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PubMed2006

Cellular responses of the ciliate, Tetrahymena thermophila, to far infrared irradiation.

Infrared rays from sunlight permeate the earth's atmosphere, yet little is known about their interactions with living organisms. To learn whether they affect cell structure and function, we tested the ciliated protozoan, Tetrahymena thermophila. These unicellular eukaryotes aggregate in swarms near the surface of freshwater habitats, where direct and diffuse solar radiation impinge upon the water-air interface. We report that populations irradiated in laboratory cultures grew and mated normally, but major changes occurred in cell physiology during the stationary phase. Early on, there were significant reductions in chromatin body size and the antibody reactivity of methyl groups on lysine residues 4 and 9 in histone H3. Later, when cells began to starve, messenger RNAs for key proteins related to chromatin structure, intermediary metabolism and cellular motility increased from two- to nearly nine-fold. Metabolic activity, swimming speed and linearity of motion also increased, and spindle shaped cells with a caudal cilium appeared. Our findings suggest that infrared radiation enhances differentiation towards a dispersal cell-like phenotype in saturated populations of Tetrahymena thermophila.

Animals↗
PubMed2004

Reconstructing the origin of Helianthus deserticola: survival and selection on the desert floor.

The diploid hybrid species Helianthus deserticola inhabits the desert floor, an extreme environment relative to its parental species Helianthus annuus and Helianthus petiolaris. Adaptation to the desert floor may have occurred via selection acting on transgressive, or extreme, traits in early hybrids between the parental species. We explored this possibility through a field experiment in the hybrid species' native habitat using H. deserticola, H. annuus, H. petiolaris, and two populations of early-generation (BC(2)) hybrids between the parental species, which served as proxies for the ancestral genotype of the ancient hybrid species. Character expression was evaluated for each genotypic class. Helianthus deserticola was negatively transgressive for stem diameter, leaf area, and flowering date, and the latter two traits are likely to be advantageous in a desert environment. The BC(2) hybrids contained a range of variation that overlapped these transgressive trait means, and an analysis of phenotypic selection revealed that some of the selective pressures on leaf size and flowering date, but not stem diameter, would move the BC(2) population toward the H. deserticola phenotype. Thus, H. deserticola may have originated from habitat-mediated directional selection acting on hybrids between H. annuus and H. petiolaris in a desert environment.

Adaptation, Physiological↗
PubMed2006

Examination of the watershed-wide distribution of Escherichia coli along Southern Lake Michigan: an integrated approach.

Recent research has highlighted the occurrence of Escherichia coli in natural habitats not directly influenced by sewage inputs. Most studies on E. coli in recreational water typically focus on discernible sources (e.g., effluent discharge and runoff) and fall short of integrating riparian, nearshore, onshore, and outfall sources. An integrated "beachshed" approach that links E. coli inputs and interactions would be helpful to understand the difference between background loading and sewage pollution; to develop more accurate predictive models; and to understand the differences between potential, net, and apparent culturable E. coli. The objective of this study was to examine the interrelatedness of E. coli occurrence from various coastal watershed components along southern Lake Michigan. The study shows that once established in forest soil, E. coli can persist throughout the year, potentially acting as a continuous non-point source of E. coli to nearby streams. Year-round background stream loading of E. coli can influence beach water quality. E. coli is present in highly variable counts in beach sand to depths just below the water table and to distances at least 5 m inland from the shore, providing a large potential area of input to beach water. In summary, E. coli in the fluvial-lacustrine system may be stored in forest soils, sediments surrounding springs, bank seeps, stream margins and pools, foreshore sand, and surface groundwater. While rainfall events may increase E. coli counts in the foreshore sand and lake water, concentrations quickly decline to prerain concentrations. Onshore winds cause an increase in E. coli in shallow nearshore water, likely resulting from resuspension of E. coli-laden beach sand. When examining indicator bacteria source, flux, and context, the entire "beachshed" as a dynamic interacting system should be considered.

Bathing Beaches↗
PubMed2000

Infectious disease and worldwide declines of amphibian populations, with comments on emerging diseases in coral reef organisms and in humans.

Many populations of amphibians are declining on all six continents on which they occur. Some causes of amphibian declines, such as habitat destruction, direct application of xenobiotics, and introduction of predators or competitors, are clearly attributable to human activities. Infectious disease appears to be the direct cause of mass amphibian die-offs in relatively undisturbed areas of the world where anthropomorphic environmental disruption is minimal. In these cases, it is not yet clear whether these epizootics result from the natural evolution of new pathogens or from environmental changes that promote the emergence of pathogenic forms and/or that weaken the immune defenses of amphibians. Because some aspects of pathogen-related amphibian mass mortalities are similar to outbreaks of new diseases in humans and coral reef organisms, amphibian declines may be part of a much larger pattern than previously appreciated.

Amphibians↗
PubMed2002

Using Geographical Information Systems to identify and target sites for creation and restoration of native woodlands: a case study of the Chiltern Hills, UK.

Rare and threatened habitats in Europe must be restored and enhanced in accordance with the European Union's Habitats and Species Directive. In the United Kingdom, conservation and expansion objectives for species and habitats are outlined in the Species Action Plans and Habitat Action Plans. Site identification for these measures has to date been ad hoc without consideration of either the existing "stock" of the natural resource or the ability of the surrounding land use to deliver the enhancement (enlargement) of a given habitat. Using a Geographical Information System, we outline a targeting system for creating new woodland in association with existing ancient woodland in the Chiltern Hills Area of Outstanding Natural Beauty. The aim was to create woodland blocks of at least 100 ha, as being of the most benefit to biodiversity. We identified existing patches of woodland between 20 and 50 ha as cores for habitat expansion and classified land use in terms of its suitability and proximity to these core areas for tree planting to meet the targets of the statutory body. Our results suggest that the targeting method employed is a useful tool for habitat restoration.

Conservation of Natural Resources↗
PubMed2006

Divergent timing and patterns of species accumulation in lowland and highland neotropical birds.

Late Pliocene and Pleistocene climatic instability has been invoked to explain the buildup of Neotropical biodiversity, although other theories date Neotropical diversification to earlier periods. If these climatic fluctuations drove Neotropical diversification, then a large proportion of species should date to this period and faunas should exhibit accelerated rates of speciation. However, the unique role of recent climatic fluctuations in promoting diversification could be rejected if late Pliocene and Pleistocene rates declined. To test these temporal predictions, dateable molecular phylogenies for 27 avian taxa were used to contrast the timing and rates of diversification in lowland and highland Neotropical faunas. Trends in diversification rates were analyzed in two ways. First, rates within taxa were analyzed for increasing or decreasing speciation rates through time. There was a significant trend within lowland taxa towards decreasing speciation rates, but no significant trend was observed within most highland taxa. Second, fauna wide diversification rates through time were estimated during one-million-year intervals by combining rates across taxa. In the lowlands, rates were highest during the late Miocene and then decreased towards the present. The decline in rates observed both within taxa and for the fauna as a whole probably resulted from density dependent cladogenesis. In the highlands, faunawide rates did not vary greatly before the Pleistocene but did increase significantly during the last one million years of the Pleistocene following the onset of severe glacial cycles in the Andes. These contrasting patterns of species accumulation suggest that lowland and highland regions were affected differently by recent climatic fluctuations. Evidently, habitat alterations associated with global climate change were not enough to promote an increase in the rate of diversification in lowland faunas. In contrast, direct fragmentation of habitats by glaciers and severe altitudinal migration of montane vegetation zones during climatic cycles may have resulted in the late Pleistocene increase in highland diversification rates. This increase resulted in a fauna with one third of its species dating to the last one million years.

Animals↗
PubMed2001

Characteristics of larval anopheline (Diptera: Culicidae) habitats in Western Kenya.

A longitudinal survey of mosquito larval habitats was carried out in Asembo Bay, western Kenya, during the rainy season of 1998. All pools of standing water along a 700-m transect were sampled twice per week. For each habitat, eight environmental variables were recorded and a sample of anopheline larvae was collected for identification. In total, 1,751 Anopheles gambiae s.l. and 2,784 Anopheles funestus Giles were identified. Identification of An. gambiae s.l. by polymerase chain reaction (PCR) indicated that 240 (14.7%) were An. gambiae Giles and 858 (52.4%) were An. arabiensis Patton; PCR failed to identify 539 (32.9%) specimens. Repeated measures logistic regression analysis indicated that An. gambiae and An. arabiensis larvae were associated with small, temporary habitats with algae and little or no aquatic vegetation. Anopheles funestus larvae were associated with larger, semipermanent bodies of water containing aquatic vegetation and algae. Direct comparison of habitat characteristics associated with either An. gambiae or An. arabiensis revealed that algae were associated more commonly with habitats containing An. gambiae; no other differences were detected. Chi-square analysis indicated that these species were collected from the same habitat more frequently than would be expected by chance alone. Together, these results indicate that An. gambiae and An. arabiensis have similar requirements for the larval environment and that, at least in western Kenya, they do not segregate into separate habitats.

Animals↗
PubMed2004

The maintenance (or not) of polygenic variation by soft selection in heterogeneous environments.

On the basis of single-locus models, spatial heterogeneity of the environment coupled with strong population regulation within each habitat (soft selection) is considered an important mechanism maintaining genetic variation. We studied the capacity of soft selection to maintain polygenic variation for a trait determined by several additive loci, selected in opposite directions in two habitats connected by dispersal. We found three main types of stable equilibria. Extreme equilibria are characterized by extreme specialization to one habitat and loss of polymorphism. They are analogous to monomorphic equilibria in singe-locus models and are favored by similar factors: high dispersal, weak selection, and low marginal average fitness of intermediate genotypes. At the remaining two types of equilibria the population mean is intermediate but variance is very different. At fully polymorphic equilibria all loci are polymorphic, whereas at low-variance equilibria at most one locus remains polymorphic. For most parameters only one type of equilibrium is stable; the transition between the domains of fully polymorphic and low-variance equilibria is typically sharp. Low-variance equilibria are favored by high marginal average fitness of intermediate genotypes, in contrast to single-locus models, in which marginal overdominance is particularly favorable for maintenance of polymorphism. The capacity of soft selection to maintain polygenic variation is thus more limited than extrapolation from single-locus models would suggest, in particular if dispersal is high and selection weak. This is because in a polygenic model, variance can evolve independently of the mean, whereas in the single-locus two-allele case, selection for an intermediate mean automatically leads to maintenance of polymorphism.

Animals↗
PubMed1985

Isolation and Screening of Yeasts That Ferment d-Xylose Directly to Ethanol.

Natural habitats of yeasts were examined for the presence of strains able to produce ethanol from d-xylose. Black knots, insect frass, and tree exudates were screened by enrichment in liquid d-xylose-yeast extract medium. These and each d-xylose-assimilating yeast in a collection from cactus fruits and Drosophila spp. were tested for alcohol production from this sugar. Among the 412 isolates examined, 36 produced more than 1 g of ethanol liter from 20 g of d-xylose liter, all under aerated conditions. Closer examination of the strains indicated that their time courses of d-xylose fermentation followed different patterns. Some strains produced more biomass than ethanol, and among these, ethanol may or may not be assimilated rapidly after depletion of d-xylose. Others produced more ethanol than biomass, but all catabolized ethanol after carbohydrate exhaustion. Ethanol production appeared best at low pH values and under mild aeration. Possible correlations between the nutritional profiles of the yeasts and their ability to produce ethanol from d-xylose were explored by multivariate analysis. d-Xylose appeared slightly better utilized by yeasts which rate poorly in terms of fermentation. The fermentation of d-glucose had no bearing on d-xylose fermentation. No specific nutritional trait could discriminate well between better d-xylose fermentors and other yeasts.

Journal Article↗
PubMed2006

Shellfish dredging pushes a flexible avian top predator out of a marine protected area.

There is a widespread concern about the direct and indirect effects of industrial fisheries; this concern is particularly pertinent for so-called "marine protected areas" (MPAs), which should be safeguarded by national and international law. The intertidal flats of the Dutch Wadden Sea are a State Nature Monument and are protected under the Ramsar convention and the European Union's Habitat and Birds Directives. Until 2004, the Dutch government granted permission for ~75% of the intertidal flats to be exploited by mechanical dredgers for edible cockles (Cerastoderma edule). Here we show that dredged areas belonged to the limited area of intertidal flats that were of sufficient quality for red knots (Calidris canutus islandica), a long-distance migrant molluscivore specialist, to feed. Dredging led to relatively lower settlement rates of cockles and also reduced their quality (ratio of flesh to shell). From 1998 to 2002, red knots increased gizzard mass to compensate for a gradual loss in shellfish quality, but this compensation was not sufficient and led to decreases in local survival. Therefore, the gradual destruction of the necessary intertidal resources explains both the loss of red knots from the Dutch Wadden Sea and the decline of the European wintering population. This study shows that MPAs that do not provide adequate protection from fishing may fail in their conservation objectives.

Animals↗
PubMed1995

Phylogenetic identification and in situ detection of individual microbial cells without cultivation.

The frequent discrepancy between direct microscopic counts and numbers of culturable bacteria from environmental samples is just one of several indications that we currently know only a minor part of the diversity of microorganisms in nature. A combination of direct retrieval of rRNA sequences and whole-cell oligonucleotide probing can be used to detect specific rRNA sequences of uncultured bacteria in natural samples and to microscopically identify individual cells. Studies have been performed with microbial assemblages of various complexities ranging from simple two-component bacterial endosymbiotic associations to multispecies enrichments containing magnetotactic bacteria to highly complex marine and soil communities. Phylogenetic analysis of the retrieved rRNA sequence of an uncultured microorganism reveals its closest culturable relatives and may, together with information on the physicochemical conditions of its natural habitat, facilitate more directed cultivation attempts. For the analysis of complex communities such as multispecies biofilms and activated-sludge flocs, a different approach has proven advantageous. Sets of probes specific to different taxonomic levels are applied consecutively beginning with the more general and ending with the more specific (a hierarchical top-to-bottom approach), thereby generating increasingly precise information on the structure of the community. Not only do rRNA-targeted whole-cell hybridizations yield data on cell morphology, specific cell counts, and in situ distributions of defined phylogenetic groups, but also the strength of the hybridization signal reflects the cellular rRNA content of individual cells. From the signal strength conferred by a specific probe, in situ growth rates and activities of individual cells might be estimated for known species. In many ecosystems, low cellular rRNA content and/or limited cell permeability, combined with background fluorescence, hinders in situ identification of autochthonous populations. Approaches to circumvent these problems are discussed in detail.

Bacteria↗
PubMed2001

Strategic environmental assessment of plans and programs: a methodology for estimating effects on biodiversity.

We developed a methodology for biodiversity evaluations within the process of Strategic Environmental Assessment and we applied it to the estimation of the effect of two Regional Plans of Development on all bird species inhabiting the Castilla y León region (northwestern Spain). The methodology is based on the evaluation of the effects of main development actions on the habitat requirements of species. From these evaluations, and from data on the current distribution and population size (number of individuals) of each species, we estimated the most likely pattern of distribution and population size after the full implementation of the plans for each species. The impacts of the plans were quantified as the differences between the pre- and postproject patterns after codifying them to compensate for differences in the quality of the information available among species. Overall, we conclude that the proposed methodology fulfills the requirements for its use within the SEA process as it allows for the assessment of cumulative impacts on every species, highlighting the development directions and the habitat types with major impacts, and ascertaining whether impacts affect species with either low or high conservation and/or economic value. Generalization of the proposed methodology to other regions or species will require wildlife-habitat models adequate for SEA analyses, so that we also propose guidelines for the development and validation of these models.

Animals↗
PubMed2006

Serum IgM levels against select marine bacteria in the Atlantic sharpnose shark (Rhizoprionodon terraenovae) from three estuaries.

The Atlantic sharpnose shark (Rhizoprionodon terraenovae) is abundant and easily captured throughout the southeastern United States. Therefore this species serves as an ideal model for generating basic immunological reagents to establish baseline information regarding the immunophysiology of sharks in the wild, and for attempting to correlate shark immune responses to potential pathogens with the quality of the habitat in which they reside. Sharpnose shark serum IgM was purified over a protein-A column and used to generate mouse polyclonal anti-sera to develop indirect ELISAs for quantifying bacteria-specific IgM antibody titers against Vibrio anguillarium, Vibrio cholerae, Vibrio parahaemolyticus, Vibrio charchariae, Escherichia coli, Mycobacterium fortuitum, and Mycobacterium marinum. Serum samples from Atlantic sharpnose sharks were collected in Charleston, SC, Beaufort, SC, and New Brunswick, GA estuaries during the early summer, and again from Charleston, SC in the fall of the same year. Relative antibody titers against E. coli, V. anguillarium, and V. parahaemolyticus differed among the three sampling locations, suggesting differences in microbial abundance or immunological responses in sharks from three locations. Overall, antibody titers in Charleston, SC sharks increased between summer and fall. A combination of chronic exposure to specific bacteria and increased antibody responses due to elevated water temperatures are likely responsible for elevated specific IgM in these sharks sampled in the fall. To our knowledge, this is the first study to examine IgM responses in elasmobranchs collected directly from their habitat.

Animals↗
PubMed1999

Isolation and characterization of microsatellite loci in black rhinoceros (Diceros bicornis).

The black rhinoceros (Diceros bicornis) is currently one of the most endangered African mammals as a direct result o habitat destruction and intensive poaching. A microsatellite library was constructed to address a number of population genetic questions. This paper describes the isolation of five black rhinoceros microsatellite loci. Three of these loci were found to be polymorphic. In addition, the paper demonstrates the utility for cross-hybridization of these primers in other species of rhinoceros.

Animals↗
PubMed2003

Ecological impact assessment in data-poor systems: a case study on metapopulation persistence.

Legislation on the protection of biodiversity (e.g., European Union Habitat and Bird Directives) increasingly requires ecological impact assessment of human activities. However, knowledge and understanding of relevant ecological processes and species responses to different types of impact are often incomplete. In this paper we demonstrate with a case study how impact assessment can be carried out for situations where data are scarce but some expert knowledge is available. The case study involves two amphibian species, the great crested newt (Triturus cristatus) and the natterjack toad (Bufo calamita) in the nature reserve the Meinweg in the Netherlands, for which plans are being developed to reopen an old railway track called the Iron Rhine. We assess the effects of this railway track and its proposed alternatives (scenarios) on the metapopulation extinction time and the occupancy times of the patches for both species using a discrete-time stochastic metapopulation model. We quantify the model parameters using expert knowledge and extrapolated data. Because of our uncertainty about these parameter values, we perform a Monte Carlo uncertainty analysis. This yields an estimate of the probability distribution of the model predictions and insight into the contribution of each distinguished source of uncertainty to this probability distribution. We show that with a simple metapopulation model and an extensive uncertainty analysis it is possible to detect the least harmful scenario. The ranking of the different scenarios is consistent. Thus, uncertainty analysis can enhance the role of ecological impact assessment in decision making by making explicit to what extent incomplete knowledge affects predictions.

Animals↗
PubMed2006

Herbivore-induced infochemicals influence foraging behaviour in two intertidal predators.

Herbivore-induced defences appear ubiquitous across most biomes and habitats. Yet the direct correlation between induced changes in host plant chemistry and the population dynamics of the herbivore remain untested in many systems. In plant-herbivore interactions in the terrestrial environment, indirect or tritrophic interactions appear a successful way in which changes in the host plant chemistry induced by prior herbivory can impact on herbivore populations via increased success of natural enemies. This set of interactions remains untested in the marine system. Here, we present work from experiments using orthogonal contrasts of plants with different prior treatments (control, mechanical damage or herbivory) and the presence or absence of herbivores on the foraging behaviour of a crab, Carcinus maenas, and a fish, Lipophrys pholis. These experiments were carried out using a novel flow-through flume, i.e. as a choice chamber supplied by turbulent water from independent cue sources. Our results show that in the Ascophyllum nodosum (plant)-Littorina obtusata (herbivore) system infochemicals from induced plants can directly influence predator foraging behaviour. L. pholis was attracted to the presence of a feeding L. obtusata, but was also more attracted to odours from herbivore-induced tissue than odours from mechanically damaged or naïve A. nodosum. C. maenas was more attracted to odours from herbivore-induced tissue compared to naïve tissue, regardless of the presence of L. obtusata. This is the first demonstration of such behavioural consequences of herbivore-induced changes in plants for marine systems.

Analysis of Variance↗
PubMed2006

UV-induced mortality in encapsulated intertidal embryos: are mycosporine-like amino acids an effective sunscreen?

Mycosporine-like amino acids (MAAs) are believed to protect a variety of marine organisms against the negative effects of ultraviolet radiation (UVR). However, their role in protecting developing intertidal encapsulated embryos remains untested. In the present study, we focused on the UV protective role of natural concentrations of MAAs for two intertidal gastropod species, Bembicium nanum and Siphonaria denticulata, which lay egg masses in habitats exposed to direct sunlight. We predicted that in both species, a higher concentration of MAAs within the egg mass would increase the likelihood of embryonic survivorship in the presence of UVR. Egg masses from both species were collected along the rocky shores of southeastern New South Wales, and a portion from each was subjected to one of three separate spectral treatments: full spectrum, UV-B block, and UV block. Proportions of surviving embryos were recorded following 72 hr exposure to spectral treatment. In addition, MAAs in each egg mass were quantified. Levels of variation in MAA concentration were striking, with S. denticulata egg masses showing more intraspecific variation than those of B. nanum. Surprisingly, survivorship under all spectral treatments was extremely high for both species, irrespective of MAA concentration. Under full spectrum treatments, B. nanum survivorship and total MAA concentration were significantly and positively correlated; however, MAA accounted for just 23.6% (R = 0.486) of the variation in survivorship. In contrast, survivorship in S. denticulata was not correlated with MAA concentration under full spectrum light. We conclude that the dependence on MAAs as photoprotection may be species-specific; however, it is likely that both species possess alternative mechanisms that minimize the negative effects of UVR.

Amino Acids↗
PubMed2004

Discrimination of aqueous and aeolian paleoenvironments by atomic force microscopy-- a database for the characterization of martian sediments.

In the search for aqueous habitats on Mars direct proof of (ancient) flowing water is still lacking, although remote sensing has provided indications of young fluvial systems. To demonstrate that such proof can be given, we examined surface marks on recent terrestrial sand grains by atomic force microscopy (AFM) and applied a quantitative three-dimensional analysis that can numerically distinguish between aeolian and aquatic transport mechanisms in sedimentary deposits on Earth. The surfaces of natural quartz grains as well as olivine, feldspar pyroxene, and monazite sands of known origin were imaged, each image yielding a three-dimensional map of the mineral surface. A fully automated analysis of distribution patterns of the structural elements that constitute the grain surfaces shows that wind-transported quartz grains have short linear elements irregularly distributed on the surface. Linear elements on water-transported grains, however, are longer with orientations that reflect the mineral symmetry. Because the surface patterns found on aqueous grains are due to preferential etching, they can be used as diagnostic fingerprints for the existence of past or present aqueous transport systems. We used a cluster analysis of the cross-correlation distance of distribution patterns in the structures of aeolian and aquatic sand grains to build a phenogram that provides a map for the relationship of the various sediments found on earth. The analysis shows that the method is highly significant and that water and wind transport can clearly be differentiated. In particular, feldspar and olivine sands contributed even more to the discrimination than quartz grains, which indicated that the method is promising for its application on future missions to Mars. Assuming that martian aqueous sand grains exhibit similar erosional patterns to mineral grains on Earth, simple AFM experiments on a Mars lander would be capable of proving the activity of flowing water in modern runoff systems and of analyzing the paleoenvironments of Mars.

Exobiology↗