bluuebunny/crossref_metadata_2025 huggingface dataset:
Evidence of peak‐to‐peak dynamics in ecology
Authors: Rinaldi Sergio , Candaten Matteo , Casagrandi Renato
Published: March 2003

Remarkably irregular peaks characterize the dynamics of many plant and animal populations. As such peaks are often associated with undesirable consequences (e.g. pest outbreaks, epidemics, forest fires), the forecast of the forthcoming peak is a problem of major concern. Here we show, through the analysis of a number of models and of some of the longest and most celebrated ecological time‐series, that the intensity of the forthcoming peak can often be predicted simply from the previous peaks. When this is possible, one can also predict the time of occurrence of the forthcoming peak.
Estimating spatial coupling in epidemiological systems: a mechanistic approach
Authors: Keeling Matt J. , Rohani Pejman
Published: March 2003

In recent years, ecologists and epidemiologists have paid increasing attention to the influence of spatial structure in shaping the dynamics and determining the persistence of populations. This is fundamentally affected by the concept of ‘coupling’—the flux of individuals moving between separate populations. In this paper, we contrast how coupling is typically implemented in epidemic models with more detailed approaches. Our aim is to link the popular phenomenological formulations with the results of mechanistic models. By concentrating on the behaviour of simple epidemic systems, we relate explicit movement patterns with observed levels of coupling, validating the standard formulation. The analysis is then extended to include a brief study of how the correlation between stochastic populations is affected by coupling, the underlying deterministic dynamics and the relative population sizes.
Long‐term oscillations in grassland productivity induced by drought
Authors: Haddad Nick M. , Tilman David , Knops Johannes M. H.
Published: March 2003

Disturbances such as drought have immediate impacts on ecosystem functioning, but little is known about long‐term dynamic consequences of disturbance. Here, we show that a major drought perturbed prairie grassland from nearly constant average annual production, and induced 9 years of oscillations with a 2‐year period. This pattern occurred in unmanipulated plots in many widely separated fields that were part of two different long‐term studies. Using direct and indirect tests, we could reject the hypothesis that the oscillations were externally imposed by climate or herbivores. Weak evidence supported the hypothesis that oscillations were internally generated, caused by a litter and nitrogen dependent feedback on productivity. This hypothesis was supported by the results of two other long‐term studies, in which burning and, separately, nitrogen addition eliminated the 2‐year oscillations in plant production. However, more direct evidence failed to support the litter hypothesis. A final, but untested hypothesis was suggested by the observation that production tended to be synchronized amongst dominant plants. Drought may have synchronized production dynamics amongst plants with biennially greater allocation to above‐ground growth. Regardless of the specific mechanism, our results show that a single disturbance may have long‐lasting effects on the dynamics of plant production.
Experimental evidence that partner choice is a driving force in the payoff distribution among cooperators or mutualists: the cleaner fish case
Authors: Bshary Redouan , Grutter Alexandra S.
Published: March 2003

Supply and demand largely determine the price of goods on human markets. It has been proposed that in animals, similar forces influence the payoff distribution between trading partners in sexual selection, intraspecific cooperation and interspecific mutualism. Here we present the first experimental evidence supporting biological market theory in a study on cleaner fish, Labroides dimidiatus. Cleaners interact with two classes of clients: choosy client species with access to several cleaners usually do not queue for service and do not return if ignored, while resident client species with access to only one cleaning station do queue or return. We used plexiglas plates with equal amounts of food to simulate these behaviours of the two client classes. Cleaners soon inspected ‘choosy’ plates before ‘resident’ plates. This supports previous field observations that suggest that client species with access to several cleaners exert choice to receive better (immediate) service.
Relative fitness of aphids: effects of plant quality and ants
Authors: Stadler B. , Dixon A.F.G. , Kindlmann Pavel
Published: March 2003

We investigated the response of four species of aphids (Metopeurum fuscoviride, Brachycaudus cardui, Aphis fabae, and Macrosiphoniella tanacetaria) on tansy (Tanacetum vulgare) to plant quality and attendance by an ant, Lasius niger. The aphids experienced one of four different environments for two consecutive generations. Ant‐attendance significantly affected the time needed to reach maximum fecundity only in Me. fuscoviride and plant quality in Me. fuscoviride and B. cardui. Maximum daily fecundity was positively affected by plant quality and the magnitude of the effect was inversely associated with the degree of myrmecophily. Ant‐attendance had a positive effect on maximum fecundity only in the obligate myrmecophile, Me. fuscoviride. The intrinsic rate of population increase, rm, on high quality plants, was lowest for the obligate myrmecophile, intermediate for the facultative myrmecophiles and highest for the unattended species. On high quality plants the fitness of Me. fuscoviride was more adversely affected by the developmental stage of the plant and absence of ants than that of A. fabae or Ma. tanacetaria, which were able to maintain a high relative fitness in all the environments. The implications for aphids experiencing different degrees of ant‐attendance and seasonal changes in plant quality are discussed.
Field evidence of trait‐mediated indirect interactions in a rocky intertidal food web
Authors: Trussell Geoffrey C. , Ewanchuk Patrick J. , Bertness Mark D.
Published: March 2003

Studies on the implications of food web interactions to community structure have often focused on density‐mediated interactions between predators and their prey. This approach emphasizes the importance of predator regulation of prey density via consumption (i.e. lethal effects), which, in turn, leads to cascading effects on the prey’s resources. A more recent and contrasting view emphasizes the importance of non‐lethal predator effects on prey traits (e.g. behaviour, morphology), or trait‐mediated interactions. On rocky intertidal shores in New England, green crab (Carcinus maenas) predation is thought to be important to patterns of algal abundance and diversity by regulating the density of herbivorous snails (Littorina littorea). We found, however, that risk cues from green crabs can dramatically suppress snail grazing, with large effects on fucoid algal communities. Our results suggest that predator‐induced changes in prey behaviour may be an important and under‐appreciated component of food web interactions and community dynamics on rocky intertidal shores.
Growth responses of littoral mayflies to the phosphorus content of their food
Authors: Frost P. C. , Elser J. J.
Published: March 2003

We examined how mayfly growth rates and body stoichiometry respond to changing phosphorus (P) content in food. In two experiments, mayfly nymphs were given high or low quantities of food at different carbon:phosphorus (C:P) ratios and their growth was measured. Low food quantity resulted in negative growth rates in both experiments, regardless of food P content. However, under high food availability, mayfly growth was affected by the type of food eaten, with low C:P ratio food producing more rapid growth. In addition, mayfly growth increased somewhat when P‐poor food was artificially enriched with inorganic P although this effect was not statistically significant. Mayfly body P content was inversely related to body size but increased in animals fed artificially P‐enriched food. A model was constructed to simulate mass balance constraints on mayfly growth imposed by the relative supply of two elements (C and P) in food. The model shows that mayfly growth should be limited by food P content at moderately low C:P ratios (c. 120, by mass). Given high C:P ratios (mean c. 270, by mass) in periphyton from oligotrophic boreal lakes, our experimental and theoretical results indicate that stoichiometric constraints are important factors affecting benthic food webs in lakes from the Canadian Shield and perhaps in other systems with similarly high C:P ratios in periphyton.
Marine reserves have rapid and lasting effects
Authors: Halpern Benjamin S. , Warner Robert R.
Published: March 2003

Marine reserves are becoming a popular tool for marine conservation and resource management worldwide. In the past, reserves have been created with little understanding of how they actually affect the areas they are intended to protect. A few recent reviews have evaluated how reserves in general affect the density and biomass of organisms within them, but little work has been done to assess temporal patterns of these impacts. Here we review 112 independent measurements of 80 reserves to show that the higher average values of density, biomass, average organism size, and diversity inside reserves (relative to controls) reach mean levels within a short (1–3 y) period of time and that the values are subsequently consistent across reserves of all ages (up to 40 y). Therefore, biological responses inside marine reserves appear to develop quickly and last through time. This result should facilitate their use in the management of marine resources.
Food web complexity and chaotic population dynamics
Authors: Fussmann Gregor F. , Heber Gerd
Published: March 2003

In mathematical models, very simple communities consisting of three or more species frequently display chaotic dynamics which implies that long‐term predictions of the population trajectories in time are impossible. Communities in the wild tend to be more complex, but evidence for chaotic dynamics from such communities is scarce. We used supercomputing power to test the hypothesis that chaotic dynamics become less frequent in model ecosystems when their complexity increases. We determined the dynamical stability of a universe of mathematical, nonlinear food web models with varying degrees of organizational complexity. We found that the frequency of unpredictable, chaotic dynamics increases with the number of trophic levels in a food web but decreases with the degree of complexity. Our results suggest that natural food webs possess architectural properties that may intrinsically lower the likelihood of chaotic community dynamics.
The Arctic Oscillation predicts effects of climate change in two trophic levels in a high‐arctic ecosystem
Authors: Aanes Ronny , Sæther Bernt‐Erik , Smith Fiona M. , Cooper Elisabeth J. , Wookey Philip A. , Øritsland Nils Are
Published: March 2003

During recent decades there has been a change in the circulation of atmospheric pressure throughout the Northern Hemisphere. These variations are expressed in the recently described Arctic Oscillation (AO), which has shown an upward trend (associated with winter warming in the eastern Arctic) during the last three decades. We analysed a 12‐year time series on growth ofCassiope tetragona(Lapland Cassiope) and a 21‐year time series on abundance of a Svalbard reindeer population. High values of the AO index were associated with reduced plant growth and reindeer population growth rate. The North Atlantic Oscillation index was not able to explain a significant proportion of the variance in either plant growth or reindeer population fluctuations. Thus, the AO index may be a better predictor for ecosystem effects of climate change in certain high‐arctic areas compared to the NAO index.
Positive indirect effects in a coral reef fish community
Authors: Webster Michael S. , Almany Glenn R.
Published: March 2003

Indirect effects occur when two species interact through one or more intermediate species. Theoretical studies indicate that indirect interactions between two prey types that share common predators can be positive, neutral or negative. We document a positive indirect interaction between different types of prey fish on coral reefs in Australia. A high abundance of one type of prey fish (cardinalfishes: Apogonidae) resulted in higher recruitment, abundance and species richness of other prey fish. Our evidence indicates that these effects were not due to differential settlement but were instead due to differential post‐settlement predation. We hypothesize that resident piscivores altered their foraging behaviour by concentrating on highly abundant cardinal‐fish when they were present, leaving recruits of other species relatively unmolested. Indirect effects were evident within 48 h of settlement and persisted throughout the 42‐day experiment, highlighting the importance of early post‐settlement processes in these communities.
Annual variation in nesting numbers of marine turtles: the effect of sea surface temperature on re‐migration intervals
Authors: Solow Andrew R , Bjorndal Karen A. , Bolten Alan B
Published: March 2003

The assessment of marine turtle populations is complicated by large inter‐annual variations in nesting numbers. This variability has been attributed to synchrony in the re‐migration intervals (i.e., intervals between successive nesting years) of individuals. It has been hypothesized that this synchrony arises from environmental variations that affect the feeding conditions at sea. This paper presents the first direct test of this hypothesis. The analysis identifies a significant effect of sea surface temperature on the re‐migration interval in the largest Atlantic population of green turtles.
Dissecting adaptive clinal variation: markers, inversions and size/stress associations in Drosophila melanogaster from a central field population
Authors: Weeks Andrew R. , McKechnie Stephen W. , Hoffmann Ary A.
Published: March 2003

Many organisms show latitudinal variation for quantitative traits that is assumed to be due to climatic adaptation. These clines provide an opportunity to study the genetics of the adaptive process both at the phenotypic and the underlying molecular levels. Yet researchers rarely try to link variation in quantitative traits to their underlying molecular genetic basis. We describe a novel approach for exploring the genetic basis for clinal variation in size and stress traits in Drosophila melanogaster. We look for associations between genetic markers and traits that exhibit clinal patterns on the east coast of Australia using a single, geographically central population. There are strong associations between markers found within In(3R)Payne and variation in size, suggesting that this inversion explains much of the clinal variation in this trait. We also find that development time is associated with the Adh allozyme locus, cold resistance is negatively associated with the In(3L)Payne inversion and a genetic marker for Hsp70, a heat‐shock protein, is associated with heat resistance. Finally we discuss the importance of inversions in clinal variation for quantitative traits and for identifying quantitative trait loci.
Variation in butterfly egg adhesion: adaptation to local host plant senescence characteristics?
Authors: Fordyce James A. , Nice Chris C.
Published: March 2003

Most butterflies that overwinter as diapausing eggs have evolved oviposition behaviours where egg placement is near or on perennating portions of their host plant. We describe an alternative strategy used by alpine populations of a Lycaenid butterfly species complex where eggs are not attached strongly to the leaf substrate and subsequently fall off the plant. Other populations occurring at lower elevations attach their eggs strongly to the plant. In the laboratory, we measured the amount of force required to detach eggs from the leaf substrate. Eggs of the non‐alpine populations required more than five times the force required to detach eggs of the alpine population. Field surveys of the host plant characteristics used by various populations suggest that easy detachment may be adaptive for alpine populations because, unlike the host plants used by other populations, nearly all of the preceding year's vegetative growth is blown away by strong winds during the winter months.
Population stability is higher in more diverse annual plant communities
Authors: Valone Thomas J. , Hoffman Catherine D.
Published: March 2003

AbstractTheoretical work suggests a paradoxical effect of diversity on the temporal stability of ecological systems: increasing diversity should result in decreased stability of populations while community stability is enhanced. While empirical work indicates that community stability tends to increase with diversity, investigations of the effect of diversity on populations have resulted in few clear patterns. Here, we examine relationships between community diversity and population stability in unmanipulated annual plant communities. We show that, counter to theory, the temporal stability of annual plant populations increases with diversity. In addition, and again counter to theoretical assumptions, mean population size tends to increase with diversity, a pattern most likely due to variation in local productivity. The fact that community diversity, population size and the temporal stability of populations covaried positively suggests that abiotic factors such as productivity may govern population stability to such an extent as to override potential effects of diversity.
Evidence for long‐distance, chemical gall induction by an insect
Authors: Sopow Stephanie L. , Shorthouse Joseph D. , Strong Ward , Quiring Dan T.
Published: March 2003

AbstractWe report that a chemical stimulus from a herbivore, a galling insect, changes plant morphology and physiology to benefit the herbivore. Previous studies could not determine whether insect galls are induced by mechanical or chemical stimuli because feeding and oviposition both occurred at the site of gall formation. We report that the mouthparts of a spruce‐galling insect,Adelges cooleyi, were inserted in stem phloem cells far from induced galls, that tissues between mouthparts and galls appeared normal, and that the ability to initiate galls was inversely correlated with distance from buds (potential gall sites). Thus the effects of chemical stimuli were unambiguously separated from any mechanical influence of probing stylets or ovipositors. Our results strongly suggest that galls were induced by a chemical stimulus transported to buds via vascular tissue and that its efficacy was dose‐dependent.
Ecological replacement of native red squirrels by invasive greys driven by disease
Authors: Tompkins D. M. , White A. R. , Boots M.
Published: March 2003

Although a parapoxvirus harmful to red squirrels is present in UK squirrel populations it has not been considered a major cause of red squirrel decline, and replacement by the introduced grey squirrel, mainly because diseased individuals are rarely observed. By developing a generic model we show that parapoxvirus is likely to have played a crucial role in the red squirrel decline even though the prevalence of infection is low. Conservationists are quite rightly concerned with the invasion of exotic organisms such as the grey squirrel. Our work emphasizes that they, along with other ecologists, should pay particular attention to pathogens, even when they occur at low prevalence.
Anthropogenic impacts and historical decline in body size of rocky intertidal gastropods in southern California
Authors: Roy Kaustuv , Collins Allen G. , Becker Bonnie J. , Begovic Emina , Engle John M.
Published: March 2003

Abstract The diverse fauna and flora of rocky intertidal ecosystems are being impacted by the activities of rapidly increasing coastal populations in many regions of the world. Human harvesting of intertidal species can lead to significant changes in body sizes of these taxa. However, little is known about the temporal trajectories of such size declines and more importantly, the long‐term effects of chronic human impacts. Furthermore, it is unclear whether sizes of species not directly targeted for harvesting are also declining through indirect effects. Here we use historical (extending back to 1869) and field survey data covering 200 km of mainland southern California coast to show that human activities have led to significant and widespread declines in body sizes of rocky intertidal gastropod species over the last century. These declines, initiated several decades ago, are continuing and contrary to expectation, they are not restricted to species harvested for human consumption. Data from the only national park in this area, where conservation laws are strictly imposed, demonstrate that negative ecological impacts can be ameliorated if existing laws are enforced.
Identification of the metabolically active members of a bacterial community in a polychlorinated biphenyl‐polluted moorland soil
Authors: Nogales Balbina , Moore Edward R. B. , Abraham Wolf‐Rainer , Timmis Kenneth N.
Published: March 2003

The presumptive metabolically active members of a bacterial community in a moorland soil in Germany, highly polluted with polychlorinated biphenyls (PCBs), were identified by sequencing of cloned reverse transcription–polymerase chain reaction (RT–PCR) amplification products of 16S rRNA generated from total RNA extracts. Analysis of the 16S rRNA clone library revealed a considerable diversity of metabolically active bacteria in the soil, despite the acidic pH and high concentrations of PCBs. Cloned sequence types clustered within the Proteobacteria (34% alpha‐, 33% beta‐ and 7% gamma‐subclasses), the Holophaga–Acidobacterium phylum (14%), the Actinobacteria (6.5%) and the Planctomycetales (2%). Three cloned sequence types were not affiliated to any described phylogenetic group. An unusual feature of this soil was the abundance of sequence types within the beta‐subclass of the Proteobacteria, most of which were similar to the 16S rRNA gene sequences of species from only two genera, Burkholderia and Variovorax. Three other numerous 16S rRNA sequence types were similar to the sequences of Sphingomonas species, members of the Rhodopila globiformis group and Acidobacterium capsulatum. Some of the sequence types retrieved were similar to the 16S rRNA sequences of bacterial isolates able to degrade a variety of organic pollutants, including PCBs. As the PCB contamination is the major source of measurable carbon in this soil, some of the 16S rRNA sequence types detected and presumed to represent the metabolically active members of the community indicate the organisms likely to be involved, directly or indirectly, in the utilization of the PCBs as carbon and energy sources.
Diversity and community structure within anoxic sediment from marine salinity meromictic lakes and a coastal meromictic marine basin, Vestfold Hills, Eastern Antarctica
Authors: Bowman John P. , Rea Suzanne M. , McCammon Sharee A. , McMeekin Tom A.
Published: March 2003

16S rDNA clone library analysis was used to examine the biodiversity and community structure within anoxic sediments of several marine‐type salinity meromictic lakes and a coastal marine basin located in the Vestfolds Hills area of Eastern Antarctica. From 69 to 130 (555 total) 16S rDNA clones were analysed from each sediment sample, and restriction fragment length polymorphism (RFLP) and sequence analysis grouped the clones into 202 distinct phylotypes (a clone group with sequence similarity of > 0.98). A number of phylotypes and phylotype groups predominated in all libraries, with a group of 10 phylotypes (31% of clones) forming a novel deep branch within the low G + C Gram‐positive division. Other abundant phylotypes detected in several different clone libraries grouped with Prochlorococcus cyanobacteria, diatom chloroplasts, delta proteobacteria (Desulfosarcina group, Syntrophus and Geobacter/Pelobacter/Desulphuromonas group), order Chlamydiales (Parachlamydiaceae) and Spirochaetales (wall‐less Antarctic spirochaetes). Most archaeal clones detected (3.1% of clones) belonged to a highly diverged group of Euryarchaeota clustering with clones previously detected in rice soil, aquifer sediments and hydrothermal vent material. Little similarity existed between the phylotypes detected in this study and other clone libraries based on marine sediment, suggesting that an enormous prokaryotic diversity occurs within marine and marine‐derived sediments.
Studies on the in situ physiology of Thiothrix spp. present in activated sludge
Authors: Nielsen Per Halkjær , De Muro Marilena Aquino , Nielsen Jeppe Lund
Published: March 2003

The in situ physiology of the filamentous sulphur bacterium Thiothrix spp. was investigated in an industrial wastewater treatment plant with severe bulking problems as a result of overgrowth of Thiothrix. Identification and enumeration using fluorescence in situ hybridization (FISH) with species‐specific 16S and 23S rRNA probes revealed that 5–10% of the bacteria in the activated sludge were Thiothrix spp. By using a combination of FISH and microautoradiography it was possible to study the in situ physiology of probe‐defined Thiothrix filaments under different environmental conditions. The Thiothrix filaments were very versatile and showed incorporation of radiolabelled acetate and/or bicarbonate under heterotrophic, mixotrophic and chemolithoautotrophic conditions. The Thiothrix filaments were active under anaerobic conditions (with or without nitrate) in which intracellular sulphur globules were formed from thiosulphate and acetate was taken up. Thiothrix‐specific substrate uptake rates and growth rates in activated sludge samples were determined under different conditions. Doubling times of 6–9 h under mixotrophic conditions and 15–30 h under autotrophic conditions were estimated. The key properties that Thiothrix might be employing to outcompete other microorganisms in activated sludge were probably related to the mixotrophic growth potential with strong stimulation of acetate uptake by thiosulphate, as well as stimulation of bicarbonate incorporation by acetate in the presence of thiosulphate.
Anaerobic respiratory growth of Vibrio harveyi, Vibrio fischeri and Photobacterium leiognathi with trimethylamine N‐oxide, nitrate and fumarate: ecological implications
Authors: Proctor Lita M. , Gunsalus Robert P.
Published: March 2003

Two symbiotic species, Photobacterium leiognathi and Vibrio fischeri, and one non‐symbiotic species, Vibrio harveyi, of the Vibrionaceae were tested for their ability to grow by anaerobic respiration on various electron acceptors, including trimethylamine N‐oxide (TMAO) and dimethylsulphoxide (DMSO), compounds common in the marine environment. Each species was able to grow anaerobically with TMAO, nitrate or fumarate, but not with DMSO, as an electron acceptor. Cell growth under microaerophilic growth conditions resulted in elevated levels of TMAO reductase, nitrate reductase and fumarate reductase activity in each strain, whereas growth in the presence of the respective substrate for each enzyme further elevated enzyme activity. TMAO reductase specific activity was the highest of all the reductases. Interestingly, the bacteria‐colonized light organs from the two squids, Euprymna scolopes and Euprymna morsei, and the light organ of the ponyfish, Leiognathus equus, also had high levels of TMAO reductase enzyme activity, in contrast to non‐symbiotic tissues. The ability of these bacterial symbionts to support cell growth by respiration with TMAO may conceivably eliminate the competition for oxygen needed for both bioluminescence and metabolism.
The responses of photosynthesis and oxygen consumption to short‐term changes in temperature and irradiance in a cyanobacterial mat (Ebro Delta, Spain)
Authors: Epping Eric , Kühl Michael
Published: March 2003

We have evaluated the effects of short‐term changes in incident irradiance and temperature on oxygenic photosynthesis and oxygen consumption in a hypersaline cyanobacterial mat from the Ebro Delta, Spain, in which Microcoleus chthonoplastes was the dominant phototrophic organism. The mat was incubated in the laboratory at 15, 20, 25 and 30°C at incident irradiances ranging from 0 to 1000 µmol photons m−2 s−1. Oxygen microsensors were used to measure steady‐state oxygen profiles and the rates of gross photosynthesis, which allowed the calculation of areal gross photosynthesis, areal net oxygen production, and oxygen consumption in the aphotic layer of the mat. The lowest surface irradiance that resulted in detectable rates of gross photosynthesis increased with increasing temperature from 50 µmol photons m−2 s−1 at 15°C to 500 µmol photons m−2 s−1 at 30°C. These threshold irradiances were also apparent from the areal rates of net oxygen production and point to the shift of M. chthonoplastes from anoxygenic to oxygenic photosynthesis and stimulation of sulphide production and oxidation rates at elevated temperatures. The rate of net oxygen production per unit area of mat at maximum irradiance, J0, did not change with temperature, whereas, JZphot, the flux of oxygen across the lower boundary of the euphotic zone increased linearly with temperature. The rate of oxygen consumption per volume of aphotic mat increased with temperature. This increase occurred in darkness, but was strongly enhanced at high irradiances, probably as a consequence of increased rates of photosynthate exudation, stimulating respiratory processes in the mat. The compensation irradiance (Ec) marking the change of the mat from a heterotrophic to an autotrophic community, increased exponentially in this range of temperatures.
Novel forms of ring‐hydroxylating dioxygenases are widespread in pristine and contaminated soils
Authors: Yeates Christine , Holmes Andrew J. , Gillings Michael R.
Published: March 2003

Ring‐hydroxylating dioxygenases (RHDs) are of central importance to bacterial recycling of aromatic hydrocarbons, including anthropogenic pollutants. The database of presently characterized RHDs is biased towards those from organisms readily isolated on anthropogenic substrates. To investigate the extent to which RHDs from extant organisms reflect the natural diversity of these enzymes, we developed a polymerase chain reaction (PCR) method for retrieval of RHD gene fragments from environmental samples. Gene libraries from two contaminated and two pristine soil samples were constructed. None of the inferred peptides from clones examined were identical to previously described RHDs; however, all showed significant sequence homology and contained key catalytic residues. On the basis of sequence identity, the environmental clones clustered into six distinct groups, only one of which included known RHDs. One of the new sequence groupings was particularly widespread, being recovered from all soil samples tested. Comparison of inferred peptide sequences of the environmental clones and known RHDs showed the former to have greater sequence variation at sites thought to influence accessibility of the active site than that seen between currently known RHDs. We conclude that presently characterized RHDs do not adequately represent the diversity of function found in in situ forms.
Members of the Cytophaga–Flavobacterium–Bacteroides phylum as intracellular bacteria of acanthamoebae: proposal of ‘Candidatus Amoebophilus asiaticus’
Authors: Horn Matthias , Harzenetter Marit D. , Linner Tanja , Schmid Ernst N. , Müller Karl‐Dieter , Michel Rolf , Wagner Michael
Published: March 2003

Three Gram‐negative, rod‐shaped bacteria that were found intracellularly in two environmental and one clinical Acanthamoeba sp. isolates were analysed. Two endocytobionts showing a parasitic behaviour were propagated successfully outside their amoebal host cells and were identified subsequently by comparative 16S rRNA sequence analysis as being most closely affiliated with Flavobacterium succinicans (99% 16S rRNA sequence similarity) or Flavobacterium johnsoniae (98% 16S rRNA sequence similarity). One endocytobiont could neither be cultivated outside its original Acanthamoeba host (Acanthamoeba sp. TUMSJ‐321) nor transferred into other amoebae. Electron microscopy revealed that the amoebal trophozoites and cysts were almost completely filled with cells of this endosymbiont which are surrounded by a host‐derived membrane. According to 16S rRNA sequence analysis, this endosymbiont could also be assigned to the Cytophaga–Flavobacterium–Bacteroides (CFB) phylum, but was not closely affiliated to any recognized species within this phylogenetic group (less than 82% 16S rRNA sequence similarity). Identity and intracellular localization of this endosymbiont were confirmed by application of a specific fluorescently labelled 16S rRNA‐targeted probe. Based on these findings, we propose classification of this obligate Acanthamoeba endosymbiont as ‘Candidatus Amoebophilus asiaticus’. Comparative 18S rRNA sequence analysis of the host of ‘Candidatus Amoebophilus asiaticus’ revealed its membership with Acanthamoeba 18S rDNA sequence type T4 that comprises the majority of all Acanthamoeba isolates.
Following spread of fire blight in Western, Central and Southern Europe by molecular differentiation of Erwinia amylovora strains with PFGE analysis
Authors: Jock Susanne , Donat Victoria , López Maria M. , Bazzi Carlo , Geider Klaus
Published: March 2003

Fire blight has been detected recently in several areas of northern Spain and north‐eastern Italy. To follow spread of the disease within Europe, more than 120 Erwinia amylovora strains isolated from 1957–1900 in England, France, Germany, The Netherlands, Belgium, Poland, Italy and Spain were assayed using pulsed‐field gel electrophoresis (PFGE) analysis of genomic DNA after XbaI digestion. Pattern types Pt1 and Pt4 were found for strains from England. Pt1 was also found in central Europe and eastern France, Pt4 in western France. Pt2 appeared first in Egypt, from where strains with this pattern disseminated northwards as far as into the Balkans. Pt3 was typical for northern France and Belgium. Strains from Spain displayed the pattern types Pt3 and Pt4. In Italy, Pt2 was found in the south‐eastern areas, Pt3 in the north‐eastern areas, and Pt1 was found very recently in orchards adjacent to the Austrian border, together with Pt3. Despite barely controlled trade with fire blight host plants and associated plant products within Europe, the PFGE patterns of the E. amylovora isolates were ordered indicating sequential spread. On the other hand, the appearance of Pt3 in northern Italy and central Spain can be explained by the import of contaminated plants by nurseries.
Occurrence and activity of Archaea in aerated activated sludge wastewater treatment plants
Authors: Gray Neil D. , Miskin Ian P. , Kornilova Oksana , Curtis Thomas P. , Head Ian M.
Published: March 2003

The occurrence, distribution and activity of archaeal populations within two aerated, activated sludge wastewater treatment systems, one treating domestic waste and the second treating mixed domestic and industrial wastewater, were investigated by denaturing gradient gel electrophoresis (DGGE) analysis of polymerase chain reaction (PCR)‐amplified ribosomal RNA gene fragments and process measurements. In the plant receiving mixed industrial and domestic waste the archaeal populations found in the mixed liquor were very similar to those in the influent sewage, though a small number of DGGE bands specific to the mixed liquor were identified. In contrast, the activated sludge treating principally domestic waste harboured distinct archaeal populations associated with the mixed liquor that were not prevalent in the influent sewage. We deduce that the Archaea in the plant treating mixed wastewater were derived principally
from the influent, whereas those in the plant treating solely domestic waste were
actively growing in the treatment plant. Archaeal 16S rRNA gene sequences related
to the Methanosarcinales, Methanomicrobiales and the Methanobacteriales were detected. Methanogenesis was measured in activated sludge samples incubated under oxic and anoxic conditions, demonstrating that the methanogens present in both activated sludge plants were active only in anoxic incubations. The relatively low rates of methanogenesis measured indicated that, although active, the methanogens play a minor role in carbon turnover in activated sludge.
A chlorophyll a fluorescence‐based Lemna minor bioassay to monitor microbial degradation of nanomolar to micromolar concentrations of linuron
Authors: Hulsen Kris , Minne Veerle , Lootens Peter , Vandecasteele Paul , Höfte Monica
Published: March 2003

A plant–microbial bioassay, based on the aquatic macrophyte Lemna minor L. (duckweed), was used to monitor biodegradation of nano‐ and micromolar concentrations of the phenylurea herbicide linuron. After 7 days of exposure to linuron, log‐logistic‐based dose–response analysis revealed significant growth inhibition on the total frond area of L. minor when linuron concentrations ≥ 80 nM were added to the bioassay. A plant‐protective effect was obtained for all concentrations > 80 nM by inoculation with either a bacterial consortium or Variovorax paradoxus WDL1, which is probably the main actor in this consortium. The outcome of the plant–microbe–toxicant interaction was also assessed using pulse amplitude‐modulated chlorophyll a fluorescence and chlorophyll a fluorescence imaging. Linuron toxicity to L. minor became apparent as a significant decrease in the effective quantum yield (ΔF/Fm′) within 90 min after exposure of the plants to linuron concentrations ≥ 160 nM. Inoculation of the bioassay with the linuron‐degrading bacteria neutralized the effect on the effective quantum yield at concentrations ≥ 160 nM, indicating microbial degradation of these concentrations. The chlorophyll a fluorescence‐based Lemna bioassay described here offers a sensitive, fast and cost‐effective approach to study the potential of biodegrading microorganisms to break down minute concentrations of photosynthesis‐inhibiting xenobiotics.
The genome structure of Pseudomonas putida: high‐resolution mapping and microarray analysis
Authors: Stjepandic´ Diana , Weinel Christian , Hilbert Helmut , Koo Hean L. , Diehl Frank , Nelson Karen E. , Tümmler Burkhard , Hoheisel Jörg D.
Published: March 2003

As part of a collaborative project aimed at sequencing and functionally analysing the entire genome of Pseudomonas putida strain KT2440, a physical clone map was produced as an initial resource. To this end, a high‐coverage cosmid library was arrayed and ordered by clone hybridizations. Restriction fragments generated by rare‐cutting enzymes and plasmids containing the rrn operon and 23S rDNA of Pseudomonas aeruginosa were used as probes and, parts of the cosmids were end‐sequenced. This provided the information necessary for merging and comparing the macro‐restriction map, cosmid clone order and sequence information, thereby assuring co‐linearity of the eventual sequence assembly with the actual genome. A tiling path of clones was selected, from the shotgun clones used for sequencing, for the production of DNA microarrays that represent the entire genome including its non‐coding portions.
Pseudomonas aeruginosa biofilms react with and precipitate toxic soluble gold
Authors: Karthikeyan S. , Beveridge T. J.
Published: March 2003

The interaction between biofilms of Pseudomonas aeruginosa PAO1 and 0.01–5 mM gold chloride was investigated using flow‐cells. Scanning confocal laser microscopy (SCLM) of these biofilms revealed the formation of two distinct structural features: (i) confluent areas of uniform thickness and (ii) cell clusters which often emerged as 30–40 µm, tall narrow pillars (or pedestals) of cells and exopolymeric substance (EPS). When 5‐day‐old, quasi‐steady state biofilms (as indicated by the stability of film thickness and overall structure) were exposed to relatively high AuCl3 (i.e. 0.5–5 mM) for 30 min at 20°C, reduction of the auric ion resulted in the formation of both extracellular and intracellular metallic gold colloids, as revealed by transmission electron microscopy (TEM). Most mineralization occurred on cell surfaces with lesser amounts within cells and little throughout the EPS. Little to no mineralization of gold was seen at 0.01–0.1 mM concentrations. As initial AuCl3 concentrations approached 0.5 mM or greater, more gold particles were seen and cell viability, as determined by a BacLight® live/dead viability probe, approached zero. At an intermediate concentration of 0.1 mM, the live:dead ratio increased to 4:1. However, when planktonic cells were exposed to this same 0.1 mM concentration, it resulted in a 4‐log reduction in viable counts as determined by plating. The higher resistance of biofilm cells to 0.1 mM gold can be attributed to its binding to the EPS and cell surfaces of the biofilm which ensured a (presumably) low effective cytoplasmic concentration of gold (i.e. no gold crystals were seen in cells by TEM). In addition, SCLM revealed the formation of larger extracellular gold crystals at the substratum (coverslip) level of the biofilms, with a higher proportion of crystals detected beneath pillars (cell cluster structures), suggesting the possibility of unique cell types, more reduced microenvironments at the base of each cluster, or a combination of both. These results suggest that the biomineralization of gold is impacted by biofilm structure.
A fluorimetric method for the estimation of G+C mol% content in microorganisms by thermal denaturation temperature
Authors: Gonzalez J. M. , Saiz‐Jimenez C.
Published: March 2003

G+C mol% content in microorganisms is one of the recommended characteristics for the standard description of bacterial species. In this study we present a novel fluorimetric method to estimate the G+C mol% content in microorganisms. Double‐stranded DNA was specifically stained with SYBR Green I, and its thermal denaturalization was followed by measuring a decrease in fluorescence using a real‐time PCR thermocycler. Unlike most previous determinations of G+C mol%, in this study only DNA from microorganisms with an available completely sequenced genome were used to prepare the calibration curves. Calibration curves showed a linear relationship between G+C mol% content and melting temperature and they were performed both in the absence and presence of 30% formamide. This protocol proves to be a rapid and inexpensive method to estimate DNA base ratios of novel microorganisms.
Rectoceles: value of videodefaecography in selection of treatment policy
Authors: Marti  , Roche  , Déléaval
Published: March 2003

Videodefaecography allows identification of three different types of rectoceles: type I or digitiform rectocele, type II or rectocele with a lax rectovaginal septum, an anterior mucosal prolapse and a deep pouch of Douglas, and a type III in which a rectocele is associated with intussusception or even rectal prolapse. Furthermore, videodefaecography gave information on functional mechanisms resulting in incontinence or constipation. Surgical treatment should be tailored to the radiological and clinical findings: endoanal approach in type I, posterior colpomyorhaphy in type II and double abdomino‐vaginal approach in type III. One hundred and fifty cases were prospectively treated according to this policy. Recurrence occurred in one out of 150 cases (1.3%). Incontinence was cured in 93% and constipation in 88%.
Introducing the circular stapling device atraumatically with the use of a second anvil
Authors: Pikarsky  , Singh  , Wexner
Published: March 2003

Inserting a second anvil to the blunt end of circular stapling devices, when open placement of the distal purse‐string is employed, lessens the risk of injury to the anal canal and allows smooth introduction. Once inserted, the anvil is easily removed and the anastomosis is constructed in the usual fashion.
Indications for performing transanal endoscopic microsurgery (TEM) in rectal cancer patients
Authors: Ikeda  , Mori  , Abe  , Koyanagi  , Akahoshi  , Sugimachi
Published: March 2003

Objective

The aim of this study was to clarify the application of a local excision using TEM for rectal cancer.

Patients and methods

Fifteen patients were preoperatively diagnosed to have cancer invasion in the submucosa (T1) and thus were treated by TEM, while 13 others were preoperatively diagnosed to have cancer invasion reaching the muscularis propria (T2) and thus were treated by a radical operation. Surgical specimens from all 28 patients were pathologically examined and compared with the preoperative evaluation.

Results

The mean operating time for TEM was 53 min. The accuracy of the preoperative evaluation for the depth of cancer invasion was 68% (19/28). In the 15 patients with preoperative evaluation of T1 cancer, two pathologically showed cancer invasion into muscularis propria. In the 13 patients with a preoperative evaluation of T2 cancer, three pathologically showed cancer invasion within the submucosa.

Conclusion

Since some patients with a preoperative evaluation of T2 rectal cancer showed the possibility of a complete cure with a local excision, preoperative T2 stage rectal cancer is considered to be a good candidate for a local excision using TEM.
Clinicopathological management of the patient with a malignant colorectal adenoma
Authors: Haboubi  , Scott
Published: March 2003

A malignant adenoma of the colorectum is defined as an adenoma in which cancer has invaded by direct continuity through the muscularis mucosae into the submucosa [ 1]. The biological basement membrane of the colon is the muscularis mucosae. Thus the term ‘cancer’ cannot be applied to a neoplastic polyp which is confined to the mucosa and does not have the potential to metastases [
2–4]. The term polypoid carcinoma is reserved for a polyp which is entirely replaced by carcinoma. There is however no practical benefit in distinguishing between the terms malignant adenoma and polypoid carcinoma [
1,
4,
5]. The term carcinoma‐in‐situ is used by some to describe an adenoma containing severe dysplasia. Not having invaded through the muscularis mucosa, it is not a carcinoma. When the diagnosis of malignant polyp is presented by the clinician to the patient, a decision is needed as to whether the polypectomy on its own is sufficient therapy or whether the patient should be subjected to surgical resection. What are the pathological and clinical factors that contribute to this decision? This review examines the issues that require consideration to arrive at a balanced view of this difficult dilemma and to allow the patient to give informed consent to the management option decided upon.