bluuebunny/crossref_metadata_2025 huggingface dataset:
Prediction of the energy dissipation rate in ductile crack propagation
Authors: ATKINS A. G. , CHEN Z. , COTTERELL B.
Published: March 2003

In this paper, energy dissipation rate D vs. Δa curves in ductile fracture are predicted using a ‘conversion’ between loads, load‐point displacements and crack lengths predicted by NLEFM and those found in real ELPL propagation. The NLEFM/ELPL link was recently discovered for the DCB testpiece, and we believe it applies to other cracked geometries. The predictions for D agree with experimental results. The model permits a crack tip toughness R(Δa) which rises from Jc and saturates out when (if) steady state propagation is reached after a transient stage in which all tunnelling, crack tip necking and shear lip formation is established. JR is always greater than the crack tip R(Δa) and continues to rise even after R(Δa) levels off.

The analysis is capable of predicting the usual D vs. Δa curves in the literature which have high initial values and fall monotonically to a plateau at large Δa. It also predicts that D curves for CCT testpieces should be higher than those for SENB/CT, as found in practice. The possibility that D curves at some intermediate Δa may dip to a minimum below the levelled‐off value at large Δa is predicted and confirmed by experiment. Recently reported D curves that have smaller initial D than the D‐values after extensive propagation can also be predicted. The testpiece geometry and crack tip R(Δa) conditions required to produce these different‐shaped D vs. Δa curves are established and confirmed by comparison with experiment.

The energy dissipation rate D vs. Δa is not a transferable property as it depends on geometry. The material characteristic R(Δa) may be the ‘transferable property’ for scaling problems in ELPL fracture. How it can be deduced from D vs. Δa curves (and by implication, JR vs. Δa curves) is established.
Equivalent initial flaw size testing and analysis of transport aircraft skin splices
Authors: FAWAZ S. A.
Published: March 2003

The equivalent initial flaw size (EIFS) concept was developed nearly 30 years ago in an attempt to account for the initial quality, both manufacturing and material properties, of a structural detail prone to fatigue cracking. Widespread use of this concept has been limited due to the large amount of test data required to develop a reliable EIFS distribution. In this effort, an EIFS distribution was determined for four types of flat, production like transport aircraft fuselage skin joints loaded by remote tension. Two crack growth prediction codes, AFGROW and FASTRAN, were used to not only develop the EIFS but also to compare the crack growth algorithms in each code. The EIFS calculations are prone to compounding errors in the crack growth analysis due to the changing stress intensity factor solutions and stress fields as the crack gets longer. Thus, only including EIFS calculations for mechanically small cracks, crack lengths less than 1.27 mm, results in a mean EIFS of 18.0 μm with a standard deviation of 3.78 μm.
Chick parasitism by blowflies affects feeding rates in a Mediterranean population of blue tits
Authors: Hurtrez‐Boussès Sylvie , Blondel Jacques , Perret Philippe , Fabreguettes Jacques , Renaud François Renaud
Published: March 2003

Offspring fitness depends on interactions between parental care and environmental constraints. It has been suggested that in altricial birds parents are able to compensate for the detrimental effects of ectoparasites by improving food provisioning. We tested this prediction in a population of blue tits highly parasitized by blowfly larvae. The frequency of parental feeding visits was significantly higher in parasitized broods than in broods experimentally deparasitized. Despite a strong increase in parental care, chicks of parasitized broods were lighter, smaller, and more anaemic than chicks in deparasitized broods. Parents invest more in feeding parasitized young but cannot fully compensate for the negative effects of parasites, hence young are in poor condition at fledging.
Parasitoid clutch size and irreversible evolution
Authors: Mayhew  , Ode  , Hardy  , Rosenheim
Published: March 2003

Previously, theoretical and empirical studies suggested that parasitoids developing in small multiple‐egg broods would evolve siblicidal behaviour, making such brood sizes rare and single‐egg broods an evolutionary absorbing state. Recent evidence, however, suggests that small gregarious broods are relatively stable in many parasitoid taxa, and that gregarious development has evolved many times from solitary development. This suggests that new research is needed to assess how nonsiblicidal behaviour can spread and become stable. We discuss some potentially rewarding possibilities.
An avian equivalent of make‐up?
Authors: Piersma  , Dekker  , Damsté
Published: March 2003

We report that a long‐distance migrating shorebird, the red knot, makes a complete switch from commonly occurring monoester preen waxes to a much rarer class of higher‐molecular‐weight diester waxes at the time of take‐off to the high arctic breeding grounds. The cold arctic climate would have required a lowering of wax‐viscosity, and thus, a shift in the reverse direction. We propose that a sexually selected need for a brilliant plumage has lead to this conter‐intuitive temporary shift from monoesters to diester waxes. The difficulty of application of the diester preen waxes under cold conditions would ensure the reliability of the quality‐signalling function of this most probably sexually selected trait.
Alternative causes for range limits: a metapopulation perspective
Authors: Holt R.D. , Keitt T.H.
Published: March 2003

All species have limited distributions at broad geographical scales. At local scales, the distribution of many species is influenced by the interplay of the three factors of habitat availability, local extinctions and colonization dynamics. We use the standard Levins metapopulation model to illustrate how gradients in these three factors can generate species’ range limits. We suggest that the three routes to range limits have radically different evolutionary implications. Because the Levins model makes simplifying assumptions about the spatial coupling of local populations, we present numerical studies of spatially explicit metapopulation models that complement the analytical model. The three routes to range limits give rise to distinct spatiotemporal patterns. Range limits in one species can also arise because of environmental gradients impinging upon other species. We briefly discuss a predator–prey example, which illustrates indirect routes to range limits in a metacommunity context.
A reappraisal of the mechanisms leading to ombrotrophy in British raised mires
Authors: Hughes P.D.M.
Published: March 2003

Previous theories of raised mire initiation stress the role of autogenic processes aided by climatic forcing towards increased oceanicity. Recent evidence from stratigraphic surveys in Great Britain and Ireland, however, suggests that raised mire initiation can occur under conditions of falling or fluctuating water tables. Macrofossil assemblages from the lowermost raised peat strata can indicate repeated aeration of the newly formed peat surface. A previously unexplored mechanism for the fen‐bog transition is discussed. New research is needed to assess its importance since a sound understanding of the way in which raised mires first formed is important for mire rehabilitation and conservation.
Dispersal functions and spatial models: expanding our dispersal toolbox
Authors: Travis  , French
Published: March 2003

A brief review of recent metapopulation literature indicates that dispersal functions are generally highly simplified. We suggest that this oversight can often make the results of such models misleading. A number of factors are considered that can affect the patterns and functions of this potentially complex process, including conditional and “intel‐ligent” dispersal, and dispersal distance. If a system is to be considered in spatially explicit terms then dispersal is an essential component. It follows therefore that a more thorough consideration of this fundamental population process is to be encouraged.
Linking genetic change to community evolution: insights from studies of bacteria and bacteriophage
Authors: Bohannan B.J.M. , Lenski R.E.
Published: March 2003

A major goal of community ecology is to link biological processes at lower scales with community patterns. Microbial communities are especially powerful model systems for making these links. In this article, we review recent studies of laboratory communities of bacteria and bacteriophage (viruses that infect bacteria). We focus on the ecology and evolution of bacteriophage‐resistance as a case study demonstrating the relationship between specific genes, individual interactions, population dynamics, community structure, and evolutionary change. In laboratory communities of bacteria and bacteriophage, bacteria rapidly evolve resistance to bacteriophage infection. Different resistance mutations produce distinct resistance phenotypes, differing, for example, in whether resistance is partial or complete, in the magnitude of the physiological cost associated with resistance, and in whether the mutation can be countered by a host‐range mutation in the bacteriophage. These differences determine whether a mutant can invade, the effect its invasion has on the population dynamics of sensitive bacteria and phage, and the resulting structure of the community. All of these effects, in turn, govern the community’s response to environmental change and its subsequent evolution.
Modelling the adaptive dynamics of traits involved in inter‐ and intraspecific interactions: An assessment of three methods
Authors: Abrams
Published: March 2003

In recent years, three related methods have been used to model the phenotypic dynamics of traits under the influence of natural selection. The first is based on an approximation to quantitative genetic recursion equations for sexual populations. The second is based on evolution in asexual lineages with mutation‐generated variation. The third method finds an evolutionarily stable set of phenotypes for species characterized by a given set of fitness functions, assuming that the mode of reproduction places no constraints on the number of distinct types that can be maintained in the population. The three methods share the property that the rate of change of a trait within a homogeneous population is approximately proportional to the individual fitness gradient. The methods differ in assumptions about the potential magnitude of phenotypic differences in mutant forms, and in their assumptions about the probability that invasion or speciation occurs when a species has a stable, yet invadable phenotype. Determining the range of applicability of the different methods is important for assessing the validity of optimization methods in predicting the evolutionary outcome of ecological interactions. Methods based on quantitative genetic models predict that fitness minimizing traits will often be evolutionarily stable over significant time periods, while other approaches suggest this is likely to be rare. A more detailed study of cases of disruptive selection might reveal whether fitness‐minimizing traits occur frequently in natural communities.
Trait variability and stress: canalization, developmental stability and the need for a broad approach
Authors: Hoffmann  , Woods
Published: March 2003

Trait variability (particularly fluctuating asymmetry) may provide a general measure of environmental stress applicable across taxa but consistent empirical support is lacking. Historically, stress effects were considered to act independently on trait canalization, developmental noise and trait size. However, in trait comparisons these processes are often assumed to be associated. Here we reconsider this issue and implications for detecting stress effects using trait variability. Published studies that consider multiple environments report little association between the effects of environmental variation on trait canalization and on developmental noise measured as fluctuating asymmetry, sug‐gesting that environmental effects often act independently on these processes. To further test the usefulness of trait variability as an indicator of stress, comparisons across environ‐ments should take a broad approach and report on several measures of trait variability, rather than focusing on only one index of fluctuating asymmetry as is commonly done.
Genotyping faeces links individuals to their diet
Authors: Fedriani Jose M. , Kohn Michael H.
Published: March 2003

The detection of individual variation in foraging behaviour within wild mammal populations requires large sample sizes and relies on the multifold re‐sampling of individuals. However, limits for observational studies are posed by the rarity and nocturnal or otherwise elusive habits of many mammals. We propose that the detection of foraging variation within populations of mammals may be facilitated if conventional diet analysis from faeces is combined with DNA‐based individual identification methods using “genetic fingerprinting” from faeces. We applied our approach to a coyote (Canis latrans) population, and showed how individuals may vary from one another in their diet profiles. Two main groups of coyotes were distinguished on the basis of their relative use of small mammals and “other vertebrates” as primary food sources, and these two groups were further subdivided on the basis of their relative use of “other vertebrates” and fruit as secondary food sources. We show that, unless a faecal sampling scheme is used that maximizes the number of different individuals included in a survey, individual foraging variation that is left unaccounted for may result in downwardly biased faecal diet diversity estimates. Our approach allows the re‐sampling of individuals over time and space, and thus may be generally useful for the testing of optimal foraging theory hypotheses in mammals and also has conservation applications.
Melanism and disease resistance in insects
Authors: Wilson Kenneth , Cotter Sheena C. , Reeson Andrew F. , Pell Judith K.
Published: March 2003

There is growing evidence that insects in high‐density populations invest relatively more in pathogen resistance than those in low‐density populations (i.e. density‐dependent prophylaxis). Such increases in resistance are often accompanied by cuticular melanism, which is characteristic of the high‐density form of many phase polyphenic insects. Both melanism and pathogen resistance involve the prophenoloxidase enzyme system. In this paper the link between resistance, melanism and phenoloxidase activity is examined inSpodopteralarvae. InS. exempta, cuticular melanism was positively correlated with phenoloxidase activity in the cuticle, haemolymph and midgut. MelanicS. exemptalarvae were found to melanize a greater proportion of eggs of the ectoparasitoidEuplectrus laphygmaethan non‐melanic larvae, and melanicS. littoraliswere more resistant to the entomopathogenic fungusBeauveria bassiana(inS. exemptathe association between melanism and fungal resistance was non‐signficant). These results strengthen the link between melanism and disease resistance and implicate the involvement of phenoloxidase.
Co‐occurrence of ectoparasites of marine fishes: a null model analysis
Authors: Gotelli Nicholas J. , Rohde Klaus
Published: March 2003

We used null model analysis to test for nonrandomness in the structure of metazoan ectoparasite communities of 45 species of marine fish. Host species consistently supported fewer parasite species combinations than expected by chance, even in analyses that incorporated empty sites. However, for most analyses, the null hypothesis was not rejected, and co‐occurrence patterns could not be distinguished from those that might arise by random colonization and extinction. We compared our results to analyses of presence–absence matrices for vertebrate taxa, and found support for the hypothesis that there is an ecological continuum of community organization. Presence–absence matrices for small‐bodied taxa with low vagility and/or small populations (marine ectoparasites, herps) were mostly random, whereas presence–absence matrices for large‐bodied taxa with high vagility and/or large populations (birds, mammals) were highly structured. Metazoan ectoparasites of marine fishes fall near the low end of this continuum, with little evidence for nonrandom species co‐occurrence patterns.
Inter‐sexual differences in the immune response of Eurasian kestrel nestlings under food shortage
Authors: Fargallo Juan A. , Laaksonen Toni , Pöyri Ville , Korpimäki Erkki
Published: March 2003

When resources are limited, parents should decide the optimal number, size, and sex of progeny, and offspring should decide the optimal allocation of resources to different costly functions, such as growth and immunity. We manipulated clutch sizes of Eurasian kestrels by one egg to estimate possible cumulative effects of incubation and chick rearing costs on parental body condition, feeding effort, and offspring viability. No obvious effects of clutch size manipulations on feeding effort were found while feeding effort was adjusted to the original clutch size. Enlarged and control nests suffered from higher nestling mortality than reduced nests, and chicks of the enlarged group were in poorer body condition than chicks of the reduced group. Controlling for body mass, male chicks exhibited lower cell‐mediated immunity assessed by a cutaneous hypersensitivity response than females, but only in treatments suffering from food restrictions, as indicated by chick starvation. These novel results reveal inter‐sexual differences in physiological strategies in early life, suggesting sex‐related differences in susceptibility to disease and consequently in survival prospects of offspring.
Mechanisms of plant species impacts on ecosystem nitrogen cycling
Authors: Knops J. M. H. , Bradley K. L. , Wedin D. A.
Published: March 2003

Plant species are hypothesized to impact ecosystem nitrogen cycling in two distinctly different ways. First, differences in nitrogen use efficiency can lead to positive feedbacks on the rate of nitrogen cycling. Alternatively, plant species can also control the inputs and losses of nitrogen from ecosystems.

Our current understanding of litter decomposition shows that most nitrogen present within litter is not released during decomposition but incorporated into soil organic matter. This nitrogen retention is caused by an increase in the relative nitrogen content in decomposing litter and a much lower carbon‐to‐nitrogen ratio of soil organic matter. The long time lag between plant litter formation and the actual release of nitrogen from the litter results in a bottleneck, which prevents feedbacks of plant quality differences on nitrogen cycling. Instead, rates of gross nitrogen mineralization, which are often an order of magnitude higher than net mineralization, indicate that nitrogen cycling within ecosystems is dominated by a microbial nitrogen loop. Nitrogen is released from the soil organic matter and incorporated into microbial biomass. Upon their death, the nitrogen is again incorporated into the soil organic matter. However, this microbial nitrogen loop is driven by plant‐supplied carbon and provides a strong negative feedback through nitrogen cycling on plant productivity. Evidence supporting this hypothesis is strong for temperate grassland ecosystems. For other terrestrial ecosystems, such as forests, tropical and boreal regions, the data are much more limited. Thus, current evidence does not support the view that differences in the efficiency of plant nitrogen use lead to positive feedbacks.

In contrast, soil microbes are the dominant factor structuring ecosystem nitrogen cycling. Soil microbes derive nitrogen from the decomposition of soil organic matter, but this microbial activity is driven by recent plant carbon inputs. Changes in plant carbon inputs, resulting from plant species shifts, lead to a negative feedback through microbial nitrogen immobilization. In contrast, there is abundant evidence that plant species impact nitrogen inputs and losses, such as: atmospheric deposition, fire‐induced losses, nitrogen leaching, and nitrogen fixation, which is driven by carbon supply from plants to nitrogen fixers. Additionally, plants can influence the activity and composition of soil microbial communities, which has the potential to lead to differences in nitrification, denitrification and trace nitrogen gas losses. Plant species also impact herbivore behaviour and thereby have the potential to lead to animal‐facilitated movement of nitrogen between ecosystems.

Thus, current evidence supports the view that plant species can have large impacts on ecosystem nitrogen cycling. However, species impacts are not caused by differences in plant quantity and quality, but by plant species impacts on nitrogen inputs and losses.
Functional diversity (FD), species richness and community composition
Authors: Petchey Owen L. , Gaston Kevin J.
Published: March 2003

Functional diversity is an important component of biodiversity, yet in comparison to taxonomic diversity, methods of quantifying functional diversity are less well developed. Here, we propose a means for quantifying functional diversity that may be particularly useful for determining how functional diversity is related to ecosystem functioning. This measure of functional diversity “FD” is defined as the total branch length of a functional dendrogram. Various characteristics of FD make it preferable to other measures of functional diversity, such as the number of functional groups in a community. Simulating species' trait values illustrates how the relative importance of richness and composition for FD depends on the effective dimensionality of the trait space in which species separate. Fewer dimensions increase the importance of community composition and functional redundancy. More dimensions increase the importance of species richness and decreases functional redundancy. Clumping of species in trait space increases the relative importance of community composition. Five natural communities show remarkably similar relationships between FD and species richness.
The ecology of tool‐use in the woodpecker finch (Cactospiza pallida)
Authors: Tebbich Sabine , Taborsky Michael , Fessl Birgit , Dvorak Michael
Published: March 2003

Insects, mammals and birds are known to use tools, but empirical evidence of the ecological importance of tool‐use is scarce. Here, we present the first ecological study of tool‐use by a bird species. Woodpecker finches use twigs or cactus spines to pry arthropods out of tree‐holes. We compared tool‐use during wet and dry seasons in two different vegetation zones: the Arid Zone and the humid Scalesia Zone. In the Scalesia Zone, where food was abundant and easily accessible, woodpecker finches rarely used tools. In contrast, in the Arid Zone, where food was limited and hard to access, they obtained half of their prey using tools during the dry season. Tool‐use enabled the birds to reach particularly large and otherwise inaccessible prey hidden in tree‐holes. Our data suggest that tool‐use in the woodpecker finch has evolved in response to the dry and unpredictable conditions in the coastal zone of the Galápagos Islands.
Top‐down and bottom‐up diversity cascades in detrital vs. living food webs
Authors: Dyer Lee A. , Letourneau Deborah
Published: March 2003

Apex predators and plant resources are both critical for maintaining diversity in biotic communities, but the indirect (‘cascading’) effects of top‐down and bottom‐up forces on diversity at different trophic levels are not well resolved in terrestrial systems. Manipulations of predators or resources can cause direct changes of diversity at one trophic level, which in turn can affect diversity at other trophic levels. The indirect diversity effects of resource and consumer variation should be strongest in aquatic systems, moderate in terrestrial systems, and weakest in decomposer food webs. We measured effects of top predators and plant resources on the diversity of endophytic animals in an understorey shrubPiper cenocladum(Piperaceae). Predators and resource availability had significant direct and indirect effects on the diversity of the endophytic animal community, but the effects were not interactive, nor were they consistent between living vs. detrital food webs. The addition of fourth trophic level beetle predators increased diversity of consumers supported by living plant tissue, whereas balanced plant resources (light and nutrients) increased the diversity of primary through tertiary consumers in the detrital resources food web. These results support the hypotheses that top‐down and bottom‐up diversity cascades occur in terrestrial systems, and that diversity is affected by different factors in living vs. detrital food webs.
Phoenix clones: recovery after long‐term defoliation‐induced dormancy
Authors: Morrow Patrice A. , Olfelt Joel P.
Published: March 2003

Many long‐lived plants are known to prolong dormancy in response to abiotic stresses such as drought. We are unaware, however, of any reports of plants prolonging dormancy in response to biotic stresses such as herbivory. We monitored 140 putative Solidago missouriensis clones (hereafter ‘clones’) ≥ 13 years before, during and after intense defoliation by the specialist herbivore Trirhabda canadensis. Eight of the clones produced no above‐ground growth in the season following defoliation. Though apparently killed, these clones reappeared 1–10 years after they disappeared, with six of them robustly recovering in a single season. We used 38 RAPD markers to test the hypotheses (denoted by H and numbered with subscripts) that territories were recovered by (H1) seedling establishment or (H2) rhizomes. We compared pre‐defoliation and post‐recovery genotypes in two clones using the same 38 markers. Our data document the existence of very large clones (60–350 m2 with c. 700–20 000 ramets), and support the hypothesis that recovery is from rhizomes. Within‐clone diversity is low, and the pre‐defoliation and post‐recovery genotypes match. We consider mechanisms that could enable plants entering dormancy with depleted resources to robustly recover, and the implications of dormancy for avoiding biotic stress such as that induced by T. canadensis.
Root allocation and multiple nutrient limitation in the New Jersey Pinelands
Authors: Gleeson Scott K. , Good Ralph E.
Published: March 2003

Abstract Current understanding of the effects of resource stress on plant communities emphasizes the adaptive integration of multiple limiting factors, but it has been difficult to directly demonstrate the fundamental assumption of the adaptive control of limitation. One model predicts a positive correlation between optimal allocation to the uptake of each resource and growth response to enrichment of that resource. Here we report a test of this prediction by a fertilization experiment in the New Jersey Pinelands Biosphere Reserve where limitation was measured by growth response to nutrient enrichments, and allocation was measured by root proliferation in microsites enriched by those same nutrients. Results suggest that a stand of regenerating Pinus echinata Mill. (shortleaf pine) was jointly limited by nitrogen and potassium, with a possible small effect of phosphorus. Root allocation was proportional to growth response, which supports the assumption of adaptive control of limitation.
Humics as an electron donor for anaerobic respiration
Authors: Lovley Derek R. , Fraga Jocelyn L , Coates John D. , Blunt‐Harris Elizabeth L.
Published: March 2003

The possibility that microorganisms might use reduced humic substances (humics) as an electron donor for the reduction of electron acceptors with a more positive redox potential was investigated. All of the Fe(III)‐ and humics‐reducing microorganisms evaluated were capable of oxidizing reduced humics and/or the reduced humics analogue anthrahydroquinone‐2,6,‐disulphonate (AHQDS), with nitrate and/or fumarate as the electron acceptor. These included Geobacter metallireducens, Geobacter sulphurreducens, Geothrix fermentans, Shewanella alga, Wolinella succinogenes and ‘S. barnesii’. Several of the humics‐oxidizing microorganisms grew in medium with AHQDS as the sole electron donor and fumarate as the electron acceptor. Even though it does not reduce Fe(III) or humics, Paracoccus denitrificans could use AHQDS and reduced humics as electron donors for denitrification. However, another denitrifier, Pseudomonas denitrificans, could not. AHQDS could also serve as an electron donor for selenate and arsenate reduction by W. succinogenes. Electron spin resonance studies demonstrated that humics oxidation was associated with the oxidation of hydroquinone moieties in the humics. Studies with G. metallireducens and W. succinogenes demonstrated that the anthraquinone‐2,6‐disulphonate (AQDS)/AHQDS redox couple mediated an interspecies electron transfer between the two organisms. These results suggest that, as microbially reduced humics enter less reduced zones of soils and sediments, the reduced humics may serve as electron donors for microbial reduction of several environmentally significant electron acceptors.
Cyanobacterial–bacterial mat consortia: examining the functional unit of microbial survival and growth in extreme environments
Authors: Paerl Hans W. , Pinckney James L. , Steppe Timothy F.
Published: March 2003

Cyanobacterial–bacterial consortial associations are taxonomically complex, metabolically interactive, self‐sustaining prokaryotic communities representing pioneer and often the only biota inhabiting extreme aquatic and terrestrial environments. Laminated mats and aggregates exemplify such communities. The fossil record indicates that these associations represent the earliest extant inhabitants and modifiers (i.e. anoxic to oxic conditions) of the Earth's biosphere. Present‐day consortia flourish in physically and chemically stressed environments, including nutrient‐deplete, hypersaline, calcified, desiccated and high‐irradiance ecosystems ranging from the tropics to polar regions. Consortial members exhibit extensive metabolic diversification, but have remained structurally simple. Structural simplicity, while advantageous in countering environmental extremes, presents a ‘packaging problem’ with regard to compartmentalizing potentially cross‐inhibitory aerobic versus anaerobic growth processes. To circumvent these metabolic constraints, phototrophic cyanobacteria and microheterotrophs orient along microscale chemical (i.e. O2, pH, Eh) gradients to meet and optimize the biogeochemical processes (C, N, S cycling) essential for survival, growth and the maintenance of genetic diversity, needed to sustain life. Microscale ecophysiological, analytical, molecular (immunological and nucleic acid) techniques have helped to develop a mechanistic basis for understanding consortial growth and survival under extreme environmental conditions on Earth. Consortia are ideal model systems for developing a process‐based understanding of the structural and functional requirements for life in extreme environments representative of the Earth's earliest biosphere and possibly other planets.
Matching molecular diversity and ecophysiology of benthic cyanobacteria and diatoms in communities along a salinity gradient
Authors: Nübel Ulrich , Garcia‐Pichel Ferran , Clavero Ester , Muyzer Gerard
Published: March 2003

The phylogenetic diversity of oxygenic phototrophic microorganisms in hypersaline microbial mats and their distribution along a salinity gradient were investigated and compared with the halotolerances of closely related cultivated strains. Segments of 16S rRNA genes from cyanobacteria and diatom plastids were retrieved from mat samples by DNA extraction and polymerase chain reaction (PCR), and subsequently analysed by denaturing gradient gel electrophoresis (DGGE). Sequence analyses of DNA from individual DGGE bands suggested that the majority of these organisms was related to cultivated strains at levels that had previously been demonstrated to correlate with characteristic salinity responses. Proportional abundances of amplified 16S rRNA gene segments from phylogenetic groupings of cyanobacteria and diatoms were estimated by image analysis of DGGE gels and were generally found to correspond to abundances of the respective morphotypes determined by microscopic analyses. The results indicated that diatoms accounted for low proportions of cells throughout, that the cyanobacterium Microcoleus chthonoplastes and close relatives dominated the communities up to a salinity of 11% and that, at a salinity of 14%, the most abundant cyanobacteria were related to highly halotolerant cultivated cyanobacteria, such as the recently established phylogenetic clusters of Euhalothece and Halospirulina. Although these organisms in cultures had previously demonstrated their ability to grow with close to optimal rates over a wide range of salinities, their occurrence in the field was restricted to the highest salinities investigated.
N2‐dependent growth and nitrogenase activity in the metal‐metabolizing bacteria, Geobacter and Magnetospirillum species
Authors: Bazylinski Dennis A. , Dean Annette J. , Schüler Dirk , Phillips Elizabeth J. P. , Lovley Derek R.
Published: March 2003

Cells of Geobacter metallireducens, Magnetospirillum strain AMB‐1, Magnetospirillum magnetotacticum and Magnetospirillum gryphiswaldense showed N2‐dependent growth, the first anaerobically with Fe(III) as the electron acceptor, and the latter three species microaerobically in semi‐solid oxygen gradient cultures. Cells of the Magnetospirillum species grown with N2 under microaerobic conditions were magnetotactic and therefore produced magnetosomes. Cells of Geobacter metallireducens reduced acetylene to ethylene (11.5 ± 5.9 nmol C2H4 produced min−1 mg−1 cell protein) while growing with Fe(III) as the electron acceptor in anaerobic growth medium lacking a fixed nitrogen source. Cells of the Magnetospirillum species, grown in a semi‐solid oxygen gradient medium, also reduced acetylene at comparable rates. Uncut chromosomal and fragments from endonuclease‐digested chromosomal DNA from these species, as well as Geobacter sulphurreducens organisms, hybridized with a nifHDK probe from Rhodospirillum rubrum, indicating the presence of these nitrogenase structural genes in these organisms. The evidence presented here shows that members of the metal‐metabolizing genera, Geobacter and Magnetospirillum, fix atmospheric dinitrogen.
Differential inhibition in vivo of ammonia monooxygenase, soluble methane monooxygenase and membrane‐associated methane monooxygenase by phenylacetylene
Authors: Lontoh Sonny , DiSpirito Alan A. , Krema Cinder L. , Whittaker Mark R. , Hooper Alan B. , Semrau Jeremy D.
Published: March 2003

Phenylacetylene was investigated as a differential inhibitor of ammonia monooxygenase (AMO), soluble methane monooxygenase (sMMO) and membrane‐associated or particulate methane monooxygenase (pMMO) in vivo. At phenylacetylene concentrations > 1 µM, whole‐cell AMO activity in Nitrosomonas europaea was completely inhibited. Phenylacetylene concentrations above 100 µM inhibited more than 90% of sMMO activity in Methylococcus capsulatus Bath and Methylosinus trichosporium OB3b. In contrast, activity of pMMO in M. trichosporium OB3b, M. capsulatus Bath, Methylomicrobium album BG8, Methylobacter marinus A45 and Methylomonas strain MN was still measurable at phenylacetylene concentrations up to 1000 µM. AMO of Nitrosococcus oceanus has more sequence similarity to pMMO than to AMO of N. europaea. Correspondingly, AMO in N. oceanus was also measurable in the presence of 1000 µM phenylacetylene. Measurement of oxygen uptake indicated that phenylacetylene acted as a specific and mechanistic‐based inhibitor of whole‐cell sMMO activity; inactivation of sMMO was irreversible, time dependent, first order and required catalytic turnover. Corresponding measurement of oxygen uptake in whole cells of methanotrophs expressing pMMO showed that pMMO activity was inhibited by phenylacetylene, but only if methane was already being oxidized, and then only at much higher concentrations of phenylacetylene and at lower rates compared with sMMO. As phenylacetylene has a high solubility and low volatility, it may prove to be useful for monitoring methanotrophic and nitrifying activity as well as identifying the form of MMO predominantly expressed in situ.
Effects of community composition and growth rate on aquifer biofilm bacteria and their susceptibility to betadine disinfection
Authors: Whiteley Marvin , Ott James R. , Weaver Eric A. , McLean Robert J. C.
Published: March 2003

Biofilm formation and function was studied in mixed culture using 20 bacterial strains isolated from a karst aquifer. When co‐cultured in a glucose‐limited chemostat, Vogesella indigofera and Pseudomonas putida were the dominant planktonic and biofilm organisms respectively. Biofilm formation and resistance to the iodine disinfectant betadine were then studied with monoculture and binary cultures of V. indigofera and P. putida and a 20‐strain community. Biofilm population size [measured as colony‐forming units (CFU) cm−2] increased with increasing species diversity. Significantly larger populations formed at dilution rates (DRs) of 0.0083 h−1 than at 0.033 h−1. P. putida populations were higher and V. indigofera lower in binary than in monoculture biofilms, suggesting that P. putida outcompeted V. indigofera. In binary biofilms, V. indigofera, a betadine‐resistant organism, enhanced the survival of P. putida, a betadine‐susceptible organism. In the 20‐strain biofilms, this protective effect was not observed because of low concentrations of V. indigofera (< 1% of the total population), suggesting that resistant organisms contribute to overall biofilm disinfectant resistance. Growth at 0.033 h−1 enhanced survival of V. indigofera biofilms against betadine. Although DR did influence survival of the other communities, its effects were neither consistent nor significant. All told, biofilm formation and betadine resistance are complex phenomena, influenced by community composition, growth rate and betadine concentration.
Localization of processes involved in methanogenic degradation of rice straw in anoxic paddy soil
Authors: Glissmann Kristin , Weber Sabine , Conrad Ralf
Published: March 2003

In anoxic paddy soil, rice straw is decomposed to CH4 and CO2 by a complex microbial community consisting of hydrolytic, fermenting, syntrophic and methanogenic microorganisms. Here, we investigated which of these microbial groups colonized the rice straw and which were localized in the soil. After incubation of rice straw in anoxic soil slurries for different periods, the straw pieces were removed from the soil, and both slurry and straw were studied separately. Although the potential activities of polysaccharolytic enzymes were higher in the soil slurry than in the straw incubations, the actual release of reducing sugars was higher in the straw incubations. The concentrations of fermentation products, mainly acetate and propionate, increased steadily in the straw incubations, whereas only a little CH4 was formed. In the soil slurries, on the other hand, fermentation products were low, whereas CH4 production was more pronounced. The production of CH4 or of fermentation products in the separated straw and soil incubations accounted in sum for 54–82% of the CH4 formed when straw was not removed from the soil. Syntrophic propionate degradation to acetate, CO2 and H2 was thermodynamically more favourable in the soil than in the straw fraction. These results show that hydrolysis and primary fermentation reactions were mainly localized on the straw pieces, whereas the syntrophic and methanogenic reactions were mainly localized in the soil. The percentage of bacterial relative to total microbial 16S rRNA content was higher on the straw than in the soil, whereas it was the opposite for the archaeal 16S rRNA content. It appears that rice straw is mainly colonized by hydrolytic and fermenting bacteria that release their fermentation products into the soil pore water where they are further degraded to CH4. Hence, complete methanogenic degradation of straw in rice soil seems to involve compartmentalization.
Measuring mass transfer processes of octane with the help of an alkSalkB::gfp‐tagged Escherichia coli
Authors: Jaspers Marco C. M. , Meier Christoph , Zehnder Alexander J. B. , Harms Hauke , Van Der Meer Jan Roelof
Published: March 2003

Diffusion of octane from oily droplets in different microscale settings was measured using Escherichia coli expressing the stable green fluorescent protein (GFP) from the alkB promoter of Pseudomonas oleovorans. GFP fluorescence intensities were determined quantitatively at the single‐cell level after 1.0 or 2.5 h incubation and compared with different calibration series using known concentrations of octane. By immobilizing the E. coli sensor cells on the bottom glass plate of a microscope flow chamber, it was possible to monitor the diffusion process for octane in aqueous solution as a function of time and distance from non‐aqueous phase droplets of octane alone or oily octane mixtures. When a gas phase was included in the flow chambers, octane transport could be demonstrated from the oily mixtures to the cells through both gas and liquid phase. Assays of non‐immobilized sensor cells in microdroplets in the presence or absence of soil particles incubated with octane through the vapour phase revealed a slight reduction in the total amount of induced E. coli cells in the presence of soil. Our results indicate the power of using GFP‐marked single‐cell biosensors in determining microscale bioavailability of organic pollutants.
Isolation of bacteria and 16S rDNAs from Lake Vostok accretion ice
Authors: Christner Brent C. , Mosley‐Thompson Ellen , Thompson Lonnie G. , Reeve John N.
Published: March 2003

Lake Vostok, the largest subglacial lake in Antarctica, is separated from the surface by ≈ 4 km of glacial ice. It has been isolated from direct surface input for at least 420 000 years, and the possibility of a novel environment and ecosystem therefore exists. Lake Vostok water has not been sampled, but an ice core has been recovered that extends into the ice accreted below glacial ice by freezing of Lake Vostok water. Here, we report the recovery of bacterial isolates belonging to the Brachybacteria, Methylobacterium, Paenibacillus and Sphingomonas lineages from a sample of melt water from this accretion ice that originated 3593 m below the surface. We have also amplified small‐subunit ribosomal RNA‐encoding DNA molecules (16S rDNAs) directly from this melt water that originated from α‐ and β‐proteobacteria, low‐ and high‐G+C Gram‐positive bacteria and a member of the Cytophaga/Flavobacterium/Bacteroides lineage.
Isolation and phylogenetic characterization of acidophilic microorganisms indigenous to acidic drainage waters at an abandoned Norwegian copper mine
Authors: Johnson D. Barrie , Rolfe Stewart , Hallberg Kevin B. , Iversen Eigil
Published: March 2003

The biodiversity of culturable acidophilic microbes in three acidic (pH 2.7–3.7), metal‐rich waters at an abandoned subarctic copper mine in central Norway was assessed. Acidophilic bacteria were isolated by plating on selective solid media, and dominant isolates were identified from their physiological characteristics and 16S rRNA gene sequences. The dominant iron‐oxidizing acidophile in all three waters was an Acidithiobacillus ferrooxidans‐like eubacterium, which shared 98% 16S rDNA identity with the type strain. A strain of Leptospirillum ferrooxidans was obtained from one of the waters after enrichment in pyrite medium, but this iron oxidizer was below detectable levels in the acidic waters themselves. In two sites, there were up to six distinct heterotrophic acidophiles, present at 103 ml−1. These included Acidiphilium‐like isolates (one closely related to Acidiphilium rubrum, a second to Acidiphilium cryptum and a third apparently novel isolate), an Acidocella‐like isolate (96% 16S rDNA identity to Acidocella facilis) and a bacterium that shared 94.5% 16S rDNA identity to Acidisphaera rubrifaciens. The other numerically significant heterotrophic isolate was not apparently related to any known acidophile, with the closest match (96% 16S rDNA sequence identity) to an acetogen, Frateuria aurantia. The results indicated that the biodiversity of acidophilic bacteria, especially heterotrophs, in acidic mine waters may be much greater than previously recognized.
Inhibition of biofilm formation and swarming of Escherichia coli by (5Z)‐4‐bromo‐5‐(bromomethylene)‐3‐butyl‐2(5H)‐furanone
Authors: Ren Dacheng , Sims James J. , Wood Thomas K.
Published: March 2003

The quorum‐sensing disrupter (5Z)‐4‐bromo‐5‐(bromomethylene)‐3‐butyl‐2(5H)‐furanone (furanone) of the alga Delisea pulchra was found to inhibit the swarming motility of Escherichia coli completely at 13 µg cm−2 (also at 20 µg ml−1) but did not inhibit its growth rate at 13–52 µg cm−2 or from 20 to 100 µg ml−1. Swimming was not inhibited by the furanone at 20–40 µg ml−1. In addition, confocal scanning laser microscopy revealed that this furanone at 60 µg ml−1 inhibited the biofilm formation of E. coli, as it decreased its thickness by 55%, reduced the number of water channels and decreased the percentage of live cells by 87%. This suggests that natural furanone may be used as a new method to control bacterial biofilms that does not involve toxicity. Furanone at 10 µg ml−1 also inhibited by 3300‐fold the quorum sensing of Vibrio harveyi via autoinducer 1 (AI‐1) and inhibited by 5500‐fold that of V. harveyi via of autoinducer 2 (AI‐2) as well as inhibited by 26 600‐fold the quorum sensing of E. coli via AI‐2; hence, this furanone is a non‐specific intercellular signal antagonist.
Population dynamics of type I and II methanotrophic bacteria in rice soils
Authors: Macalady Jennifer L. , McMillan Andrew M. S. , Dickens Angela F. , Tyler Stanley C. , Scow Kate M.
Published: March 2003

Methane‐oxidizing bacteria (methanotrophs) consume a significant but variable fraction of greenhouse‐active methane gas produced in wetlands and rice paddies before it can be emitted to the atmosphere. Temporal and spatial dynamics of methanotroph populations in California rice paddies were quantified using phospholipid biomarker analyses in order to evaluate the relative importance of type I and type II methanotrophs with depth and in relation to rice roots. Methanotroph population fluctuations occurred primarily within the top 0–2 cm of soil, where methanotroph cells increased by a factor of 3–5 over the flooded rice‐growing season. The results indicate that rice roots and rhizospheres were less important than the soil–water interface in supporting methanotroph growth. Both type I and type II methanotrophs were abundant throughout the year. However, only type II populations were strongly correlated with soil porewater methane concentrations and rice growth.