bluuebunny/crossref_metadata_2025 huggingface dataset:
Are communities saturated? On the relationship between α, β and γ diversity
Authors: Loreau Michel
Published: March 2003

A popular way to suggest a regional influence on local species diversity has been to plot local versus regional diversity. The form of these curves has been interpreted as evidence for or against “community saturation” due to species interactions. This interpretation, however, is unwarranted. Using the concepts of α, β and γ diversity, I show that local–regional richness curves are determined by the way total diversity is partitioned between its α and β components, which itself is a matter of scale. Changing the scale of the local community amounts to changing the scale at which the heterogeneity of the interactions between organisms and their environment manifests itself, and hence the balance between α and β diversity. Community saturation may occur because of physical limitations, but there are no theoretical grounds for the belief that species interactions set an absolute upper limit to diversity at any scale. A distinction between different meanings of the concept of “saturation” is proposed to clarify this issue. I argue that the challenge now is to understand the relationship between α and β diversity at multiple scales, and the processes that determine it.
Biodiversity lessens the risk of cascading extinction in model food webs
Authors: Borrvall Charlotte , Ebenman Bo , Tomas Jonsson Tomas Jonsson
Published: March 2003

Due to the complex interactions between species in food webs, the extinction of one species could lead to a cascade of further extinctions and hence cause dramatic changes in species composition and ecosystem processes. We found that the risk of additional species extinction, following the loss of one species in model food webs, decreases with the number of species per functional group. For a given number of species per functional group, the risk of further extinctions is highest when an autotroph is removed and lowest when a top predator is removed. In addition, stability decreases when the distribution of interaction strengths in the webs is changed from equal to skew (few strong and many weak links). We also found that omnivory appears to stabilize model food webs. Our results indicate that high biodiversity may serve as an insurance against radical ecosystem changes.
Consuming and grouping: recource‐mediated animal aggregation
Authors: Wilson  , Richards
Published: March 2003

We demonstrate that a simplistic foraging rule for a consumer in a spatially explicit resource environment leads to consumer grouping. Although consumer groups sweeping through the renewing resource environment represents the model’s dynamical attractor, for short time scales (represented by a constant total consumer population) three different distributions emerge. At low consumer density, population distributions are variable and spatially fixed, but not grouped. Moving groups erupt at intermediate consumer densities. At high consumer density, there is no spatial variability in the resource and consumer densities. Similar results have been observed in a variety of empirical systems. The results suggest interesting insights will arise by examining social interactions within a resource‐consumer modeling framework.
A catastrophic mass‐mortality episode of gorgonians and other organisms in the Ligurian Sea (North‐western Mediterranean), summer 1999
Authors: Cerrano C. , Bavestrello G. , Bianchi C.N. , Cattaneo‐vietti R. , Bava S. , Morganti C. , Morri C. , Picco P. , Sara G. , Schiaparelli S. , Siccardi A. , Sponga F.
Published: March 2003

In the late summer of 1999, an extensive mortality of gorgonians and other epi‐benthic organisms was observed in the Ligurian Sea (Mediterranean Sea) from the Tuscan Archipelago to Marseille. Quantitative data from Tino Island and Portofino Promontory indicated that the proportion of affected gorgonians ranged from 60% to 100% in populations having a density of 9–27.8 colonies m−2, suggesting that millions of sea fans died along the coast of Liguria. This mass mortality episode coincided with a sudden increase of sea water temperature down to more than 50 m depth. Laboratory analyses showed that the colonies stressed by high temperature also underwent extensive attack by microrganisms (protozoans and fungi), which are interpreted as opportunistic pathogens.
Dependence of sustainability on the configuration of marine reserves and larval dispersal distance
Authors: Botsford  , Hastings  , Gaines
Published: March 2003

Marine reserves hold promise for maintaining biodiversity and sustainable fishery management, but studies supporting them have not addressed a crucial aspect of sustainability: the reduction in viability of populations with planktonic larvae dispersing along a coastal habitat with noncontiguous marine reserves. We show how sustainability depends on the fraction of natural larval settlement (FNLS) remaining after reserves are implemented, which in turn depends on reserve configuration and larval dispersal distance. Sustainability requires FNLS to be greater than an empir‐ically determined minimum. Maintaining an adequate value for all species requires either a large, unlikely fraction (> 35%) of coastline in reserves, or reserves that are larger than the mean larval dispersal distance of the target species. FNLS is greater for species dispersing shorter distances, which implies reserves can lead to: (1) changes in community composition and (2) genetic selection for shorter dispersal distance. Dependence of sustainability on dispersal distance is a new source of uncertainty.
Population synchrony and environmental variation: an experimental demonstration
Authors: Benton T.G. , Lapsley C.T. , Beckerman A.P.
Published: March 2003

Understanding the causes of population synchrony is an important issue for population management. Its study in field populations involves disentangling the effects of dispersal and correlated environmental noise. Here we report on an experimental investigation of the synchronizing effects of noise in closed laboratory populations of a soil mite, Sancassania berlesei. Mite life‐histories are highly plastic with respect to resource availability (which is a function of food supply and population density). By varying the food supply we imposed environmental variation. We show that (a) population synchrony is a function of environmental synchrony, (b) perceived population synchrony depends on the life‐history stage counted, and (c) average population synchrony tends to be lower than environmental synchrony: even when populations were supplied with food with a correlation of 1.0, the correlation between populations was 0.63 (bootstrapped 95%CI 0.54–0.71). This supports recent theoretical work suggesting that the Moran theorem (indicating that population synchrony equals environmental synchrony) generally overestimates the population synchrony of nonlinear systems.
Mechanisms of positive biodiversity–production relationships: insights provided by δ13C analysis in experimental Mediterranean grassland plots
Authors: Caldeira Maria C. , Ryel Ronald J. , Lawton John H. , Pereira João S.
Published: March 2003

We investigated the role of water use in a Mediterranean grassland, in which diversity was experimentally manipulated, and a positive relationship was observed between plant species richness and productivity. Soil moisture patterns and stable carbon isotope ratios (δ13C) in leaves indicated greater water use by plants growing in species‐rich mixtures compared to monocultures. These results suggest that complementarity or facilitation may be the mechanism responsible for the positive relationship between plant diversity and ecosystem processes.
Taxon size predicts rates of rarity in vascular plants
Authors: Schwartz Mark W. , Simberloff
Published: March 2003

We surveyed rarity in the vascular plants of the continental U.S.A. and Canada and the vascular plants of Hawaii to test the hypothesis that rates of rarity are independent of taxonomic group size. We demonstrated that taxonomic groups of plants with few species consistently contained fewer than the expected numbers of rare species. This pattern was apparent at the levels of genus, family, order and class. We also found that the pattern remained when we examined rates of rarity by comparing sister taxa that share a common ancestor. This pattern may arise from either differential speciation and extinction patterns or taxonomic bias in species designations (lumping and splitting). The pattern of lineages with few species demonstrating reduced rates of rarity is opposite to that previously observed in mammals and birds. If the protection of representatives from a diversity of lineages is a conservation objective, plant conservation is facilitated by the fact that relatively few species‐poor lineages contain rare species.
Habitat patchiness and plant species richness
Authors: Bascompte Jordi , Rodríguez Miguel Á.
Published: March 2003

The pattern of woody species richness decline with a decrease in woody vegetation cover was studied within a tallgrass prairie. The decline in species richness is highly non‐linear, with a well‐defined threshold below which species richness collapses. This relationship can be understood after considering information on how landscape structure changes with woody vegetation cover, and how species richness is related to landscape structure.
Procedure for separating the selection effect from other effects in diversity–productivity relationship
Authors: Špaèková Iva , Lepš Jan
Published: March 2003

In a greenhouse pot experiment we cultivated six meadow species in a replacement series design. The plants were grown at two sowing densities in monocultures and all possible species combinations. Our aim was to separate the selection effect from other diversity effects. This distinction is based on the notion that true overyielding is not a consequence of the selection effect. We suggest a hierarchical procedure, which is based on a repeated division of samples into the pots with the most productive species present and missing. Overyielding can be then demonstrated by a positive dependence of productivity on species richness in the subsets with the most productive species present. Although we found a strong dependence of biomass on species richness in the entire data set, the hierarchical method revealed no evidence of overyielding. Above‐ground biomass in a monoculture was a good predictor of species success in a species mix.
A rodent plague on prairie diversity
Authors: Howe H. F. , Brown J. S. , Zorn‐Arnold B.
Published: March 2003

Selective vole (Microtus pennsylvanicus) suppression of prairie grasses and forbs in experimental restorations suggests why many of the plants are likely to be uncommon in nature. Vole herbivory reduced densities of legumes and grasses and increased unpalatable forbs in replicated plantings in Illinois: six otherwise common species (Dalea purpurea, Desmanthus illinoensis, Elymus canadensis, Panicum virgatum, Phalaris arundinacea, Sorghastrum nutans) declined 27–89% in abundance, whereas two species (Echinacea purpurea and Rudbeckia hirta) increased by 61% and 1023%. Species number dropped by 19% and plant diversity (Simpson’s D) by 37% in one treatment to which voles had access. Plots were planted with 18 prairie species of the region, but in even distributions of 35 or 350 seeds species−1 m−2, rather than skewed in favour of large C4 grasses common in native remnants. Manipulation of plant composition and vole access revealed what are likely to be formative effects of rodent herbivory on vegetative composition. These experimental tallgrass communities appear to be assembling from plant species that voles prefer not to eat.
Variation in nuclear DNA content across environmental gradients: a quantile regression analysis
Authors: Knight Charles A. , Ackerly David D.
Published: March 2003

The nuclear DNA content of angiosperms varies by several orders of magnitude. Previous studies suggest that variation in 2C DNA content (i.e. the amount of DNA in G1 phase nuclei, also referred to as the 2C‐value) is correlated with environmental factors, but there are conflicting reports in the literature concerning the nature of these relationships. We examined variation in 2C DNA content for 401 species in the ecologically diverse California flora in relation to the mean July maximum temperature, January minimum temperature, and annual precipitation within the geographical ranges of these species. Species with small 2C‐values predominate in all environments. Species with large 2C‐values occur at intermediate July maximum temperatures, and decline in frequency at both extremes of the July temperature gradient, and with decreasing annual precipitation. Our analysis demonstrates the utility of quantile regression for statistical inference of complex distributions such as these. The method supports our observation that relationships between nuclear DNA content and environmental factors are stronger for species with large 2C‐values.
Conservation of tropical forest birds in countryside habitats
Authors: Hughes Jennifer B. , Daily Gretchen C. , Ehrlich Paul R.
Published: March 2003

The pressing need to increase agricultural production often seems at odds with conserving biodiversity. We find that if managed properly, the tropical countryside may provide a substantial opportunity for tropical bird conservation. We detected 144 bird species from 29 families in agricultural areas outside of extensive native forest in southern Costa Rica. The majority of the species detected were observed foraging, often kilometres from extensive native forest. We estimate that 46% of those native to this region (excluding nocturnal species and waterfowl) are utilizing the countryside in some manner. Forecasts of biodiversity change under various land‐use scenarios indicate that policies that affect habitat composition could greatly impact the persistence of these species in the countryside. In particular, if tall trees and edge habitats were removed from this landscape, we predict that bird richness in the countryside would decline by approximately 40%.
Arbuscular mycorrhizal fungi affect phytophagous insect specialism
Authors: Gange Alan C. , Stagg Penny G. , Ward Lena K.
Published: March 2003

The majority of phytophagous insects eat very few plant species, yet the ecological and evolutionary forces that have driven such specialism are not entirely understood. The hypothesis that arbuscular mycorrhizal (AM) fungi can determine phytophagous insect specialism, through differential effects on insect growth, was tested using examples from the British flora. In the UK, plant families and species in the family Lamiaceae that are strongly mycorrhizal have higher proportions of specialist insects feeding on them than those that are weakly mycorrhizal. We suggest that AM fungi can affect the composition of insect assemblages on plants and are a hitherto unconsidered factor in the evolution of insect specialism.
Prospects for conserving biodiversity in Amazonian extractive reserves
Authors: Moegenburg Susan M. , Levey Douglas J.
Published: March 2003

Non‐timber forest product (NTFP) extraction is a popular alternative to timber extraction that figures prominently in efforts to utilize tropical forests sustainably. But the ability to conserve biodiversity through NTFP management, particularly in extractive reserves in Amazonia, has remained untested. We found that intensive management of Euterpe oleracea (Palmae) fruit, one of the most important extractive products in the Amazon, has substantial impacts on biodiversity, whereas moderate management does not. We mimicked traditional levels of fruit harvest in a replicated experiment over one fruiting season. High‐intensity harvest (75% of fruits removed) reduced avian frugivore species diversity by 22%. Low‐intensity harvest (40% of fruits removed), however, had no effect on diversity. On a larger scale, we found that forests with enriched densities of E. oleracea supported more fruit‐eating birds but fewer non fruit‐eating birds than non‐enriched forests. Taken together, these results suggest that intensive NTFP management to meet market demands may trigger substantial ecological impacts, at least at the level of our study. E. oleracea harvest should be limited where conservation of biodiversity is a goal.
Detecting evolutionary rate heterogeneity among mangroves and their close terrestrial relatives
Authors: Zhong Yang , Zhao Qiong , Shi Suhua , Huang Yelin , Hasegawa Masami
Published: March 2003

Mangroves form the dominant intertidal ecosystems and differ morphologically and physiologically from their close terrestrial relatives. We investigate the molecular evolutionary pattern of the typical mangrove family, i.e. Rhizophoraceae, and rate heterogeneity for the plastid matK and rbcL genes in different species of the family, as revealed by phylogenetic analyses and relative‐rate tests. Our study documents evolutionary rate heterogeneity in the Rhizophoraceae for the two genes: the mangrove genus Bruguiera has relatively slow substitution rates compared to the terrestrial genus Carallia at both synonymous and non‐synonymous sites in the matK sequences, and the synonymous and non‐synonymous substitution matrices are correlated. However, the rbcL non‐synonymous sites exhibit a high degree of rate heterogeneity among mangroves and related terrestrial groups, and uncoupling of rates with the synonymous sites. Selection is probably an important influence on the rate variation, suggesting further investigation for better understanding of various forces contributing to the rate heterogeneity and molecular adaptation in mangroves.
Differential selection of baculovirus genotypes mediated by different species of host food plant
Authors: Hodgson David J. , Vanbergen Adam J. , Hartley Susan E. , Hails Rosie S. , Cory Jenny S.
Published: March 2003

Recent studies have demonstrated high levels of genotypic and phenotypic variation in populations of parasites, even within individual hosts. Several genetic, immunological and epidemiological mechanisms have been postulated as promoters of such variation, but little empirical work has addressed the role of host ecology. A nucleopolyhedrovirus that attacks larvae of the pine beauty moth, Panolis flammea, exists as a complex mixture of genotypes within individual host larvae. We demonstrate that the food plant species eaten by the host (Scots pine vs. lodgepole pine) differentially affects the pathogenicity and productivity of two virus genotypes originally purified from a single host individual. We hypothesize that such food plant‐mediated differential selection will promote genotypic variation between baculovirus populations, and that subsequent remixing of virus genotypes could maintain genotypic variation within individual hosts. Our results provide a tritrophic explanation for the genotypic and phenotypic complexity of host–parasite interactions with complex ecologies.
Is host‐specificity of weed biological control agents likely to evolve rapidly following establishment?
Authors: Van Klinken Rieks Dekker , Edwards Owain Rhys
Published: March 2003

Over 352 herbivore species have now been intentionally introduced into new regions as weed biological control agents. Recent evidence shows that rapid and significant evolution in host‐specificity can occur. The risk of non‐target use by biological control agents increasing to unacceptable levels through rapid evolution therefore needs to be considered. In addition, weed biological control offers many as yet largely unexploited opportunities for improving our basic understanding of host‐specificity and its evolution. We therefore evaluate the evidence that rapid evolution (1) alters the use of existing hosts, and (2) alters the fundamental host‐range. Most cited examples of so‐called host shifts from weed biological control were not the result of genetic change. There was only limited evidence of genetically altered performance on a non‐target host and no evidence of altered fundamental host‐range. We conclude, from both theory and the available data, that only altered use of existing hosts (through quantitative genetic changes) needs be considered when evaluating the risk of rapid evolution. Host‐specificity testing methodologies can be improved and adapted to better assess the risk of occurrence of post‐release evolution.
Blue tits use selected plants and olfaction to maintain an aromatic environment for nestlings
Authors: Petit Cécile , Hossaert‐McKey Martine , Perret Philippe , Blondel Jacques , Lambrechts Marcel M.
Published: March 2003

Animals use the chemical compounds of plants as a defence mechanism against enemies, and sometimes use olfaction to discriminate and select the chemical plant substances. Some birds bring to the nest plant material that has volatile compounds that protect the host and their offspring against parasitic organisms. Here we show that blue tits on the island of Corsica (Parus caeruleus ogliastrae) adorn their nests with fragments of aromatic plants. These plants have chemical compounds that are used by humans to make aromatic house cleaners and herbal medicines. We also show that individual blue tits maintain an aromatic nest environment when offspring are raised, using odour cues to determine the frequency with which they replenish the nest with fresh plant material. We provide an exceptional example of the ecologically relevant use of olfaction by birds under natural conditions. To our knowledge, we present the first experimental demonstration that a free‐ranging animal makes use of smell to maintain an aromatic environment for offspring with plants, supporting predictions of the nest protection hypothesis.
Allometric scaling of maximum population density: a common rule for marine phytoplankton and terrestrial plants
Authors: Belgrano Andrea , Allen Andrew P. , Enquist Brian J. , Gillooly James F.
Published: March 2003

A primary goal of macroecology is to identify principles that apply across varied ecosystems and taxonomic groups. Here we show that the allometric relationship observed between maximum abundance and body size for terrestrial plants can be extended to predict maximum population densities of marine phytoplankton. These results imply that the abundance of primary producers is similarly constrained in terrestrial and marine systems by rates of energy supply as dictated by a common allometric scaling law. They also highlight the existence of general mechanisms linking rates of individual metabolism to emergent properties of ecosystems.
Root herbivory induces an above‐ground indirect defence
Authors: Wäckers Felix L. , Bezemer T. Martijn
Published: March 2003

Indirect plant defences have largely been studied within the scope of above‐ground interactions. Here we provide novel evidence that root herbivory can induce an above‐ground indirect defence. Cotton plants (Gossypium herbaceum) exposed to root‐feeding wireworms (Agriotes lineatus) increased their foliar extrafloral nectar production ten‐fold in comparison to undamaged control plants. Mechanical root damage also yielded an increase in nectar production. In nature, extrafloral nectar production allows plants to recruit predators, which in turn protect the plant against above‐ground insect herbivores. Our results show that root‐feeding herbivores may alter such above‐ground defensive interactions.
Invariant properties in coevolutionary networks of plant–animal interactions
Authors: Jordano Pedro , Bascompte Jordi , Olesen Jens M.
Published: March 2003

Plant–animal mutualistic networks are interaction webs consisting of two sets of entities, plant and animal species, whose evolutionary dynamics are deeply influenced by the outcomes of the interactions, yielding a diverse array of coevolutionary processes. These networks are two‐mode networks sharing many common properties with others such as food webs, social, and abiotic networks. Here we describe generalized patterns in the topology of 29 plant–pollinator and 24 plant–frugivore networks in natural communities. Scale‐free properties have been described for a number of biological, social, and abiotic networks; in contrast, most of the plant–animal mutualistic networks (65.6%) show species connectivity distributions (number of links per species) with a power‐law regime but decaying as a marked cut‐off, i.e. truncated power‐law or broad‐scale networks and few (22.2%) show scale‐invariance. We hypothesize that plant–animal mutualistic networks follow a build‐up process similar to complex abiotic nets, based on the preferential attachment of species. However, constraints in the addition of links such as morphological mismatching or phenological uncoupling between mutualistic partners, restrict the number of interactions established, causing deviations from scale‐invariance. This reveals generalized topological patterns characteristic of self‐organized complex systems. Relative to scale‐invariant networks, such constraints may confer higher robustness to the loss of keystone species that are the backbone of these webs.
The Allee effect, stochastic dynamics and the eradication of alien species
Authors: Liebhold Andrew , Bascompte Jordi
Published: March 2003

Previous treatments of the population biology of eradication have assumed that eradication can only be achieved via 100% removal of the alien population. However, this assumption appears to be incorrect because stochastic dynamics and the Allee effect typically contribute to the extinction of very low‐density populations. We explore a model that incorporates Allee dynamics and stochasticity to observe how these two processes contribute to the extinction of isolated populations following eradication treatments of varying strength (percentage mortality). As a case study, we used historical data on the dynamics of isolated gypsy moth,Lymantria dispar, populations to fit parameters to this model. The parameterized model was then used in simulations that evaluated the efficacy of various eradication strategies. The results indicated that eradication of isolated gypsy moth populations could be easily achieved following a treatment of >80% mortality as long as populations were relatively low (indicated by <100 males captured in pheromone traps).
Top predator control of plant biodiversity and productivity in an old‐field ecosystem
Authors: Schmitz Oswald J.
Published: March 2003

Abstract Predators can have strong indirect effects on plants by altering the way herbivores impact plants. Yet, many current evaluations of plant species diversity and ecosystem function ignore the effects of predators and focus directly on the plant trophic level. This report presents results of a 3‐year field experiment in a temperate old‐field ecosystem that excluded either predators, or predators and herbivores and evaluated the consequence of those manipulations on plant species diversity (richness and evenness) and plant productivity. Sustained predator and predator and herbivore exclusion resulted in lower plant species evenness and higher plant biomass production than control field plots representing the intact natural ecosystem. Predators had this diversity‐enhancing effect on plants by causing herbivores to suppress the abundance of a competitively dominant plant species that offered herbivores a refuge from predation risk.
Indiscriminate nursing in communal breeders: a role for genomic imprinting
Authors: Roulin Alexandre , Hager Reinmar
Published: March 2003

Abstract In several communally nesting mammal species, females indiscriminately nurse each others' offspring. Previous hypotheses have suggested that the inability to recognize one's own young during lactation is the result of costs incurred from recognition errors. Here, we propose an alternative hypothesis based on sexual conflict theory and genomic imprinting. In polygynous species, males copulate with several females that may later breed communally. Under such conditions, males benefit from indiscriminate nursing of all their offspring and the reduced risk of female infanticide. This may have selected for paternally expressed genes that suppress kin recognition during lactation.
Grazing of the copepod Diaptomus connexus on purple sulphur bacteria in a meromictic salt lake
Authors: Overmann Jörg , Hall Kenneth J. , Northcote Tom G. , Beatty J. Thomas
Published: March 2003

A meromictic lake ecosystem (Mahoney Lake, BC, Canada) was investigated to elucidate the significance of chemocline bacteria in the total carbon cycle under natural conditions. In this lake, primary production by oxygenic phototrophs was insufficient to support the observed net secondary production of the calanoid copepod Diaptomus connexus and the rotifer Brachionus plicatilis, indicating the presence of additional food sources for consumers. Mahoney Lake harbours the densest population of phototrophic sulphur bacteria ever reported in a natural body of water. This layer is located at the interface between oxic and anoxic water layers and is dominated by the purple sulphur bacterium Amoebobacter purpureus. The transfer rates of A. purpureus carbon to D. connexus determined in stratified mesocosms were very low (0.71 ngC copepod−1 day−1) and accounted for only 0.6% of the observed net biomass increase in the zooplankter. Stable stratification within the mesocosms prevented an upwelling of A. purpureus into the oxic part. However, measurements of carbon fluxes, infrared fluorescence microscopy and stable carbon analysis provided cumulative evidence that, under in situ conditions, the cell carbon of purple sulphur bacteria indeed enters the aerobic food chain via the grazing activity of D. connexus. Based on a two‐source isotopic mixing model, A. purpureus represents at least 75–85% of the diet of D. connexus. Autumnal upwelling into oxic water layers and aggregation of A. purpureus cells appear to be the main factors determining the high carbon flux from purple sulphur bacteria to zooplankton under natural conditions, and most probably also play a key role in other aquatic ecosystems. Through this pathway, over 53% of the reduced organic matter of purple sulphur bacteria trapped in anoxic bottom waters is returned to the oxic realm.
Legionella: from environmental habitats to disease pathology, detection and control
Authors: Atlas Ronald M.
Published: March 2003

Studies on Legionella show a continuum from environment to human disease. Legionellosis is caused by Legionella species acquired from environmental sources, principally water sources such as cooling towers, where Legionella grows intracellularly in protozoa within biofilms. Aquatic biofilms, which are widespread not only in nature, but also in medical and dental devices, are ecological niches in which Legionella survives and proliferates and the ultimate sources to which outbreaks of legionellosis can be traced. Invasion and intracellular replication of L. pneumophila within protozoa in the environment play a major role in the transmission of Legionnaires' disease. Protozoa provide the habitats for the environmental survival and reproduction of Legionella species. L. pneumophila proliferates intracellularly in various species of protozoa within vacuoles studded with ribosomes, as it also does within macrophages. Growth within protozoa enhances the environmental survival capability and the pathogenicity (virulence) of Legionella. The growth requirements of Legionella, the ability of Legionella to enter a viable non‐culturable state, the association of Legionella with protozoa and the occurrence of Legionella within biofilms complicates the detection of Legionella and epidemiological investigations of legionellosis. Polymerase chain reaction (PCR) methods have been developed for the molecular detection of Legionella and used in environmental and epidemiological studies. Various physical and chemical disinfection methods have been developed to eliminate Legionella from environmental sources, but gaining control of Legionella in environmental waters, where they are protected from disinfection by growing within protozoa and biofilms, remains a challenge, and one that must be overcome in order to eliminate sporadic outbreaks of legionellosis.
The formation of migratory ripples in a mixed species bacterial biofilm growing in turbulent flow
Authors: Stoodley Paul , Lewandowski Zbigniew , Boyle John D. , Lappin‐Scott Hilary M.
Published: March 2003

Mixed‐species biofilms, consisting of Klebsiella pneumoniae, Pseudomonas aeruginosa, Pseudomonas fluorescens and Stenotrophomonas maltophilia, were grown in glass flow cells under either laminar or turbulent flow. The biofilms grown in laminar flow consisted of roughly circular‐shaped microcolonies separated by water channels. In contrast, biofilm microcolonies grown in turbulent flow were elongated in the downstream direction, forming filamentous ‘streamers’. Moreover, biofilms growing in turbulent flow developed extensive patches of ripple‐like structures between 9 and 13 days of growth. Using time‐lapse microscopic imaging, we discovered that the biofilm ripples migrated downstream. The morphology and the migration velocity of the ripples varied with short‐term changes in the bulk liquid flow velocity. The ripples had a maximum migration velocity of 800 μm h−1 (2.2 × 10−7 m s−1) when the liquid flow velocity was 0.5 m s−1 (Reynolds number = 1800). This work challenges the commonly held assumption that biofilm structures remain at the same location on a surface until they eventually detach.
Changes in the community structure of ammonia‐oxidizing bacteria during secondary succession of calcareous grasslands
Authors: Kowalchuk George A. , Stienstra Atie W. , Heilig  , Stephen John R. , Woldendorp Jan W.
Published: March 2003

The community structure of β‐subclass Proteobacteria ammonia‐oxidizing bacteria was determined in semi‐natural chalk grassland soils at different stages of secondary succession. Both culture‐mediated (most probable number; MPN) and direct nucleic acid‐based approaches targeting genes encoding 16S rRNA and the AmoA subunit of ammonia monooxygenase were used. Similar shifts were detected in the composition of the ammonia oxidizer communities by both culture‐dependent and independent approaches. A predominance of Nitrosospira sequence cluster 3 in early successional fields was replaced by Nitrosospira sequence cluster 4 in late successional fields. The rate of this shift differed between the two areas examined. This shift occurred in a background of relative stability in the dominant bacterial populations in the soil, as determined by domain‐level polymerase chain reaction–denaturing gradient gel electrophoresis (PCR–DGGE). Molecular analysis of enrichment cultures obtained using different ammonia concentrations revealed biases towards Nitrosospira sequence cluster 3 or Nitrosospira sequence cluster 4 under high‐ or low‐ammonia conditions respectively. High‐ammonia MPNs suggested a decease in ammonia oxidizer numbers with succession, but low‐ammonia MPNs and competitive PCR targeting amoA failed to support such a trend. Ammonia turnover rate, not specific changes in plant diversity and species composition, is implicated as the major determinant of ammonia oxidizer community structure in successional chalk grassland soils.
Impact of oxygen on metabolic fluxes and in situ rates of reductive acetogenesis in the hindgut of the wood‐feeding termite Reticulitermes flavipes
Authors: Tholen Anne , Brune Andreas
Published: March 2003

The symbiotic digestion of lignocellulose in the hindgut of the wood‐feeding termite Reticulitermes flavipes is characterized by two major metabolic pathways: (i) the oxidation of polysaccharides to acetate by anaerobic hydrogen‐producing protozoa; and (ii) the reduction of CO2 by hydrogenotrophic acetogenic bacteria. Both reactions together would render the hindgut largely homoacetogenic. However, the results of this study show that the situation is more complex. By microinjection of radiolabelled metabolites into intact agarose‐embedded hindguts, we showed that the in situ rates of reductive acetogenesis (3.3 nmol termite−1 h−1) represent only 10% of the total carbon flux in the living termite, whereas 30% of the carbon flux proceeds via lactate. The rapid turnover of the lactate pool (7.2 nmol termite−1 h−1) consolidates the previously reported presence of lactic acid bacteria in the R. flavipes hindgut and the low lactate concentrations in the hindgut fluid. However, the immediate precursor of lactate remains unknown; the low turnover rates of injected glucose (< 0.5 nmol termite−1 h−1) indicate that free glucose is not an important intermediate under in situ conditions. The influence of the incubation atmosphere on the turnover rate and the product pattern of glucose and lactate confirmed that the influx of oxygen via the gut epithelium and its reduction in the hindgut periphery have a significant impact on carbon and electron flow within the hindgut microbial community. The in situ rates of reductive acetogenesis were not significantly affected by the presence of oxygen or exogenous H2, which is in agreement with a localization of homoacetogens in the anoxic gut lumen rather than in the oxic periphery. This adds strong support to the hypothesis that the co‐existence of methanogens and homoacetogens in this termite is based on the spatial arrangement of the different populations of the gut microbiota. A refined model of metabolic fluxes in the hindgut of R. flavipes is presented.
Developmental pathway for biofilm formation in curli‐producing Escherichia coli strains: role of flagella, curli and colanic acid
Authors: Prigent‐Combaret Claire , Prensier Gérard , Le Thi Thanh Thuy , Vidal Olivier , Lejeune Philippe , Dorel Corinne
Published: March 2003

This work was performed to establish a model describing bacterial surface structures involved in biofilm development, in curli‐overproducing Escherichia coli K‐12 strains, at 30°C, and in minimal growth medium. Using a genetic approach, in association with observations of sessile communities by light and electron microscopic techniques, the role of protein surface structures, such as flagella and curli, and saccharidic surface components, such as the E. coli exopolysaccharide, colanic acid, was determined. We show that, in the context of adherent ompR234 strains, (i) flagellar motility is not required for initial adhesion and biofilm development; (ii) both primary adhesion to inert surfaces and development of multilayered cell clusters require curli synthesis; (iii) curli display direct interactions with the substratum and form interbacterial bundles, allowing a cohesive and stable association of cells; and (iv) colanic acid does not appear critical for bacterial adhesion and further biofilm development but contributes to the biofilm architecture and allows for the formation of voluminous biofilms.
Comparison of microbial populations in model and natural rumens using 16S ribosomal RNA‐targeted probes
Authors: Ziemer Cherie J. , Sharp Richard , Stern Marshall D. , Cotta Michael A. , Whitehead Terence R. , Stahl David A.
Published: March 2003

A model rumen system, dual‐flow continuous culture fermenters, was evaluated by two comparative criteria in two experiments using ribosomal (r)RNA‐targeted DNA probes to compare key microbial groups in samples. The initial experiment measured temporal changes in population structure during adaptation of ruminal microbial populations in fermenters over 240 h. The fermenter inoculum contained 34.9% Bacteria, 60.1% Eukarya and 6.8% Archaea measured as a fraction of total small subunit (SSU) rRNA quantified using a universal probe. The cellulolytic bacterial genus Fibrobacter comprised 9.5% of total SSU rRNA in the inoculum. After 240 h of fermenter operation, the average abundance was 80.9% Bacteria, 6.1% Eukarya, 5.1% Archaea and Fibrobacter genus accounted for 6.6% of the total SSU rRNA. Divergence between ruminal and fermenter population structure was evaluated in the second experiment and samples were classified as ruminal, inoculum or fermenter (96, 120, 144 and 168 h of fermenter operation). Fermenter samples had higher relative abundances of Bacteria (84.5%) and Archaea (2.1%) and lower relative abundances of Eukarya (1.8%) than ruminal samples (average 48.0% Bacteria, 1.3% Archaea and 61.5% Eukarya). The relative abundance of Fibrobacter was similar in all samples, averaging 2.5%. The ruminal and fermenter samples had similar proportions of F. succinogenes and F. succinogenes subgroup 3 (as a percentage of Fibrobacter SSU rRNA). Fibrobacter succinogenes subgroup 1 and F. intestinalis proportions of Fibrobacter were lower in fermenter samples (8.2% and 0.7% respectively) than in ruminal samples (28.4% and 2.2% respectively). Fermenters were able to maintain a core prokaryotic community structure similar to the native microbial community in the rumen. Although protozoa populations were lost, maintenance of Fibrobacter and archaeal populations indicated that the model system supported a functional community structure similar to the rumen. This model rumen system may serve as a suitable tool for studying aspects of ruminal microbial ecology and may resolve some of the relationships between microbial community structure and function by providing control of experimental conditions.
Use of green fluorescent protein and luciferase biomarkers to monitor survival and activity of Arthrobacter chlorophenolicus A6 cells during degradation of 4‐chlorophenol in soil
Authors: Elväng Annelie M. , Westerberg Karolina , Jernberg Cecilia , Jansson Janet K.
Published: March 2003

The recently isolated novel species Arthrobacter chlorophenolicus A6 is capable of growth on and degradation of high concentrations of 4‐chlorophenol (up to 350 μg ml−1) as the sole carbon and energy source. This strain shows promise for bioremediation of environmental sites contaminated with high levels of chlorophenols. In this study, green fluorescent protein (gfp) or luciferase (luc) genes were used as biomarkers for monitoring cell number and activity, respectively, during degradation of 4‐chlorophenol by A. chlorophenolicus cells. The individual marked strains, Arthrobacter chlorophenolicus A6L (luc‐tagged) and Arthrobacter chlorophenolicus A6G (gfp‐tagged), were monitored during degradation of 250 μg ml−1 4‐chlorophenol in pure culture and 175 μg g−1 4‐chlorophenol in soil microcosms. Both gene‐tagged strains were capable of cleaning up the contaminated soil during 9 d incubation. During the bioremediation experiments, the luc‐tagged cells were monitored using luminometry and the gfp‐tagged cells using flow cytometry, in addition to selective plate counting for both strains. The cells remained at high population levels in the soil (evidenced by GFP‐fluorescent cell counts) and the A. chlorophenolicus A6L population was metabolically active (evidenced by luciferase activity measurements). These results demonstrate that the Arthrobacter chlorophenolicus A6 inoculum is effective for cleaning‐up soil containing high concentrations of 4‐chlorophenol.
In situ identification of polyphosphate‐ and polyhydroxyalkanoate‐accumulating traits for microbial populations in a biological phosphorus removal process
Authors: Liu Wen‐Tso , Nielsen Alex T. , Wu Jer‐Horng , Tsai Chin‐Sun , Matsuo Yoshitaka , Molin Søren
Published: March 2003

Polyphosphate‐ and polyhydroxyalkanoate (PHA)‐accumulating traits of predominant microorganisms in an efficient enhanced biological phosphorus removal (EBPR) process were investigated systematically using a suite of non‐culture‐dependent methods. Results of 16S rDNA clone library and fluorescence in situ hybridization (FISH) with rRNA‐targeted, group‐specific oligonucleotide probes indicated that the microbial community consisted mostly of the α‐ (9.5% of total cells), β‐ (41.3%) and γ‐ (6.8%) subclasses of the class Proteobacteria, Flexibacter–Cytophaga (4.5%) and the Gram‐positive high G+C (HGC) group (17.9%). With individual phylogenetic groups or subgroups, members of Candidatus Accumulibacter phosphatis in the β‐2 subclass, a novel HGC group closely related to Tetrasphaera spp., and a novel γ‐proteobacterial group were the predominant populations. Furthermore, electron microscopy with energy‐dispersive X‐ray analysis was used to validate the staining specificity of 4,6‐diamino‐2‐phenylindole (DAPI) for intracellular polyphosphate and revealed the composition of polyphosphate granules accumulated in predominant bacteria as mostly P, Ca and Na. As a result, DAPI and PHA staining procedures could be combined with FISH to identify directly the polyphosphate‐ and PHA‐accumulating traits of different phylogenetic groups. Members of Accumulibacter phosphatis and the novel gamma‐proteobacterial group were observed to accumulate both polyphosphate and PHA. In addition, one novel rod‐shaped group, closely related to coccus‐shaped Tetrasphaera, and one filamentous group resembling Candidatus Nostocoidia limicola in the HGC group were found to accumulate polyphosphate but not PHA. No cellular inclusions were detected in most members of the α‐Proteobacteria and the Cytophaga–Flavobacterium group. The diversified functional traits observed suggested that different substrate metabolisms were used by predominant phylogenetic groups in EBPR processes.
Ribotyping of rhizobia nodulatingAcacia mangiumandParaserianthes falcatariafrom different geographical areas in Indonesia using PCR‐RFLP‐SSCP (PRS) and sequencing
Authors: Clapp Justin P. , Mansur Irdika , Dodd John C. , Jeffries Peter
Published: March 2003

Acacia mangiumandParaserianthes falcatariaare leguminous tree species widely grown for timber in Indonesia and other tropical countries, yet little is known about the identity of their rhizobial symbionts. Polymerase chain reaction‐restriction fragment length polymorphism‐single‐strand conformational polymorphism (PRS) analysis of the 16S rRNA gene was used along with sequencing to assess the diversity of 57 rhizobia isolated from nodules ofA. mangiumandP. falctariain Indonesia. In total, 26 rhizobia isolated fromA. mangiumwere analysed by PRS and sequencing. The PRS patterns indicated that 12 (46%) clustered withBradyrhizobium elkanii, 13 (50%) withB. lianoningense/japonicumand one (4%) withMesorhizobium loti. Thirty‐one isolates were analysed fromP. falcataria: five (16%) clustered withB. elkaniiand 26 (84%) withB. lianoningense/japonicum.These results were confirmed by phylogenetic analysis of sequences. Intraspecific diversity of the 16S rRNA genes from rhizobia nodulatingA. mangiumandP. falcatariarevealed by PRS was low, only one genotype was found within the isolates that clustered withB. elkaniiand two within theB. liaoningense/japonicumgroup. TheseBradyrhizobiumspecies are apparently ubiquitous throughout the Indonesian archipelago and it is clear why the two tree species are able to successfully establish outside their native range without the need for inoculation with indigenous rhizobia.