP, but its variabilityis high enough to make its measurement advisable.     

Structure and diversity of HLA-B27-specific T cell epitopes. Analysis with site-directed mutants mimicking HLA-B27 subtype polymorphism.

HLA-B27 subtype polymorphism is amenable to differential recognition by CTL. Site-directed mutagenesis was used to construct a series of HLA-B27 mutants reproducing most of the changes occurring in the natural subtypes. The reactivity of 21 anti-HLA-B27 CTL clones was examined with these mutants to address three issues concerning the alloreactive response against HLA-B27: 1) diversity of clonotypic specificities, 2) structural features of the epitopes recognized by these clones, and 3) role of individual positions in the differential recognition of HLA-B27 subtypes. Virtually all CTL clones displayed unique reaction patterns with the mutants, indicating a corresponding diversity of epitopes. However, these share some molecular features, such as certain amino acid residues and related locations. Individual mutations induced complex effects on multiple B27-specific CTL epitopes, revealing some of their very precise stereochemical constrains. An important feature of HLA-B27 subtype polymorphism is that every individual change was relevant, altering recognition by many CTL clones. Although the specific set affected by each mutation was partially different, the global number of clones affected by most changes was very similar. This suggests that the antigenic profile of any given subtype is not dominated by one particular change but is uniquely defined by its corresponding set of changes. An exception was the change at position 152, which totally abrogated recognition by all 20 anti-B*2705 CTL clones. This effect decisively influences the profound differences in T cell recognition between B*2705 and the two subtypes, B*2704 and B*2706, carrying this change. The results are compatible with the idea that HLA-B27 allorecognition may involve multiple peptides bound to the alloantigen on the cell surface.