Effects of two contrasting canopy manipulations on growth and water use of London plane (Platanus x acerifolia) trees

Aims: Two contrasting canopy manipulations were compared to unpruned controls on London plane trees, to determine the effects on canopy regrowth, soil and leaf water relations. Methods: ‘Canopy reduction’, was achieved by removing the outer 30 % length of all major branches and ‘canopy thinning’, by removing 30 % of lateral branches arising from major branches. Results: Total canopy leaf areas recovered within two and three years of pruning for the canopy-thinned and reduced trees respectively. Canopy reduction increased mean leaf size, nitrogen concentration, canopy leaf area density and conserved soil moisture for up to 3 years, whereas canopy thinning had no effects. Another experiment compared more severe canopy reduction to unpruned trees. This produced a similar growth response to the previous experiment, but soil moisture was conserved nearer to the trunk. Analysis of 13C and 18O signals along with leaf water relations and soil moisture data suggested that lower boundary layer conductance within the canopy-reduced trees restricted tree water use, whereas for the canopy-thinned trees the opposite occurred. Conclusions: Only canopy reduction conserved soil moisture and this was due to a combination of reduced total canopy leaf area and structural changes in canopy architecture

Bacterial Niche-Specific Genome Expansion Is Coupled with Highly Frequent Gene Disruptions in Deep-Sea Sediments

The complexity and dynamics of microbial metagenomes may be evaluated by genome size, gene duplication and the disruption rate between lineages. In this study, we pyrosequenced the metagenomes of microbes obtained from the brine and sediment of a deep-sea brine pool in the Red Sea to explore the possible genomic adaptations of the microbes in response to environmental changes. The microbes from the brine and sediments (both surface and deep layers) of the Atlantis II Deep brine pool had similar communities whereas the effective genome size varied from 7.4 Mb in the brine to more than 9 Mb in the sediment. This genome expansion in the sediment samples was due to gene duplication as evidenced by enrichment of the homologs. The duplicated genes were highly disrupted, on average by 47.6% and 70% for the surface and deep layers of the Atlantis II Deep sediment samples, respectively. The disruptive effects appeared to be mainly due to point mutations and frameshifts. In contrast, the homologs from the Atlantis II Deep brine sample were highly conserved and they maintained relatively small copy numbers. Likely, the adaptation of the microbes in the sediments was coupled with pseudogenizations and possibly functional diversifications of the paralogs in the expanded genomes. The maintenance of the pseudogenes in the large genomes is discussed

Microbial diversity in waters, sediments and microbial mats evaluated using fatty acid-based methods

The review summarises recent advances towards a greater comprehensive assessment of microbial diversity in aquatic environments using the fatty acid methyl esters and phospholipid fatty acids approaches. These methods are commonly used in microbial ecology because they do not require the culturing of micro-organisms, are quantitative and reproducible and provide valuable information regarding the structure of entire microbial communities. Because some fatty acids are associated with taxonomic and functional groups of micro-organisms, they allow particular groups of micro-organisms to be distinguished. The integration of fatty acid-based methods with stable isotopes, RNA and DNA analyses enhances our knowledge of the role of micro-organisms in global nutrient cycles, functional activity and phylogenetic lineages within microbial communities. Additionally, the analysis of fatty acid profiles enables the shifts in the microbial diversity in pristine and contaminated environments to be monitored. The main objective of this review is to present the use of lipid-based approaches for the characterisation of microbial communities in water columns, sediments and biomats

Two-structure thermodynamics for the TIP4P/2005 model of water covering supercooled and deeply stretched regions

One of the most promising frameworks for understanding the anomalies of cold and supercooled water postulates the existence of two competing, interconvertible local structures. If the non-ideality in the Gibbs energy of mixing overcomes the ideal entropy of mixing of these two structures, a liquid-liquid phase transition, terminated at a liquid-liquid critical point, is predicted. Various versions of the “two-structure equation of state” (TSEOS) based on this concept have shown remarkable agreement with both experimental data for metastable, deeply supercooled water and simulations of molecular water models. However, existing TSEOSs were not designed to describe the negative pressure region and do not account for the stability limit of the liquid state with respect to the vapor. While experimental data on supercooled water at negative pressures may shed additional light on the source of the anomalies of water, such data are very limited. To fill this gap, we have analyzed simulation results for TIP4P/2005, one of the most accurate classical water models available. We have used recently published simulation data, and performed additional simulations, over a broad range of positive and negative pressures, from ambient temperature to deeply supercooled conditions. We show that, by explicitly incorporating the liquid-vapor spinodal into a TSEOS, we are able to match the simulation data for TIP4P/2005 with remarkable accuracy. In particular, this equation of state quantitatively reproduces the lines of extrema in density, isothermal compressibility, and isobaric heat capacity. Contrary to an explanation of the thermodynamic anomalies of water based on a “retracing spinodal,” the liquid-vapor spinodal in the present TSEOS continues monotonically to lower pressures upon cooling, influencing but not giving rise to density extrema and other thermodynamic anomalies