bluuebunny/crossref_metadata_2025 huggingface dataset:
Impacts of landscape structure on butterfly range expansion
Authors: Hill J.K. , Collingham Y.C. , Thomas C.D. , Blakeley D.S. , Fox R. , Moss D. , Huntley B.
Published: March 2003

Since the 1940s, the distributions of several butterfly species have been expanding in northern Europe, probably in response to climate warming. We focus on the speckled wood butterfly Pararge aegeria in order to determine impacts of habitat availability on expansion rates. We analyse observed expansion rates since 1940 and also use a spatially explicit mechanistic model (MIGRATE) to simulate range expansion in two areas of the UK which differ in their distribution of breeding habitat (woodland). Observed and simulated expansion rates were in very close agreement but were 42%–45% slower in an area that had 24% less woodland. Unlike P. aegeria, the majority of butterfly species are not currently expanding, almost certainly because of lack of suitable habitat. Incorporating the spatial distribution of habitat into investigations of range changes is likely to be important in determining those species that can and cannot expand, and for predicting potential future range changes.
Chaos and population control of insect outbreaks
Authors: Desharnais Robert A. , Costantino R.F. , Cushing J.M. , Henson Shandelle M. , Dennis Brian
Published: March 2003

We used small perturbations in adult numbers to control large fluctuations in the chaotic demographic dynamics of laboratory populations of the flour beetle Tribolium castaneum. A nonlinear mathematical model was used to identify a sensitive region of phase space where the addition of a few adult insects would result in a dampening of the life stage fluctuations. Three experimental treatments were applied: one in which perturbations were made whenever the populations were inside the sensitive region (“in‐box treatment”), another where perturbations were made whenever the populations were outside the sensitive region (“out‐box treatment”), and an unperturbed control. The in‐box treatment caused a stabilization of insect densities at numbers well below the peak values exhibited by the out‐box and control populations. This study demonstrates how small perturbations can be used to influence the chaotic dynamics of an ecological system.
Effects of perceived danger on flower choice by bees
Authors: Dukas Reuven
Published: March 2003

Studies on animal–flower interactions have mostly neglected the third trophic level of pollinators’ predators, even though antipredatory behaviour of pollinators may affect patterns of pollinator visitation, pollen transfer and floral traits. In three experiments, it was found that honeybees showed sensitivity to perceived danger at flowers by preferring apparently safe flowers over equally rewarding alternatives harbouring either a dead bee or a spider, and avoiding revisitation of a site where the bees had escaped a simulated predation attempt. These results suggest that bees, like other animals, take antipredatory measures, which may have far reaching effects on animal–flower interactions.
Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness
Authors: Gotelli Nicholas J. , Colwell Robert K.
Published: March 2003

Species richness is a fundamental measurement of community and regional diversity, and it underlies many ecological models and conservation strategies. In spite of its importance, ecologists have not always appreciated the effects of abundance and sampling effort on richness measures and comparisons. We survey a series of common pitfalls in quantifying and comparing taxon richness. These pitfalls can be largely avoided by using accumulation and rarefaction curves, which may be based on either individuals or samples. These taxon sampling curves contain the basic information for valid richness comparisons, including category–subcategory ratios (species‐to‐genus and species‐to‐individual ratios). Rarefaction methods – both sample‐based and individual‐based – allow for meaningful standardization and comparison of datasets. Standardizing data sets by area or sampling effort may produce very different results compared to standardizing by number of individuals collected, and it is not always clear which measure of diversity is more appropriate. Asymptotic richness estimators provide lower‐bound estimates for taxon‐rich groups such as tropical arthropods, in which observed richness rarely reaches an asymptote, despite intensive sampling. Recent examples of diversity studies of tropical trees, stream invertebrates, and herbaceous plants emphasize the importance of carefully quantifying species richness using taxon sampling curves.
Contrasting effects of solar UV radiation on dissolved organic sources for bacterial growth
Authors: Tranvik Lars J. , Bertilsson Stefan
Published: March 2003

The photochemical transformation of dissolved organic matter (DOM) in lakes and oceans has been shown to either reduce or enhance bacterial utilization. We compared the effects of UV radiation on the bacterial use of DOM in a wide range of lakes. Although complex DOM was converted in all irradiated samples into carboxylic acids that are readily utilized by bacteria, irradiation in several lakes resulted in a decreased ability of DOM to support bacterial growth. The effect of irradiation on the ability of DOM to promote bacterial growth was a positive function of the terrestrial humic matter, and a negative function of indigenous algal production. We suggest that the net effect of irradiation is a result of counteracting but concurrent processes rendering DOM either labile or recalcitrant. Humic DOM is predominantly transformed into forms of increased lability, whereas photochemical transformation into compounds of decreased bacterial substrate quality dominates in algal‐derived DOM. Hence, solar‐induced photochemical reactions interact with microbial degraders in different ways, depending on the origin and nature of the organic matter, affecting the transfer of energy within aquatic food webs, as well as the degradation and preservation of detrital organic matter, in different directions.
Coevolutionary interactions in a host–parasite system
Authors: Soler Juan José , Martínez Juan Gabriel , Soler Manuel , Møller Anders Pape
Published: March 2003

Interactions between parasitic cuckoos and their hosts represent a classic example of coevolution, where adaptations in the parasite to exploit the host select for defences, which in turn select for new parasite adaptations. Current interactions between the two parties may be at an evolutionary equilibrium or, alternatively, a coevolutionary arms race may be taking place. By taking into account the effect of gene flow in 15 European magpie (Pica pica) populations, we studied the coevolutionary interactions with its brood parasite, the great spotted cuckoo (Clamator glandarius). Our results suggest that, in Europe, magpies and cuckoos are engaged in an ongoing coevolutionary process because, despite controlling for the large amounts of gene flow among different magpie populations, we still found a positive relationship between host defence (i.e. foreign egg recognition and rejection) and parasite selection pressure.
Antioxidants, showy males and sperm quality
Authors: Blount Jonathan D. , Møller Anders Pape , Houston David C.
Published: March 2003

The fertility of males sometimes correlates with their ornamental display, but we do not have a mechanistic explanation to universally link these traits. We suggest that both sperm quality (fertility; integrity of DNA), and the substrates responsible for male ornamentation, may be vulnerable to free radical attack, which can be mitigated by antioxidants. Support for these ideas is at present weak, and requires validation in ecological contexts. We hypothesize that a link between ornamentation and sperm quality could arise if antioxidants are in limited supply, and the showiest males may be preferred because they are most likely to be fertile, or to provide sperm with undamaged genotypes that could give rise to fit offspring.
Towards a solution of the plankton paradox: the importance of physiology and life history
Authors: Huisman Jef , Johansson Anna M. , Folmer Eelke O. , Weissing Franz J.
Published: March 2003

Phytoplankton communities reveal an astonishing biodiversity, whereas classical competition theory seems to suggest that only a few competing species can survive. Recently we suggested a new solution to this plankton paradox. In theory, at least, competition between multiple species can generate complex dynamics that can support a large number of species. How likely is it then, in reality, that competitive chaos indeed promotes biodiversity? To obtain some insight, we simulated multispecies competition according to five different physiological scenarios. For random species parameters, biodiversity was generally low. Assuming plausible physiological trade‐offs, the simulations revealed switches back and forth between equilibrium and nonequilibrium dynamics, and a higher biodiversity. An extremely high biodiversity, with sometimes more than 100 species on three resources, was observed in simulations that assumed a cyclic relation between competitive abilities and resource contents. We conclude that physiological and life‐history patterns have a major impact on the likelihood of nonequilibrium dynamics and on the biodiversity of plankton communities.
Protandrous arrival timing to breeding areas: a review
Authors: Morbey Yolanda E. , Ydenberg Ronald C.
Published: March 2003

Protandry, the earlier arrival of males to breeding areas than females, is a common pattern of sex‐biased timing in many animal taxa (e.g. some insects, fish, amphibians, reptiles, birds and mammals). The adaptive significance of protandry is not fully understood and, since the 1970s, at least seven hypotheses for protandry have been proposed. We describe each of these hypotheses and summarize what is known about each. In three of these hypotheses, the relative arrival timing of males and females has no direct fitness consequences for males or females, but selection for different timing in each sex indirectly produces protandry. In the other four hypotheses, the difference between male and female timing has fitness consequences for males or females and selection directly maintains the fitness‐maximizing degree of sex‐biased timing. The hypotheses are not mutually exclusive, and the degree of multiple mating by males and the occurrence of male territoriality seem to determine the relative importance of each hypothesis. In order to understand the adaptive significance of sex‐biased timing, future studies need to consider all the alternatives and to assess the costs and benefits to males of early arrival relative to calendar date, to other males and to females.
Genetic differences in growth of an invasive tree species
Authors: Siemann Evan , Rogers William E.
Published: March 2003

Invasive plants are often more vigorous in their introduced ranges than in their native ranges. This may reflect an innate superiority of plants from some habitats or an escape from their enemies. Another hypothesis proposes that invasive plants evolve increased competitive ability in their introduced range. We present the results of a 14‐year common garden experiment with the Chinese Tallow Tree (Sapium sebiferum) from its native range (Asia), place of introduction to North America (Georgia) and areas colonized a century later (Louisiana and Texas). Invasive genotypes, especially those from recently colonized areas, were larger than native genotypes and more likely to produce seeds but had lower quality, poorly defended leaves. Our results demonstrate significant post‐invasion genetic differences in an invasive plant species. Post‐introduction adaptation by introduced plants may contribute to their invasive success and make it difficult to predict problem species.
Sperm environment affects offspring quality in broadcast spawning marine invertebrates
Authors: Marshall Dustin John , Styan Craig Andrew , Keough Michael James
Published: March 2003

The provisioning of offspring can have far‐reaching consequences for later life in a wide range of organisms and generally this provisioning is thought to be under maternal influence or control. In experiments with a broadcast‐spawning ascidian, we found that the size of offspring was determined by egg size and the abundance of sperm present during fertilization. Larger eggs were fertilized at low sperm concentrations, whilst smaller eggs were successfully fertilized at high sperm concentrations. These differences in fertilized egg size resulted in differences in the development rate, hatching success and mean size of the subsequent larvae. Our results suggest that, in contrast to females that reproduce by other mating systems, free‐spawning mothers lack some control over the provisioning of offspring. Furthermore, because males can alter the sperm environment, they can exert paternal (non‐genetic) control over key offspring characteristics.
Food web structure and climate effects on the dynamics of small mammals and owls in semi‐arid Chile
Authors: Lima Mauricio , Stenseth Nils C. , Jaksic Fabian M.
Published: March 2003

Population dynamics of small mammals and predators in semi‐arid Chile is positively correlated with rainfall associated with incursions of El Niño (El Niño Southern Oscillation: ENSO). However, the causal relationships between small mammal fluctuations, predator oscillations, and climatic disturbances are poorly understood. Here, we report time series models for three species of small mammal prey and two species of owl predators. The large differences in population fluctuations between the three small mammal species are related to differences in their respective feedback structures. The analyses reveal that per capita growth rate of the leaf‐eared mouse is a decreasing function of log density and of log barn owl abundance together with a positive rainfall effect. In turn, per capita population growth rate (R‐function) of the barn owl is a negative function of log barn owl abundance and a positive function of leaf‐eared mouse abundance, suggesting a predator–prey interaction. The dramatic population fluctuations exhibited by leaf‐eared mouse (Phyllotis darwini) are caused by climate effects coupled with a complex food web architecture.
The interaction between predation and competition: a review and synthesis
Authors: Chase Jonathan M. , Abrams Peter A. , Grover James P. , Diehl Sebastian , Chesson Peter , Holt Robert D. , Richards Shane A. , Nisbet Roger M. , Case Ted J.
Published: March 2003

This review discusses the interface between two of the most important types of interactions between species, interspecific competition and predation. Predation has been claimed to increase, decrease, or have little effect on, the strength, impact or importance of interspecific competition. There is confusion about both the meaning of these terms and the likelihood of, and conditions required for, each of these outcomes. In this article we distinguish among three measures of the influence of predation on competitive outcomes: short‐term per capita consumption or growth rates, long‐term changes in density, and the probability of competitive coexistence. We then outline various theoretical mechanisms that can lead to qualitatively distinct effects of predators. The qualitative effect of predators can depend both on the mechanism of competition and on the definition of competitive strength/impact. In assessing the empirical literature, we ask: (1) What definitions of competitive strength/impact have been assumed? (2) Does strong evidence exist to support one or more of the possible mechanisms that can produce a given outcome? (3) Do biases in the choice of organism or manipulation exist, and are they likely to have influenced the conclusions reached? We conclude by discussing several unanswered questions, and espouse a stronger interchange between empirical and theoretical approaches to this important question.
Indirect effect of aquatic insect emergence on a terrestrial insect population through by birds predation
Authors: Murakami Masashi , Nakano Shigeru
Published: March 2003

A manipulative field experiment was performed to determine the effect of birds, subsidized by aquatic insect emergence, on the insect herbivores in a riparian deciduous forest. Insectivorous birds were observed more frequently in the riparian forest than in upland forest away from the stream, utilizing both herbivorous insects feeding on the riparian vegetation and aquatic insects emerging from the stream as their prey. Field experiments revealed that the insect herbivore population in the riparian forest was more depressed by bird predation than that in the upland forest. This suggests that allochthonous prey input to the in situ prey population was responsible for a modification in the interaction between birds and herbivorous insects, resulting in a heterogeneous food web structure in the forest.
An ecological cost of plant defence: attractiveness of bitter cucumber plants to natural enemies of herbivores
Authors: Agrawal Anurag A. , Janssen Arne , Bruin Jan , Posthumus Maarten A. , Sabelis Maurice W.
Published: March 2003

Plants produce defences that act directly on herbivores and indirectly via the attraction of natural enemies of herbivores. We examined the pleiotropic effects of direct chemical defence production on indirect defence employing near‐isogenic varieties of cucumber plants (Cucumis sativus) that differ qualitatively in the production of terpenoid cucurbitacins, the most bitter compounds known. In release–recapture experiments conducted in greenhouse common gardens, blind predatory mites were attracted to plants infested by herbivorous mites. Infested sweet plants (lacking cucurbitacins), however, attracted 37% more predatory mites than infested bitter plants (that produce constitutive and inducible cucurbitacins). Analysis of the headspace of plants revealed that production of cucurbitacins was genetically correlated with large increases in the qualitative and quantitative spectrum of volatile compounds produced by plants, including induced production of (E )‐β‐ocimene (3E )‐4,8‐dimethyl‐1,3,7‐nonatriene, (E,E)‐α‐farnesene, and methyl salicylate, all known to be attractants of predators. Nevertheless, plants that produced cucurbitacins were less attractive to predatory mites than plants that lacked cucurbitacins and predators were also half as fecund on these bitter plants. Thus, we provide novel evidence for an ecological trade‐off between direct and indirect plant defence. This cost of defence is mediated by the effects of cucurbitacins on predator fecundity and potentially by the production of volatile compounds that may be repellent to predators.
Complexity in conservation: lessons from the global decline of amphibian populations
Authors: Blaustein Andrew R. , Kiesecker Joseph M.
Published: March 2003

As part of an overall “biodiversity crisis” many amphibian populations are in decline throughout the world. Numerous causes have been invoked to explain these declines. These include habitat destruction, climate change, increasing levels of ultraviolet radiation, environmental contamination, disease, and the introduction of non‐native species. In this paper, we argue that amphibian population declines are caused by different abiotic and biotic factors acting together in a context‐dependent fashion. Moreover, different species and different populations of the same species may react in different ways to the same environmental insult. Thus, the causes of amphibian population declines will vary spatially and temporally. Although some generalizations (e.g. those concerning environmental stress and disease outbreaks) can be made about amphibian population declines, we suggest that these generalizations take into account the context‐dependent dynamics of ecological systems.
Latency in response of barn swallowHirundo rusticapopulations to changes in breeding habitat conditions
Authors: Ambrosini Roberto , Bolzern Anna Maria , Canova Luca , Saino Nicola
Published: March 2003

Inclusion of past, in addition to current ecological conditions can improve the realism of animal‐habitat models, because populations may show delayed responses to changing environments. We studied the relationships between the distribution of barn swallows (Hirundo rusticaL.) in 2001 and ecological factors between 1986 and 2001. Livestock farming was the best predictor of swallow distribution. Maximum predictive power of swallow abundance was achieved by livestock farming data 7 years before the census and significantly earlier than 2001, as shown by a bootstrap analysis. Breeding philopatry, social facilitation of breeding habitat choice may delay response of barn swallow populations to rapidly changing ecological conditions in anthropogenic habitats. By bootstrapping the set of farms and applying our predictive distribution models to livestock farming data in the past and those predicted for the near future we forecast no significant change in swallow populations until 2015. This study suggests that population studies should incorporate historical ecological data.
A cross‐ecosystem comparison of the strength of trophic cascades
Authors: Shurin Jonathan B. , Borer Elizabeth T. , Seabloom Eric W. , Anderson Kurt , Blanchette Carol A. , Broitman Bernardo , Cooper Scott D. , Halpern Benjamin S.
Published: March 2003

Although trophic cascades (indirect effects of predators on plants via herbivores) occur in a wide variety of food webs, the magnitudes of their effects are often quite variable. We compared the responses of herbivore and plant communities to predator manipulations in 102 field experiments in six different ecosystems: lentic (lake and pond), marine, and stream benthos, lentic and marine plankton, and terrestrial (grasslands and agricultural fields). Predator effects varied considerably among systems and were strongest in lentic and marine benthos and weakest in marine plankton and terrestrial food webs. Predator effects on herbivores were generally larger and more variable than on plants, suggesting that cascades often become attenuated at the plant–herbivore interface. Top‐down control of plant biomass was stronger in water than on land; however, the differences among the five aquatic food webs were as great as those between wet and dry systems.
Large tree mortality and the decline of forest biomass following Amazonian wildfires
Authors: Barlow Jos , Peres Carlos A. , Lagan Bernard O. , Haugaasen Torbjorn
Published: March 2003

Surface fires in Amazonian forests could contribute as much as 5% of annual carbon emissions from all anthropogenic sources during severe El Niño years. However, these estimates are based on short‐term figures of post‐burn tree mortality, when large thicker barked trees (representing a disproportionate amount of the forest biomass) appear to resist the fires. On the basis of a longer term study, we report that the mortality of large trees increased markedly between 1 and 3 years, more than doubling current estimates of biomass loss and committed carbon emissions from low‐intensity fires in tropical forests.
Dispersal and transient dynamics in metapopulations
Authors: Labra Fabio A. , Lagos Nelson A. , Marquet Pablo A.
Published: March 2003

Abstract Recent studies of spatially explicit metapopulation models have shown the existence of complex transient behaviour (supertransients and mesotransients) characterized by spontaneous changes in the system's dynamics after thousands or hundreds of generations, respectively. Their detection in simple ecological models has been taken as evidence that transient dynamics may be common in nature. In this study, we explore the generality of these phenomena in a simple one‐dimensional spatially explicit metapopulation model. We investigate how frequently supertransient behaviour emerges in relation to the shape and type of the dispersal kernel used (normal and Laplace), system size, boundary conditions and how sensitive they are to initial conditions. Our results show that supertransients are rare, are heavily affected by initial conditions and occur for a small set of dispersal parameter values, which vary according to kernel type, system size, and boundary conditions. Similarly, mesotransients emerge over a very narrow range of dispersal parameter values and are rare under all circumstances. Thus, transient dynamics are not likely to be either common or widespread in simple models of ecological systems.
Mixed infections and insect–pathogen interactions
Authors: Thomas Matthew B. , Watson Emma L. , Valverde‐Garcia Pablo
Published: March 2003

Abstract Most studies of insect–pathogen interactions consider the direct interaction between one disease agent and one species of host. However, given that hosts are subject to challenge from many pathogen/parasite species, mixed infections are probably common. In this study, using the desert locust and two species of fungal entomopathogen, we show how mixed infection with a largely avirulent pathogen can alter the virulence and reproduction of a second, highly virulent pathogen. We find that two strains of the avirulent pathogen vary in their interaction with the virulent pathogen, depending on the order of infection and environmental conditions. We propose that avirulent pathogens, which have largely been overlooked to date, could play a significant role in host–pathogen dynamics, with implications for biological control and evolution of virulence.
Do species evenness and plant density influence the magnitude of selection and complementarity effects in annual plant species mixtures?
Authors: Polley H. Wayne , Wilsey Brian J. , Derner Justin D.
Published: March 2003

Abstract Plant species richness influences primary productivity via mechanisms that (1) favour species with particular traits (selection effect) and (2) promote niche differentiation between species (complementarity). Influences of species evenness, plant density and other properties of plant communities on productivity are poorly defined, but may depend on whether selection or complementarity prevails in species mixtures. We predicted that selection effects are insensitive to species evenness but increase with plant density, and that the converse is true for complementarity. To test predictions, we grew three species of annuals in monocultures and in three‐species mixtures in which evenness of established plants was varied at each of three plant densities in a cultivated field in Texas, USA. Above‐ground biomass was smaller in mixtures than expected from monocultures because of negative ‘complementarity’ and a negative selection effect. Neither selection nor complementarity varied with species evenness, but selection effects increased at the greatest plant density as predicted.
Molecular screening for alkane hydroxylase genes in Gram‐negative and Gram‐positive strains
Authors: Smits Theo H. M. , Röthlisberger Martina , Witholt Bernard , Van Beilen Jan B.
Published: March 2003

We have developed highly degenerate oligonucleotides for polymerase chain reaction (PCR) amplification of genes related to the Pseudomonas oleovorans GPo1 and Acinetobacter sp. ADP1 alkane hydroxylases, based on a number of highly conserved sequence motifs. In all Gram‐negative and in two out of three Gram‐positive strains able to grow on medium‐ (C6–C11) or long‐chain n‐alkanes (C12–C16), PCR products of the expected size were obtained. The PCR fragments were cloned and sequenced and found to encode peptides with 43.2–93.8% sequence identity to the corresponding fragment of the P. oleovorans GPo1 alkane hydroxylase. Strains that were unable to grow on n‐alkanes did not yield PCR products with homology to alkane hydroxylase genes. The alkane hydroxylase genes of Acinetobacter calcoaceticus EB104 and Pseudomonas putida P1 were cloned using the PCR products as probes. The two genes allow an alkane hydroxylase‐negative mutant of Acinetobacter sp. ADP1 and an Escherichia coli recombinant containing all P. oleovorans alk genes except alkB, respectively, to grow on n‐alkanes, showing that the cloned genes do indeed encode alkane hydroxylases.
Reduction of (per)chlorate by a novel organism isolated from paper mill waste
Authors: Bruce Royce A. , Achenbach Laurie A. , Coates John D.
Published: March 2003

As part of a study on the microbiology of chlorate reduction, several new dissimilatory chlorate‐reducing bacteria were isolated from a broad diversity of environments. One of these, strain CKB, was selected for a more complete characterization. Strain CKB was enriched and isolated from paper mill waste with acetate as the sole electron donor and chlorate as the sole electron acceptor. Strain CKB is a completely oxidizing, non‐fermentative, Gram‐negative, facultative anaerobe. Cells of strain CKB are 0.5 × 2 μm and are highly motile, with a single polar flagellum. In addition to acetate, strain CKB can use propionate, butyrate, lactate, succinate, fumarate, malate or yeast extract as electron donors, with chlorate as the sole electron acceptor. Strain CKB can also couple chlorate reduction to the oxidation of ferrous iron, sulphide, or the reduced form of the humic substances analogue 2,6‐anthrahydroquinone disulphonate. Fe(II) is oxidized to insoluble amorphous Fe(III) oxide, whereas sulphide is oxidized to elemental sulphur. Growth is not associated with this metabolism, even when small quantities of acetate are added as a potential carbon source. In addition to chlorate, strain CKB can also couple acetate oxidation to the reduction of oxygen or perchlorate. Chlorate is completely reduced to chloride. Strain CKB has an optimum temperature of 35°C, a pH optimum of 7.5 and a salinity optimum of 1% NaCl. Strain CKB can grow in chlorate and perchlorate concentrations of 80 or 20 mM respectively. Under anaerobic conditions, strain CKB can dismutate chlorite into chloride and O2, and is only the second organism shown to be capable of this metabolism. Oxidized minus reduced spectra of whole‐cell suspensions of strain CKB showed absorbance maxima at 423, 523 and 552 nm, which are indicative of the presence of c‐type cytochrome(s). Analysis of the complete sequence of the 16S rDNA indicates that strain CKB is a member of the beta subclass of the Proteobacteria. The phototroph Rhodocyclus tenuis is the closest known relative. When tested, strain CKB could not grow by phototrophy and did not contain bacteriochlorophyll. Phenotypically and phylogenetically, strain CKB differs from all other described bacteria and represents the type strain of a new genus and species.
The hexY genes of Erwinia carotovora ssp. carotovora and ssp. atroseptica encode novel proteins that regulate virulence and motility co‐ordinately
Authors: Shih Yu‐Ling , Harris Stephen J. , Borner Georg , Rivet Michèle M. , Salmond George P. C.
Published: March 2003

Mutations located in a new gene, hexY, in Erwinia carotovora ssp. carotovora (Ecc ) and ssp. atroseptica (Eca ) cause strong upregulation of production of exoenzyme virulence factors and motility. The hexY gene encodes a novel 14.4 kDa protein with no known homologues. The hexY mRNA transcript has an unusually long (525 bp) 5′ untranslated region, which may be important for post‐transcriptional regulation. An elevated level of transcription of two exoenzyme genes, pelC and celV, was observed in the HexY mutant background. The levels of cellulase and protease in a HexY mutant were independent of the presence of PGA, suggesting a role for HexY in the induction of these enzymes seen upon PGA addition. Electron microscopy revealed that HexY cells were hyperflagellated, perhaps contributing to the hypermotility phenotype of this mutant. The HexY mutant M5 exhibited enhanced maceration capacity on potato tubers. Therefore, the hexY gene and its gene product may define another level of regulation of virulence determinants in Ecc and Eca.
Green algal extracellular products regulate antialgal toxin production in a cyanobacterium
Authors: Kearns Katherine Dowell , Hunter Mark D.
Published: March 2003

Many bacterial genes and virulence factors are regulated by interbacterial and/or host–parasite chemical signals. We demonstrate that toxin production by a free‐living freshwater cyanobacterium is regulated in part by the presence of extracellular products of a eukaryotic green alga. In growth experiments, extracellular products made by the cyanobacterium Anabaena flos‐aquae contained both anatoxin and microcystin, and significantly reduced the yield of Chlamydomonas reinhardtii, a green alga. Based on experiments in which we added purified toxins to C. reinhardtii cultures, we believe that microcystin was responsible for the growth reduction. A. flos‐aquae produced anatoxin constitutively when grown alone, but anatoxin concentration increased in the presence of C. reinhardtii elicitors. Microcystin accumulation depended on the growth phase; however, high concentrations of C. reinhardtii extracellular products completely inhibited microcystin accumulation. Our results demonstrate that cyanobacterial toxin production may be regulated by complex growth phase‐dependent and environmental chemical cues, and suggest that secreted chemicals can mediate the outcome of competition between the cyanobacterium A. flos‐aquae and the green alga C. reinhardtii.
Disruption of the Paenibacillus polymyxa levansucrase gene impairs its ability to aggregate soil in the wheat rhizosphere
Authors: Bezzate Samira , Aymerich Stéphane , Chambert Régis , Czarnes Sonia , Berge Odile , Heulin Thierry
Published: March 2003

Inoculation of wheat roots with Paenibacillus (formerly Bacillus) polymyxa CF43 increases the mass of root‐adhering soil. We tested the role of levan, a fructosyl polymer produced by strain CF43, in the aggregation of soil adhering to wheat roots. The P. polymyxa gene homologous to the Bacillus subtilis sacB gene encoding levansucrase was cloned and sequenced. The corresponding gene product synthesises high molecular weight levan. A P. polymyxa mutant strain, SB03, whose sacB gene is disrupted, was constructed using heterogramic conjugation. Effects of wheat inoculation with the wild type and the mutant strain were compared using two different cultivated silt loam soils in four independent pot experiments. Roots of wheat plantlets inoculated with CF43 or SB03 were colonized after 7–14 days at the same level, and root and shoot masses were not significantly different from those of the non‐inoculated control plants. The ratio of root‐adhering soil dry mass to root tissue dry mass was significantly higher for plants inoculated with strain CF43 than for those inoculated with mutant strain SB03: + 30% in Orgeval soil and + 100% in Dieulouard soil. Thus the levan produced by P. polymyxa is implicated in the aggregation of root‐adhering soil on wheat.
Crenarchaeota colonize terrestrial plant roots
Authors: Simon Holly M. , Dodsworth Jeremy A. , Goodman Robert M.
Published: March 2003

Microorganisms that colonize plant roots are recruited from, and in turn contribute substantially to, the vast and virtually uncharacterized phylogenetic diversity of soil microbiota. The diverse, but poorly understood, microorganisms that colonize plant roots mediate mineral transformations and nutrient cycles that are central to biosphere functioning. Here, we report the results of epifluorescence microscopy and culture‐independent recovery of small subunit (SSU) ribosomal RNA (rRNA) gene sequences showing that members of a previously reported clade of soil Crenarchaeota colonize both young and senescent plant roots at an unexpectedly high frequency, and are particularly abundant on the latter. Our results indicate that non‐thermophilic members of the Archaea inhabit an important terrestrial niche on earth and direct attention to the need for studies that will determine their possible roles in mediating root biology.
Artificial selection of microbial ecosystems for 3‐chloroaniline biodegradation
Authors: Swenson William , Arendt Jeff , Wilson David Sloan
Published: March 2003

We present a method for selecting entire microbial ecosystems for bioremediation and other practical purposes. A population of ecosystems is established in the laboratory, each ecosystem is measured for a desired property (in our case, degradation of the environmental pollutant 3‐chloroaniline), and the best ecosystems are used as ‘parents’ to inoculate a new generation of ‘offspring’ ecosystems. Over many generations of variation and selection, the ecosystems become increasingly well adapted to produce the desired property. The procedure is similar to standard artificial selection experiments except that whole ecosystems, rather than single individuals, are the units of selection. The procedure can also be understood in terms of complex system theory as a way of searching a vast combinatorial space (many thousands of microbial species and many thousands of genes within species) for combinations that are especially good at producing the desired property. Ecosystem‐level selection can be performed without any specific knowledge of the species that comprise the ecosystems and can select ensembles of species that would be difficult to discover with more reductionistic methods. Once a ‘designer ecosystem’ has been created by ecosystem‐level selection, reductionistic methods can be used to identify the component species and to discover how they interact to produce the desired effect.
Microenvironments and distribution of nitrifying bacteria in a membrane‐bound biofilm
Authors: Schramm Andreas , De Beer Dirk , Gieseke Armin , Amann Rudolf
Published: March 2003

The distribution of nitrifying bacteria of the genera Nitrosomonas, Nitrosospira, Nitrobacter and Nitrospira was investigated in a membrane‐bound biofilm system with opposed supply of oxygen and ammonium. Gradients of oxygen, pH, nitrite and nitrate were determined by means of microsensors while the nitrifying populations along these gradients were identified and quantified using fluorescence in situ hybridization (FISH) in combination with confocal laser scanning microscopy. The oxic part of the biofilm which was subjected to high ammonium and nitrite concentrations was dominated by Nitrosomonas europaea‐like ammonia oxidizers and by members of the genus Nitrobacter. Cell numbers of Nitrosospira sp. were 1–2 orders of magnitude lower than those of N. europaea. Nitrospira sp. were virtually absent in this part of the biofilm, whereas they were most abundant at the oxic–anoxic interface. In the totally anoxic part of the biofilm, cell numbers of all nitrifiers were relatively low. These observations support the hypothesis that N. europaea and Nitrobacter sp. can out‐compete Nitrosospira and Nitrospira spp. at high substrate and oxygen concentrations. Additionally, they suggest microaerophilic behaviour of yet uncultured Nitrospira sp. as a factor of its environmental competitiveness.
Microbiology of the ‘G‐bacteria’ in activated sludge
Authors: Seviour Robert J. , Maszenan Abdul M. , Soddell Jacques A. , Tandoi Valter , Patel Bharat K. C. , Kong Yunhong , Schumann Peter
Published: March 2003

This review discusses a group of bacteria, the ‘G‐bacteria’, which have a distinctive morphology of cocci in tetrads, sheets or clusters, that are seen in large numbers in many activated sludge biomass samples. Isolates of ‘G‐bacteria’ that have been grown axenically are phylogenetically diverse. The Gram‐negative members include several α‐ and β‐proteobacteria, among which is the genus Amaricoccus, while the Gram‐positive ‘G‐bacteria’ contain several members of the actinobacteria. It is probable that other, as yet uncharacterized, ‘G‐bacteria’ exist in activated sludge. The hypothesis that these ‘G‐bacteria’ are detrimental to the process of enhanced biological phosphate removal by competing for substrates anaerobically with the phosphate‐accumulating bacteria in such systems, based as it is largely on mixed‐culture studies, receives little support from studies using those available in pure culture. The evidence on which these conclusions are founded is discussed, as are the arguments used to explain why these ‘G‐bacteria’ all appear to thrive under conditions found in certain activated sludge systems.
The effects of copper on the microbial community of a coral reef sponge
Authors: Webster Nicole S. , Webb Richard I. , Ridd Michael J. , Hill Russell T. , Negri Andrew P.
Published: March 2003

Marine sponges often harbour communities of symbiotic microorganisms that fulfil necessary functions for the well‐being of their hosts. Microbial communities associated with the sponge Rhopaloeides odorabile were used as bioindicators for sublethal cupric ion (Cu2+) stress. A combined strategy incorporating molecular, cultivation and electron microscopy techniques was adopted to monitor changes in microbial diversity. The total density of sponge‐associated bacteria and counts of the predominant cultivated symbiont (α‐proteobacterium strain NW001) were significantly reduced in response to Cu2+ concentrations of 1.7 µg l−1 and above after 14 days of exposure. The number of operational taxonomic units (OTUs) detected by restriction fragment length polymorphism (RFLP) decreased by 64% in sponges exposed to 223 µg l−1 Cu2+ for 48 h and by 46% in sponges exposed to 19.4 µg l−1 Cu2+ for 14 days. Electron microscopy was used to identify 17 predominant bacterial morphotypes, composing 47% of the total observed cells in control sponges. A reduction in the proportion of these morphotypes to 25% of observed cells was evident in sponges exposed to a Cu2+ concentration of 19.4 µg l−1. Although the abundance of most morphotypes decreased under Cu2+ stress, three morphotypes were not reduced in numbers and a single morphotype actually increased in abundance. Bacterial numbers, as detected using fluorescence in situ hybridization (FISH), decreased significantly after 48 h exposure to 19.4 µg l−1 Cu2+. Archaea, which are normally prolific in R. odorabile, were not detected after exposure to a Cu2+ concentration of 19.4 µg l−1 for 14 days, indicating that many of the microorganisms associated with R. odorabile are sensitive to free copper. Sponges exposed to a Cu2+ concentration of 223 µg l−1 became highly necrosed after 48 h and accumulated 142 ± 18 mg kg−1 copper, whereas sponges exposed to 19.4 µg l−1 Cu2+ accumulated 306 ± 15 mg kg−1 copper after 14 days without apoptosis or mortality. Not only do sponges have potential for monitoring elevated concentrations of heavy metals but also examining changes in their microbial symbionts is a novel and sensitive bioindicator for the assessment of pollution on important microbial communities.
Long‐term compositional changes after transplant in a microbial mat cyanobacterial community revealed using a polyphasic approach
Authors: Abed Raeid M. M. , Garcia‐Pichel Ferran
Published: March 2003

Using a polyphasic approach that included microscopy, cultivation and 16S rRNA‐based cultivation‐independent molecular fingerprinting, we compared the cyanobacterial composition of Solar Lake microbial mats and samples thereof transplanted and maintained in new settings for extended periods of time. Significant changes in community composition, with clear replacement of the dominant cyanobacterium, Microcoleus chthonoplastes, were detected in all cases. The most dramatic shifts occurred in a sample kept in the laboratory for 3 years, which resulted in dominance by an Oscillatoria‐like cyanobacterium whose 16S rRNA closely matched that of a morphologically similar isolate from mats in Mexico. Transfer of Solar Lake mat to an artificial experimental pond with incubation under seminatural conditions resulted in an increase in cyanobacterial diversity. Judging from the molecular signatures, two novel, previously unrecognized and phylogenetically well‐delimited cyanobacterial populations became dominant. Through cultivation, one population was shown to correspond to a filamentous, non‐heterocystous group of Cyanobacteria with very narrow trichomes (≈ 0.75–1.5 μm). The most dominant novel molecular signature, however, could not be identified by cultivation efforts or correlation with microscopy and, upon phylogenetic analyses, its 16S rRNA genes showed no particular close association to known cyanobacterial groups.
Chemical properties of catechols and their molecular modes of toxic action in cells, from microorganisms to mammals
Authors: Schweigert Nina , Zehnder Alexander J. B. , Eggen Rik I. L.
Published: March 2003

Catechols can undergo a variety of chemical reactions. In this review, we particularly focus on complex formations and the redox chemistry of catechols, which play an inportant role in the toxicity of catechols. In the presence of heavy metals, such as iron or copper, stable complexes can be formed. In the presence of oxidizing agents, catechols can be oxidized to semiquinone radicals and in a next step to o‐benzoquinones. Heavy metals may catalyse redox reactions in which catechols are involved. Further chemical properties like the acidity constant and the lipophilicity of different catechols are shortly described as well. As a consequence of the chemical properties and the chemical reactions of catechols, many different reactions can occur with biomolecules such as DNA, proteins and membranes, ultimately leading to non‐repairable damage. Reactions with nucleic acids such as adduct formation and strand breaks are discussed among others. Interactions with proteins causing protein and enzyme inactivation are described. The membrane–catechol interactions discussed here are lipid peroxidation and uncoupling. The deleterious effect of the interactions between catechols and the different biomolecules is discussed in the context of the observed toxicities, caused by catechols.
Phylogenetic structure of unusual aquatic microbial formations in Nullarbor caves, Australia
Authors: Holmes Andrew J. , Tujula Niina A. , Holley Marita , Contos Annalisa , James Julia M. , Rogers Peter , Gillings Michael R.
Published: March 2003

The nature of unusual aquatic microbial formations in flooded passages of cave systems in the Nullarbor region of Australia was investigated using electron microscopy and DNA analysis. The caves are located in a semiarid region but intersect the watertable at depths of approximately 100 m below the surface. Throughout submerged portions of the caves divers have noted the presence of unusual microbial formations. These ‘microbial mantles’ comprise sheets or tongues of mucoid material in which small crystals are embedded. Examination of the biomass revealed it to be primarily composed of densely packed, unbranched filaments, together with spherical‐, rod‐ and spiral‐shaped cells, and microcrystals of calcite in a mucoid matrix. Molecular phylogenetic analysis of the community structure revealed ∼12% of clones showed high similarity to autotrophic nitrite‐oxidizing bacteria (Nitrospira moscoviensis). The remainder of the clones exhibited a high proportion of phylogenetically novel sequence types. Chemical analysis of water samples revealed high levels of sulphate and nitrate together with significant nitrite. The community structure, the presence of nitrite in the water, and the apparent absence of aquatic macrofauna, suggest these microbial structures may represent biochemically novel, chemoautotrophic communities dependent on nitrite oxidation.