Essay - The role of ecological theory in microbial ecology

Microbial ecology is currently undergoing a revolution, with repercussions spreading throughout microbiology, ecology and ecosystem science. The rapid accumulation of molecular data is uncovering vast diversity, abundant uncultivated microbial groups and novel microbial functions. This accumulation of data requires the application of theory to provide organization, structure, mechanistic insight and, ultimately, predictive power that is of practical value, but the application of theory in microbial ecology is currently very limited. Here we argue that the full potential of the ongoing revolution will not be realized if research is not directed and driven by theory, and that the generality of established ecological theory must be tested using microbial systems.

Comparison of media for optimal recovery of Candida albicans and Candida glabrata from blood culture

Candida spp., mainly Candida albicans, are frequently responsible for complications in immunocompromised patients. There are limited data comparing recovery efficiency using simple non-selective basal broth media.

The application of the ecological footprint in two Irish urban areas: Limerick and Belfast

The ecological footprint is now a widely accepted indicator of sustainable
development. Footprinting translates resource consumption into the land area
required to sustain it, and allows for an average per capita footprint for a region
or nation to be compared with the global average. This paper reports on a project
in which footprints were calculated for two Irish cities, namely Belfast in
Northern Ireland and Limerick in the Republic of Ireland for the year 2001. As
is frequently the case at sub-national scale, data quality and availability were
often problematic, and in general data gaps were filled by means of population
proxies or national averages. A range of methods was applied to convert
resource flows to land areas. Both footprints suggest that the lifestyles of citizens
of the cities use several times more land than their global share, as has been
found for other cities.

The Doñana ecological disaster:contamination of a world heritage estuarine marsh ecosystem with acidified pyrite mine waste

One of the most important bird breeding and over wintering sites in the west of Europe, the Coto Doñana, was severely impacted by the release of 5 million cubic meters of acid waste from the processing of pyrite ore. The waste entered ecologically sensitive areas of the park (including breeding areas for internationally endangered bird species) causing sustained pH decreases from pH 8.5 to 4.5 and resulting in massive metal contamination of the impacted ecosystem. The contaminating sludge waste contained arsenic at 0.6%, lead at 1.2% and zinc at 0.8% on a dry weight basis. The acid conditions facilitated the solubilization of these metals, leading to water concentrations lethal for aquatic wildlife. The accident caused considerable fish and invertebrate kills and has severe consequences for the protected bird species dependent on the impacted habitats and adjacent areas.

A complete analytic theory for structure and dynamics of populations and communities spanning wide ranges in body size

The prediction and management of ecosystem responses to global environmental change would profit from a clearer understanding of the mechanisms determining the structure and dynamics of ecological communities. The analytic theory presented here develops a causally closed picture for the mechanisms controlling community and population size structure, in particular community size spectra, and their dynamic responses to perturbations, with emphasis on marine ecosystems. Important implications are summarised in non-technical form. These include the identification of three different responses of community size spectra to size-specific pressures (of which one is the classical trophic cascade), an explanation for the observed slow recovery of fish communities from exploitation, and clarification of the mechanism controlling predation mortality rates. The theory builds on a community model that describes trophic interactions among size-structured populations and explicitly represents the full life cycles of species. An approximate time-dependent analytic solution of the model is obtained by coarse graining over maturation body sizes to obtain a simple description of the model steady state, linearising near the steady state, and then eliminating intraspecific size structure by means of the quasi-neutral approximation. The result is a convolution equation for trophic interactions among species of different maturation body sizes, which is solved analytically using a novel technique based on a multiscale expansion.

Identifying optimal sites for natural recovery and restoration of impacted biogenic habitats in a special area of conservation using hydrodynamic and habitat suitability modelling

Selection of sites for successful restoration of impacted shellfish populations depends on understanding the dispersion capability and habitat requirements of the species involved. In Strangford Lough, Northern Ireland, the horse mussel (Modiolus modiolus) biogenic reefs cover only a fraction of their historical range with the remaining reefs badly damaged and requiring restoration. Previous experimental trials suggest that translocation of horse mussels accelerates reef recovery and has therefore been proposed as a suitable restoration technique. We used a series of coupled hydrodynamic and particle dispersal models to assess larval dispersion from remnant and translocated populations to identify suitable areas for adult live M. modiolus translocation in Strangford Lough, Northern Ireland. A maximum entropy model (MAXENT) was used to identify if dispersing larvae could reach habitat suitable for adult M. modiolus. From these we predicted if translocated mussels will reseed themselves or be able to act as larval sources for nearby reefs. The dispersal models showed that the remnant M. modiolus populations are largely self-recruiting with little connectivity between them. The majority of larvae settled near the sources and movement was largely dependent on the tides and not influenced by wind or waves. Higher reef elevation resulted in larvae being able to disperse further away from the release point. However, larval numbers away from the source population are likely to be too low for successful recruitment. There was also little connectivity between the Irish Sea and Strangford Lough as any larvae entering the Lough remained predominantly in the Strangford Narrows. The areas covered by these self-seeding populations are suitable for M. modiolus translocation according to the MAXENT model. As a result of this work and in conjunction with other field work we propose a combination of total protection of all remaining larval sources and small scale translocations onto suitable substrata in each of the identified self-recruiting areas.

Glacial to paraglacial history and forest recovery in the Oglio glacier system (Italian Alps) between 26 and 15 ka cal BP

The integrated stratigraphic, radiocarbon and palynological record from an end-moraine system of the Oglio valley glacier (Italian Alps), propagating a lobe upstream in a lateral reach, provided evidence for a complete cycle of glacial advance, culmination and withdrawal during the Last Glacial Maximum and early Lateglacial. The glacier culminated in the end moraine shortly after 25.8 +/- 0.8 ka cal BP, and cleared the valley floor 18.3-17.2 +/- 0.3 ka cal BP. A primary paraglacial phase is then recorded by fast progradation of the valley floor.

As early as 16.7 +/- 0.3 ka cal BP, early stabilization of alluvial fans and lake filling promoted expansion of cembran pine. This is an unprecedented evidence of direct tree response to depletion of paraglacial activity during the early Lateglacial, and also documents the cembran pine survival in the mountain belt of the Italian Alps during the last glaciation. Between 16.1 and 14.6 +/- 0.5 ka cal BP, debris cones emplacement points to a moisture increase favouring tree Betula and Pinus sylvestris-mugo. A climate perturbation renewed paraglacial activity. According to cosmogenic ages on glacial deposits and AMS radiocarbon ages from lake records in South-Eastern Alps such phase compares favourably with the Gschnitz stadial and with the oscillations recorded at lakes Ragogna. Langsee and Jeserzersee, most probably forced by the latest freshening phases of the Heinrich Event 1.

A further sharp pine rise marks the subsequent onset of Bolling interstadial. The chronology of the Oglio glacier compares closely with major piedmont glaciers on the Central and Eastern Alpine forelands. On the other hand, the results of the present study imply a chronostratigraphic re-assessment of the recent geological mapping of the Central Italian Alps. (C) 2012 Elsevier Ltd. All rights reserved.

Parallel and nonparallel ecological, morphological and genetic divergence in lake-stream stickleback from a single catchment

Parallel phenotypic evolution in similar environments has been well studied in evolutionary biology; however, comparatively little is known about the influence of determinism and historical contingency on the nature, extent and generality of this divergence. Taking advantage of a novel system containing multiple lake-stream stickleback populations, we examined the extent of ecological, morphological and genetic divergence between three-spined stickleback present in parapatric environments. Consistent with other lake-stream studies, we found a shift towards a deeper body and shorter gill rakers in stream fish. Morphological shifts were concurrent with changes in diet, indicated by both stable isotope and stomach contents analysis. Performing a multivariate test for shared and unique components of evolutionary response to the distance gradient from the lake, we found a strong signature of parallel adaptation. Nonparallel divergence was also present, attributable mainly to differences between river locations. We additionally found evidence of genetic substructuring across five lake-stream transitions, indicating that some level of reproductive isolation occurs between populations in these habitats. Strong correlations between pairwise measures of morphological, ecological and genetic distance between lake and stream populations supports the hypothesis that divergent natural selection between habitats drives adaptive divergence and reproductive isolation. Lake-stream stickleback divergence in Lough Neagh provides evidence for the deterministic role of selection and supports the hypothesis that parallel selection in similar environments may initiate parallel speciation.

Parsing parallel evolution:Ecological divergence and differential gene expression in the adaptive radiations of thick-lipped Midas cichlid fishes from Nicaragua

The study of parallel evolution facilitates the discovery of common rules of diversification. Here, we examine the repeated evolution of thick lips in Midas cichlid fishes (the Amphilophus citrinellus species complex) - from two Great Lakes and two crater lakes in Nicaragua - to assess whether similar changes in ecology, phenotypic trophic traits and gene expression accompany parallel trait evolution. Using next-generation sequencing technology, we characterize transcriptome-wide differential gene expression in the lips of wild-caught sympatric thick- and thin-lipped cichlids from all four instances of repeated thick-lip evolution. Six genes (apolipoprotein D, myelin-associated glycoprotein precursor, four-and-a-half LIM domain protein 2, calpain-9, GTPase IMAP family member 8-like and one hypothetical protein) are significantly underexpressed in the thick-lipped morph across all four lakes. However, other aspects of lips' gene expression in sympatric morphs differ in a lake-specific pattern, including the magnitude of differentially expressed genes (97-510). Generally, fewer genes are differentially expressed among morphs in the younger crater lakes than in those from the older Great Lakes. Body shape, lower pharyngeal jaw size and shape, and stable isotopes (dC and dN) differ between all sympatric morphs, with the greatest differentiation in the Great Lake Nicaragua. Some ecological traits evolve in parallel (those related to foraging ecology; e.g. lip size, body and head shape) but others, somewhat surprisingly, do not (those related to diet and food processing; e.g. jaw size and shape, stable isotopes). Taken together, this case of parallelism among thick- and thin-lipped cichlids shows a mosaic pattern of parallel and nonparallel evolution. © 2012 Blackwell Publishing Ltd.

Modelling recovery of Celtic Sea demersal fish community size-structure

The Large Fish Indicator (LFI) is a size-based indicator of fish community state. The indicator describes the proportion by biomass of a fish community represented by fish larger than some size threshold. From an observed peak value of 0.49 in 1990, the Celtic Sea LFI declined until about 2000 and then fluctuated around 0.10 throughout the 2000s. This decline in the LFI reflected a period of diminishing ‘large’ fish biomass, probably related to high levels of size selective fishing. During the study period, fishing mortality was maintained at consistently high values. Average biomass of ‘small’ fish fluctuated across the whole time series, showing a weak positive trend in recent years. Inter-annual variation in the LFI was increasingly driven by fluctuation in small fish biomass as large fish biomass declined. Simulations using a size-based ecosystem model suggested that recovery in Celtic Sea fish community size-structure (LFI) could demand at least 20% reductions in fishing pressure and occur on decadal timescales.

Review of Rankine Cycle Systems Components for Hybrid Engines Waste Heat Recovery

In any internal combustion engine, the amount of heat rejected from the engine, and associated systems, is a result of the engine inefficiency. Successfully recovering a small proportion of this energy would therefore substantially improve the fuel economy.

Pain and distress reactivity and recovery as early predictors of temperament in toddlers born preterm

Pain reactivity may reflect underlying mechanisms of constitutional aspects of temperament.

Fermentable sugars recovery from lignocellulosic waste-newspaper by catalytic hydrolysis

The urgent need for alternative renewable energies to supplement petroleum-based fuels and the reduction of landfill sites for disposal of solid wastes makes it increasingly attractive to produce inexpensive biofuels from the organic fraction of the municipal solid waste. Therefore, municipal waste in the form of newspaper was investigated as a potential feedstock for fermentable sugars production. Hydrolysis of newspaper by dilute phosphoric acid was carried out in autoclave Parr reactor, where reactor temperature and acid concentration were examined. Xylose concentration reached a maximum value of 14 g/100 g dry mass corresponding to a yield of 94% at the best identified conditions of 2.5 wt% HPO, 135°C, 120 min reaction time, and at 2.5 wt% HPO, 150°C, and 60 min reaction time. For glucose, an average yield of 26% was obtained at 2.5 wt% HPO, 200°C, and 30 min. Furfural and 5-hydroxymethylfurfural (HMF) formation was clearly affected by reaction temperature, where the higher the temperature the higher the formation rate. The maximum furfural formed was an average of 3 g/100 g dry mass, corresponding to a yield of 28%. The kinetic study of the acid hydrolysis was also carried out using the Saeman and the two-fraction models. It was found for both models that the kinetic constants (K) depend on the acid concentration and temperature. The degradation of HMF to levulinic acid is faster than the degradation of furfural to formic acid. Also, the degradation rate is higher than the formation rate for both inhibitors when degradation is observed.