bluuebunny/crossref_metadata_2025 huggingface dataset:
Niche segregation among Lake Malawi cichlid fishes? Evidence from stable isotope signatures
Authors: Genner  , Turner  , Barker  , Hawkins
Published: March 2003

The fish communities of the rocky littoral zone of Lake Malawi contain a large number of ecologically similar cichlid species. It has been suggested that dietary niche segregation may play a role in the coexistence of these species, but previous studies have yielded ambiguous results. Stable isotope analysis was used to determine whether five sympatric species are segregated by diet. Significant differences were found between the mean isotopic signatures of the study species, but there was considerable interspecific overlap between three species from the same subgenus that were anatomically almost indistinguishable. The implication that this was due to substantial dietary similarity was supported by stomach content analysis. We propose that ecological segregation may not always be necessary to allow coexistence of Lake Malawi cichlids.
Is zonation on coastal sand dunes determined primarily by sand burial or by salt spray? A test in New Zealand dunes
Authors: Wilson  , Sykes
Published: March 2003

There has long been controversy on which environmental factor is the predominant determinant of community zonation on sand dunes. It is demonstrated here that, on a dune system in southern New Zealand, several environmental factors that could limit growth all vary along the sea‐to‐inland sand dune zonation: soil moisture, soil nutrients, wind exposure, sand burial, salt spray and soil salinity. Correlation of the responses of 30 species to experimental stress (burial, darkness, rooting‐medium salinity and salt spray) with the zonation of the species in the field indicates that, in the four dune systems studied, sand burial and salt are both important, with salt generally being the more important. However, the relative importance of the factors differs between sites.
The structure of a plant‐pollinator food web
Authors: Memmott J.
Published: March 2003

The pollination biology literature is dominated by examples of specialization between plants and their pollinators. However, a recent review shows that it is generalization that prevails in the field, with most plants having a number of pollinators and most pollinators visiting a number of plants. Consequently, the vast majority of plant–pollinator interactions are embedded in a complex web of plant–pollinator interactions. These plant‐pollinator webs can be studied in the manner of conventional food webs and the aim of this paper is to illustrate how contemporary methods of web construction and analysis can be applied to plant‐pollinator communities.
Mass Coral Reef Bleaching: A Recent Outcome of Increased El Niño Activity?
Authors: Stone L. , Huppert A. , Rajagopalan B. , Bhasin H. , Loya Y.
Published: March 2003

Coral reefs are generally considered to be the most biologically productive of all marine ecosystems, but in recent times these vulnerable aquatic resources have been subject to unusual degradation. The general decline in reefs has been greatly accelerated by mass bleaching in which corals whiten en masse and often fail to recover. Empirical evidence indicates a coral reef bleaching cycle in which major bleaching episodes are synchronized with El Niño events that occur every 3–4 years on average. By heating vast areas of the Pacific Ocean, and affecting the Indian and Atlantic Oceans as well, El Niño causes widespread damage to reefs largely because corals are very sensitive to temperature changes. However, mass bleaching events were rarely observed before the 1970s and their abrupt appearance two decades ago remains an enigma. Here we propose a new explanation for the sudden occurrence of mass bleaching and show that it may be a response to the relative increase in El Niño experienced over the last two decades.
Evolving biodiversity
Authors: Jansen  , Mulder
Published: March 2003

We formulated a mathematical model to study the evolution of biodiversity. Our model describes a collection of sites and incorporates a simple but explicit description of the competitive processes within a site. In our model the characteristics of component species evolve towards an evolutionarily stable state and in this way an evolutionarily stable assemblage of species is formed. We show that the number of species in these assemblages matches two well‐documented patterns in biodiversity: the increase in the number of species towards the equator and the dependence of the number of species on the productivity of habitat: the average number of species rises to a maximum and then falls when plotted against increasing productivity of that habitat. Our results show that population dynamical and evolutionary processes can underlie patterns in biodiversity.
Modelling trade‐offs between mortality and fitness associated with persistent blood feeding by mosquitoes
Authors: Anderson R.A. , Roitberg B.D.
Published: March 2003

Feeding persistence of mosquitoes (that tendency to attack again within a short period if a first meal is incomplete) is a key determinant of feeding success (defined here as blood‐meal volume), especially with regard to mosquitoes that attack defensive hosts. Mortality risk from the vertebrate host is one cost that may be expected to create a trade‐off against increased fecundity from second and subsequent meals depending on the availability of blood sources and on the probability of survival until the next gonotrophic cycle. We initially used stochastic simulation models to examine potential trade‐offs in fecundity and survival for persistent and nonpersistent lines of mosquitoes that acquire blood from potentially dangerous hosts. In these models, a given strategy, i.e. persistence or the lack thereof, was fixed for the lifetime of the mosquito. Persistent blood feeding paid off relative to nonpersistent mosquitoes when feeding‐associated mortality was relatively low to moderate and when the probability of obtaining blood on a given attempt was relatively low. On the other hand, the nonpersistent strategy tended to give relatively higher fecundity when the chances of obtaining blood were high. We also examined the implications of persistence as a feeding strategy for mosquitoes that could exhibit this behaviour in a flexible manner over their lifetime in response to state. We solved for optimal feeding behaviours with a stochastic dynamic programming model set up along similar lines to the simulation model. Results from this approach lend support to the idea that the threshold blood‐meal size at which mosquitoes should continue to feed should change relative to the age of the mosquito. The modelling approaches used in this study identified important areas of future study for mosquito blood‐feeding behaviour.
“Ultraviolet spring” and the ecological consequences of catastrophic impacts
Authors: Cockell Charles S. , Blaustein Andrew R.
Published: March 2003

Asteroid and comet impacts cause ozone depletion. For the first time, we have quantified the photobiological characteristics of these events and speculate on some of the associated ecological consequences. Following the clearing of stratospheric dust after “impact winter”, levels of damaging UVB radiation (280–315 nm) could increase by at least 100%, resulting in an “ultraviolet spring”. Many of the taxa stressed by the cold and dark conditions of impact are the same that would be stressed by large increases in UVB radiation. Furthermore, depletion of dissolved organic carbon (DOC) by impact‐induced acid rain would increase UVB penetrability into freshwater systems. Although an increase in UVB radiation is an attractive hypothesis for exacerbating the demise of land animals at the Cretaceous‐Tertiary (K/T) boundary, e.g. dinosaurs, our calculations suggest the impact into rare sulphate‐rich target rock may have prevented an ultraviolet spring in this case. If the K/T impact event had occurred in any other region on Earth, the stress to the biosphere would probably have been considerably greater.
Variation in intensity of a parasitic mite (Spinturnix myoti) in relation to the reproductive cycle and immunocompetence of its bat host (Myotis myotis)
Authors: Christe  , Arlettaz  , Vogel
Published: March 2003

Given the intimate association in host–parasite systems, parasites are expected to initiate their own reproduction when vulnerable hosts become abundant and/or when adult hosts are less resistant. In this study, we examined the variation in the intensities of a blood‐sucking mite (Spinturnix myoti, Acarina) with respect to the reproductive cycle and immunocompetence of its host, the greater mouse‐eared bat Myotis myotis. Reproductive, pregnant females were less immunocompetent and harboured more parasites than nonreproductive females, whilst, during lactation, immunocompetence was positively associated with female body mass. There was a dramatic increase in the T‐cell response of gravid females with the advancement of gestation, which coincided with a diminution of individual parasite loads and a progressive switch of parasites from adults to juveniles. The latter not only harboured greater numbers of mites than adult female bats, but they also exhibited gravid parasites in higher proportions, indicating that juvenile hosts are more attractive for parasite reproduction than adult females.
Are tropical fungal endophytes hyperdiverse?
Authors: Arnold A.E. , Maynard Z. , Gilbert G.S. , Coley P.D. , Kursar T.A.
Published: March 2003

Fungal endophytes are ubiquitous fungi that inhabit healthy plant tissues without causing disease. Endophytes have been found in every plant species examined to date and may be important, but often overlooked, components of fungal biodiversity. In two sites in a lowland, moist tropical forest of central Panama, we quantified endophyte colonization patterns, richness, host preference, and spatial variation in healthy leaves of two co‐occurring, understory tree species [Heisteria concinna (Olacaceae) and Ouratea lucens (Ochnaceae)]. From 83 leaves, all of which were colonized by endophytes, we isolated 418 endophyte morphospecies (estimated 347 genetically distinct taxa), most of which were represented by only a single isolate (59%). Among morphospecies encountered in more than one leaf (nonsingletons), we found evidence of host preference and spatial heterogeneity using both morphospecies frequencies and presence/absence records. Based on these data, we postulate that tropical endophytes themselves may be hyperdiverse and suggest that extrapolative estimates that exclude them will markedly underestimate fungal species diversity.
How 17‐year cicadas keep track of time
Authors: Karban R. , Black C.A. , Weinbaum S.A.
Published: March 2003

Seventeen‐year periodical cicadas (Magicicada spp.) require 17 years to develop underground and all individuals at any location emerge synchronously within several days. The mechanisms that animals use to keep track of time are poorly understood and nothing is known about how cicada nymphs emerge after precisely 17 years. We altered the seasonal cycles of trees supporting cicada nymphs and thereby induced premature metamorphosis of the associated cicadas. This indicates that cicadas accomplish a consistently accurate 17‐year preadult development time by counting host seasonal cycles and not either by the passage of real time or by the accumulation of degree days.
Source–sink dynamics: how sinks affect demography of sources
Authors: Gundersen G. , Johannesen E. , Andreassen H.P. , Ims R.A.
Published: March 2003

Models of source–sink population dynamics have to make assumptions about whether, and eventually how, demographic parameters in source habitats are dependent on the demography in sink habitats. However, the empirical basis for making such assumptions has been weak. Here we report a study on experimental root vole populations, where estimates of demographic parameters were contrasted between source patches in source–sink (treatment) and source–source systems (control). In the presence of a sink patch (simulated by a pulsed removal of immigrants), source‐patch populations failed to increase over the breeding season, mainly due to a high spatially density‐dependent dispersal rate from source to sink patches. Theper capitarecruitment rate was almost two times higher in source–sink than in the source–source systems, but this did not compensate for the loss rate due to dispersal from source to sink patches. Sex ratio in the source–sink systems became less female biased, probably as a result of an enhanced frequency of dispersal movements in females. Good knowledge of the degree of density‐and habitat‐dependent dispersal is critical for predicting the dynamics of source–sink populations.
Biodiversity may regulate the temporal variability of ecological systems
Authors: Cottingham K.L. , Brown B.L. , Lennon J.T.
Published: March 2003

The effect of biodiversity on natural communities has recently emerged as a topic of considerable ecological interest. We review studies that explicitly test whether the number of species in a community (species richness) regulates the temporal variability of aggregate community (total biomass, productivity, nutrient cycling) and population (density, biomass) properties. Theoretical studies predict that community variability should decline with increasing species richness, while population variability should increase. Many, but not all, empirical studies support these expectations. However, a closer look reveals that several empirical studies have either imperfect experimental designs or biased methods of calculating variability. Furthermore, most theoretical studies rely on highly unrealistic assumptions. We conclude that evidence to support the claim that biodiversity regulates temporal variability is accumulating, but not unequivocal. More research, in a broader array of ecosystem types and with careful attention to methodological considerations, is needed before we can make definitive statements regarding richness‐variability relationships.
Coral bleaching: the winners and the losers
Authors: Loya Y. , Sakai K. , Yamazato K. , Nakano Y. , Sambali H. , van Woesik R.
Published: March 2003

Sea surface temperatures were warmer throughout 1998 at Sesoko Island, Japan, than in the 10 preceding years. Temperatures peaked at 2.8 °C above average, resulting in extensive coral bleaching and subsequent coral mortality. Using random quadrat surveys, we quantitatively documented the coral community structure one year before and one year after the bleaching event. The 1998 bleaching event reduced coral species richness by 61% and reduced coral cover by 85%. Colony morphology affected bleaching vulnerability and subsequent coral mortality. Finely branched corals were most susceptible, while massive and encrusting colonies survived. Most heavily impacted were the branched Acropora and pocilloporid corals, some of which showed local extinction. We suggest two hypotheses whose synergistic effect may partially explain observed mortality patterns (i.e. preferential survival of thick‐tissued species, and shape‐dependent differences in colony mass‐transfer efficiency). A community‐structural shift occurred on Okinawan reefs, resulting in an increase in the relative abundance of massive and encrusting coral species.
Predicting competition coefficients for plant mixtures: reciprocity, transitivity and correlations with life‐history traits
Authors: Freckleton R.P. , Watkinson A.R.
Published: March 2003

There are few empirical or theoretical predictions of how per capita or per individual competition coefficients for pairs of plant species should relate to each other. In contrast, there are a considerable number of general hypotheses that predict competitive ability as a function of a range of ecological traits, together with a suite of increasingly sophisticated models for competitive interactions between plant species. We re‐analyse a data set on competition between all pairwise combinations of seven species and show that competition coefficients relate strongly to differences between the maximum sizes, root allocation, emergence time and seed size of species. Regressions suggest that the best predictor of competition coefficients is the difference in the maximum size of species and that correlations of the other traits with the competition coefficients occur through effects on the maximum size. We also explore the patterns of association between coefficients across the competition matrix. We find significant evidence for coefficient reciprocity (inverse relationships between the interspecific coefficients for species pairs) and transitivity (numerically predictable hierarchies of competition between species) across competition matrices. These results therefore suggest simple null models for plant community structure when there is competition for resources.
Rare species loss alters ecosystem function – invasion resistance
Authors: Lyons Kelly G. , Schwartz Mark W.
Published: March 2003

The imminent decline in species diversity coupled with increasing exotic species introductions has provoked investigation into the role of resident diversity in community resistance to exotic species colonization. Here we present the results of a field study using an experimental method in which diversity was altered by removal of less abundant species and the resulting disturbance was controlled for by removal of an equivalent amount of biomass of the most common species from paired plots. Following these manipulations, the exotic grass, Lolium temulentum, was introduced. We found that exotic species establishment was higher in plots in which diversity was successfully reduced by removal treatments and was inversely related to imposed species richness. These results demonstrate that less common species can significantly influence invasion events and highlight the potential role of less common species in the maintenance of ecosystem function.
Complementary impact of copepods and cladocerans on phytoplankton
Authors: Sommer Ulrich , Sommer Frank , Santer Barbara , Jamieson Colleen , Boersma Maarten , Becker Claes , Hansen Thomas
Published: March 2003

The differences in the impact of two major groups of herbivorous zooplankton (Cladocera and Copepoda) on summer phytoplankton in a mesotrophic lake were studied. Field experiments were performed in which phytoplankton were exposed to different densities of two major types of herbivorous zooplankton, cladocerans and copepods. Contrary to expectation, neither of the two zooplankton groups significantly reduced phytoplankton biomass. However, there were strong and contrasting impacts on phytoplankton size structure and on individual taxa. Cladocerans suppressed small phytoplankton, while copepods suppressed large phytoplankton. The unaffected size classes compensated for the loss of those affected by enhanced growth. After contamination of the copepod mesocosms with the cladoceran Daphnia, the combined impact of both zooplankton groups caused a decline in total phytoplankton biomass.
Bacteria divert resources from growth for magellanic penguin chicks
Authors: Potti Jaime , Moreno Juan , Yorio Pablo , Briones Víctor , García‐Borboroglu Pablo , Villar Susana , Ballesteros Cristina
Published: March 2003

The influence of bacteria on the growth of their wild avian hosts is unknown. We tested experimentally whether administration of a wide‐spectrum antibiotic (cephalosporine) during early development of magellanic penguin (Spheniscus magellanicus) chicks had any effect on their growth rates in the wild. Chicks that were injected in two occasions with cephalosporine grew faster than control untreated chicks. The positive effect of medication on nestling growth disappeared after the treatment ceased, did not alter haematological indices indicative of health status, had no influence on chick survival until near independence and was related to a changed bacterial composition of the faecal microbiota of treated chicks when compared with that from control chicks. These results were similar to those obtained for poultry with antimicrobials promoting growth and chick nutrient assimilation rates. Gram‐positive bacilli in the diphtheroid genusCorynebacteriumare likely candidates to cause decreased growth rates in magellanic penguin chicks.
Biodiversity hotspots, centres of endemicity, and the conservation of coral reefs
Authors: Hughes Terry P. , Bellwood David R. , Connolly Sean R.
Published: March 2003

On land, biodiversity hotspots typically arise from concentrations of small‐range endemics. For Indo‐Pacific corals and reef fishes, however, centres of high species richness and centres of high endemicity are not concordant. Moreover ranges are not, on average, smaller inside the Central Indo‐Pacific (CI‐P) biodiversity hotspot. The disparity between richness and endemicity arises because corals and reef fishes have strongly skewed range distributions, with many species being very widespread. Consequently, the largest ranges overlap to generate peaks in species richness near the equator and the CI‐P biodiversity hotspot, with only minor contributions from endemics. Furthermore, we find no relationship between the number of coral vs. fish endemics at locations throughout the Indo‐Pacific, even though total richness of the two groups is strongly correlated. The spatial separation of centres of endemicity and biodiversity hotspots in these taxa calls for a two‐pronged management strategy to address conservation needs.
Sulphate reduction and vertical distribution of sulphate‐reducing bacteria quantified by rRNA slot‐blot hybridization in a coastal marine sediment
Authors: Sahm Kerstin , MacGregor Barbara J. , Jørgensen Bo B. , Stahl David A.
Published: March 2003

In the past, enumeration of sulphate‐reducing bacteria (SRB) by cultivation‐based methods generally contradicted measurements of sulphate reduction, suggesting unrealistically high respiration rates per cell. Here, we report evidence that quantification of SRB rRNA by slot‐blot hybridization is a valuable tool for a more realistic assessment of SRB abundance in the natural environment. The distribution of SRB was investigated in a coastal marine sediment by hybridization of membrane‐immobilized rRNA with oligonucleotide probes. As represented by general probe–target groups, SRB rRNA contributed between 18% and 25% to the prokaryotic rRNA pool. The dominant SRB were related to complete oxidizing genera (Desulphococcus,DesulphosarcinaandDesulphobacterium), whileDesulphobactercould not be detected. The vertical profile and quantity of rRNA from SRB was compared with sulphate reduction rates (SRR) measured with35SO42−tracer in whole‐core incubations. While SRB abundance was highest near the surface, peaking at around 1.5 cm, measured sulphate reduction rates were lowest in this region. A second peak of SRB rRNA was observed at the transition zone from oxidized to reduced sediment, directly above the sulphate reduction maximum. Cell numbers calculated by converting the relative contribution of SRB rRNA to the percentage of DAPI‐stained cells indicated a population size for SRB of 2.4–6.1 × 108cells cm−3wet sediment. Cellular sulphate reduction rates calculated on the basis of these estimated cell numbers were between 0.01 and 0.09 fmol SO42− cell−1day−1, which is below the rates that have been determined for pure cultures (0.2–50 fmol SO42− cell−1day−1) growing exponentially at near‐ optimal temperature with a surplus of substrates.
Changes in community composition during dilution cultures of marine bacterioplankton as assessed by flow cytometric and molecular biological techniques
Authors: Fuchs Bernhard M. , Zubkov Mikhail V. , Sahm Kerstin , Burkill Peter H. , Amann Rudolf
Published: March 2003

Dilution cultures are a common technique for measuring the growth of bacterioplankton communities. In this study, the taxonomic composition of marine bacterioplankton dilution cultures was followed in water samples from Plymouth Sound and the English Channel (UK). Bacterial abundances as well as protein and DNA content were closely monitored by flow cytometry. Denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR)‐amplified 16S rDNA fragments and fluorescence in situ hybridization (FISH) were applied directly to the water samples and to cells sorted from the dilution cultures based on their protein and DNA content. As expected, a rapid activation of bacteria occurred. However, molecular techniques showed that the community developed in the dilution culture within 1 day was significantly different from that in the original water samples. Whereas in the original samples, cells detectable by FISH were dominated by members of the Cytophaga/Flavobacterium (CF) cluster, in dilution cultures, gamma‐proteobacteria accounted for the majority of cells detected, followed by alpha‐proteobacteria. An actively growing and an apparently non‐growing population with average cellular protein contents of 24 and 4.5 fg respectively, were sorted by flow cytometry. FISH indicated mostly gamma‐ (64%) and alpha‐proteobacteria (33%) in the first active fraction and 78% members of the CF cluster in the second fraction. Sequencing of DGGE bands confirmed the FISH assignments of the latter two groups. The data presented clearly show that even relatively short‐term dilution experiments do not measure in situ growth, but rather growth patterns of an enrichment. Furthermore, it was demonstrated that the combination of flow cytometric analysis and sorting combined with FISH and DGGE analysis presented a fairly rapid method of analysing the taxonomic composition of marine bacterioplankton.
Bacterial chromosomal painting for in situ monitoring of cultured marine bacteria
Authors: Lanoil Brian D. , Carlson Craig A. , Giovannoni Stephen J.
Published: March 2003

We previously described a new method, bacterial chromosomal painting (BCP), for the in situ identification of bacterial cells. Here, we describe the application of this technique to study the ecology and physiology of cultured marine pelagic bacteria from the western Sargasso Sea (WSS). A total of 86 bacteria were isolated from seawater collected from near the surface, at a depth of 250 m and from nutrient‐amended seawater incubations. The 10 bacterial isolates that were best represented in environmental genomic DNA from the WSS were selected using reverse genome probing. BCP hybridization cell counts were used to determine the depth‐specific distribution of one of the alpha proteobacterial isolates, B5‐6, in the WSS during two thermal stratification regimes: stratified and partially mixed. The maximum cell count measured for B5‐6 at the summer deep chlorophyll maximum was approximately 4% of the total cell count. This study is the first application of BCP to natural environments.
Bacterial and archaeal populations associated with freshwater ferromanganous micronodules and sediments
Authors: Stein Lisa Y. , La Duc Myron T. , Grundl Timothy J. , Nealson Kenneth H.
Published: March 2003

Biology is believed to play a large role in the cycling of iron and manganese in many freshwater environments, but specific microbial groups indigenous to these systems have not been well characterized. To investigate the populations of Bacteria and Archaea associated with metal‐rich sediments from Green Bay, WI, we extracted nucleic acids and analysed the phylogenetic relationships of cloned 16S rRNA genes. Because nucleic acids have not been routinely extracted from metal‐rich samples, we investigated the bias inherent in DNA extraction and gene amplification from pure MnO2 using defined populations of whole cells or naked DNA. From the sediments, we screened for manganese‐oxidizing bacteria using indicator media and found three isolates that were capable of manganese oxidation. In the phylogenetic analysis of bacterial 16S rRNA gene clones, we found two groups related to known metal‐oxidizing genera, Leptothrix of the β‐Proteobacteria and Hyphomicrobium of the α‐Proteobacteria, and a Fe(III)‐reducing group related to the Magnetospirillum genus of the α‐Proteobacteria. Groups related to the metal‐reducing δ‐Proteobacteria constituted 22% of the gene clones. In addition, gene sequences from one group of methanogens and a group of Crenarchaeota, identified in the archaeal gene clone library, were related to those found previously in Lake Michigan sediments.
Complete mineralization of dodecyldimethylamine using a two‐membered bacterial culture
Authors: Kroon A. G. M. , Van Ginkel C. G.
Published: March 2003

Complete degradation of dodecyldimethylamine was achieved using a two‐membered bacterial culture isolated from activated sludge. One member, identified as Burkholderia cepacia, was capable of degrading the alkyl chain of the molecule. The other member, identified as Stenotrophomonas maltophilia, was able to degrade dimethylamine, the product of the former. Batch culture experiments revealed that the two‐membered culture consisting of B. cepacia and S. maltophilia was based on a commensalistic relationship under carbon‐limited conditions. Under nitrogen‐limited conditions, the relationship of this culture was transformed from a commensalistic to a mutualistic one. A two‐membered culture was therefore imperative for growth on dodecyldimethylamine under nitrogen‐limited conditions, whereas a pure culture of B. cepacia was capable of growth on dodecyldimethylamine under carbon‐limited conditions.
Differential expression of antenna and core genes in Prochlorococcus PCC 9511 (Oxyphotobacteria) grown under a modulated light–dark cycle
Authors: Garczarek Laurence , Partensky Frédéric , Irlbacher Horst , Holtzendorff Julia , Babin Marcel , Mary Isabelle , Thomas Jean Claude , Hess Wolfgang R.
Published: March 2003

The continuous changes in incident solar light occurring during the day oblige oxyphototrophs, such as the marine prokaryote Prochlorococcus, to modulate the synthesis and degradation rates of their photosynthetic components finely. How this natural phenomenon influences the diel expression of photosynthetic genes has never been studied in this ecologically important oxyphotobacterium. Here, the high light‐adapted strain Prochlorococcus sp. PCC 9511 was grown in large‐volume continuous culture under a modulated 12 h−12 h light–dark cycle mimicking the conditions found in the upper layer of equatorial oceans. The pcbA gene encoding the major light‐harvesting complex showed strong diel variations in transcript levels with two maxima, one before the onset of illumination and the other near the end of the photoperiod. In contrast, the mRNA level of psbA (encoding the reaction centre II subunit D1), the monocistronic transcript of psbD (encoding D2) and the dicistronic transcript of psbDC were all tightly correlated with light irradiance, with a minimum at night and a maximum at noon. The occurrence of a second peak during the dark period for the monocistronic transcript of psbC (encoding one of the PS II core Chl a antenna proteins) suggested the involvement of post‐transcriptional regulation. Differential expression of the external antenna and core genes may constitute a mechanism of regulation of the antenna size to cope with the excess photon fluxes that Prochlorococcus cells experience in the upper layer of oceans around midday. The 5′ ends of all transcripts were mapped, and a conserved motif, 5′‐TTGATGA‐3′, was identified within the putative psbA and pcbA promoters.
The structure of a local population of phytopathogenic Pseudomonas brassicacearum from agricultural soil indicates development under purifying selection pressure
Authors: Sikorski Johannes , Jahr Holger , Wackernagel Wilfried
Published: March 2003

Among the isolates of a bacterial community from a soil sample taken from an agricultural plot in northern Germany, a population consisting of 119 strains was obtained that was identified by 16S rDNA sequencing and genomic fingerprinting as belonging to the recently described species Pseudomonas brassicacearum. Analysis of the population structure by allozyme electrophoresis (11 loci) and random amplified polymorphic DNA–polymerase chain reaction (RAPD–PCR; four primers) showed higher resolution with the latter method. Both methods indicated the presence of three lineages, one of which dominated strongly. Stochastic tests derived from the neutral theory of evolution (including Slatkin's exact test, Watterson's homozygosity test and the Tajima test) indicated that the population had developed under strong purifying selection pressure. The presence of strains clearly divergent from the majority of the population can be explained by in situ evolution or by influx of strains as a result of migration or both. Phytopathogenicity of a P. brassicacearum strain determined with tomato plants reached the level obtained with the type strain of the known pathogen Pseudomonas corrugata. The results show that a selective sweep was identified in a local population. Previously, a local selective sweep had not been seen in several populations of different bacterial species from a variety of environmental habitats.
Predominant growth of Alcanivorax strains in oil‐contaminated and nutrient‐supplemented sea water
Authors: Kasai Yuki , Kishira Hideo , Sasaki Tetsuya , Syutsubo Kazuaki , Watanabe Kazuya , Harayama Shigeaki
Published: March 2003

We found that bacteria closely related to Alcanivorax became a dominant
bacterial population in petroleum‐contaminated sea water when nitrogen and phosphorus
nutrients were supplied in adequate quantity. The predominance of Alcanivorax
bacteria was demonstrated under three experimental conditions: (i) in batch cultures
of sea water containing heavy oil; (ii) in columns packed with oil‐coated gravel
undergoing a continuous sea water flow; and (iii) in a large‐scale tidal flux reactor
that mimics a beach undergoing tidal cycles with fresh sea water. These results suggest
that bacteria related to Alcanivorax are major players in the bioremediation of oil‐contaminated marine environments.
Pseudomonas aeruginosa O‐antigen chain length is determined before ligation to lipid A core
Authors: Daniels Craig , Griffiths Corrie , Cowles Bryony , Lam Joseph S.
Published: March 2003

Pseudomonas aeruginosa is a Gram‐negative opportunistic pathogen that infects immunocompromised patients and trauma victims and causes fatal lung infections in people with cystic fibrosis. This microorganism produces a number of virulence factors, one of which is lipopolysaccharide (LPS), which has been shown to mediate many biological effects including resistance to serum killing and phagocytosis. These biological activities have been correlated to the length of the O‐polysaccharide and its distribution on the outer membrane. Wzz is responsible for regulation of the size distribution of the O‐antigen. Wzz has been found to participate solely in the Wzy‐dependent pathway for LPS biosynthesis, which produces heteropolymeric O‐polysaccharide such as the B‐band LPS of P. aeruginosa. Our laboratory has previously reported characterization of a Wzz protein encoded in the B‐band O‐antigen biosynthesis cluster of PAO1. The availability of the genome sequence of P. aeruginosa PAO1 has made it possible to identify a second functional Wzz protein (PA0938, Wzz2). Gene replacement was used to generate an unmarked wzz2Δ knock‐out and a wzz2Δ/wzz1::Gm double knock‐out. As expected, the wzz2Δ strain produced LPS with modal length imparted by Wzz1, and the wzz2Δ/wzz1::Gm strain produced LPS O‐antigen with a non‐modal (random) length. Both wzz1 and wzz2 from P. aeruginosa PAO1 were cloned and expressed with an N‐terminal His6 tag. His6‐Wzz1 and His6‐Wzz2 were purified to near homogeneity by immobilized metal affinity chromatography (IMAC). These preparations were used to develop specific polyclonal antibodies against each of the proteins. In vivo protein cross‐linking followed by Western immunoblotting indicated that Wzz1 forms dimers whereas Wzz2 forms octamers. By generation of a wzz2Δ/rmlC double mutant and analysis of the LPS, we have made the novel observation that polymerization of modal chain length‐distributed O‐antigen occurred before ligation to the lipid A core. We have shown an association between the Wzz proteins and O‐antigen polymer chains using immunoprecipitation with anti‐O5 O‐antigen monoclonal antibody MF15‐4. Both Wzz1 and Wzz2 could be co‐precipitated with O5 polymer.
Discrimination and taxonomy of geographically diverse strains of nitrile‐metabolizing actinomycetes using chemometric and molecular sequencing techniques
Authors: Brandão Pedro F. B. , Clapp Justin P. , Bull Alan T.
Published: March 2003

Mycolic acid‐containing actinomycetes capable of metabolizing nitriles were recovered from deepsea sediments and terrestrial soils by enrichment culture on acetonitrile, benzonitrile, succinonitrile or bromoxynil. A total of 43 nitrile‐degrading strains were isolated and, together with previously reco‐vered nitrile‐degrading rhodococci, were identified by a polyphasic taxonomic approach, which included mycolic acid profiles, pyrolysis mass spectrometry (PyMS), genomic fingerprinting based on sequence variability of the 16S ribosomal RNA gene using polymerase chain reaction‐restriction fragment length polymorphism‐single‐strand conformational polymorphism, and 16S rRNA gene sequence comparison. Isolates phylogenetically related to Rhodococcus erythropolis
dominated the culturable microorganisms from most marine and terrestrial samples.
These isolates clustered together in a major pyrogroup that showed high congruence
with PRS profiles of the 16S rRNA gene. Such high congruence also was obtained for
other recovered isolates that were assigned to species of Rhodococcus and
Gordonia. Sequencing data validated the results obtained by PRS analysis and enabled phylogenetic relationships to be established. Some of the recovered bacteria probably represent novel microbial species. The fact that nitrile‐metabolizing microorganisms were recovered from a wide range of habitat types suggests that nitrile transforming enzymatic activity is geographically widely distributed in nature.
In vitro demonstration of anaerobic oxidation of methane coupled to sulphate reduction in sediment from a marine gas hydrate area
Authors: Nauhaus Katja , Boetius Antje , Krüger Martin , Widdel Friedrich
Published: March 2003

Anaerobic oxidation of methane (AOM) and sulphate reduction were examined in sediment samples from a marine gas hydrate area (Hydrate Ridge, NE Pacific). The sediment contained high numbers of microbial consortia consisting of organisms that affiliate with methanogenic archaea and with sulphate‐reducing bacteria. Sediment samples incubated under strictly anoxic conditions in defined mineral medium (salinity as in seawater) produced sulphide from sulphate if methane was added as the sole organic substrate. No sulphide production occurred in control experiments without methane. Methane‐dependent sulphide production was fastest between 4°C and 16°C, the average rate with 0.1 MPa (approximately 1 atm) methane being 2.5 μmol sulphide day−1 and (g dry mass sediment)−1. An increase of the methane pressure to 1.1 MPa (approximately 11 atm) resulted in a four to fivefold increase of the sulphide production rate. Quantitative measurements using a special anoxic incubation device without gas phase revealed continuous consumption of dissolved methane (from initially 3.2 to 0.7 mM) with simultaneous production of sulphide at a molar ratio of nearly 1:1. To test the response of the indigenous community to possible intermediates of AOM, molecular hydrogen, formate, acetate or methanol were added in the absence of methane; however, sulphide production from sulphate with any of these compounds was much slower than with methane. In the presence of methane, such additions neither stimulated nor inhibited sulphate reduction. Hence, the experiments did not provide evidence for one of these compounds acting as a free extracellular intermediate (intercellular shuttle) during AOM by the presently investigated consortia.
Microbial diseases of corals and global warming
Authors: Rosenberg Eugene , Ben‐Haim Yael
Published: March 2003

Coral bleaching and other diseases of corals have increased dramatically during the last few decades. As outbreaks of these diseases are highly correlated with increased sea‐water temperature, one of the consequences of global warming will probably be mass destruction of coral reefs. The causative agent(s) of a few of these diseases have been reported: bleaching of Oculina patagonica by Vibrio shiloi; black band disease by a microbial consortium; sea‐fan disease (aspergillosis) by Aspergillus sydowii; and coral white plague possibly by Sphingomonas sp. In addition, we have recently discovered that Vibrio coralyticus is the aetiological agent for bleaching the coral Pocillopora damicornis in the Red Sea. In the case of coral bleaching by V. shiloi, the major effect of increasing temperature is the expression of virulence genes by the pathogen. At high summer sea‐water temperatures, V. shiloi produces an adhesin that allows it to adhere to a β‐galactoside‐containing receptor in the coral mucus, penetrate into the coral epidermis, multiply intracellularly, differentiate into a viable‐but‐not‐culturable (VBNC) state and produce toxins that inhibit photosynthesis and lyse the symbiotic zooxanthellae. In black band disease, sulphide is produced at the coral–microbial biofilm interface, which is probably responsible for tissue death. Reports of newly emerging coral diseases and the lack of epidemiological and biochemical information on the known diseases indicate that this will become a fertile area of research in the interface between microbial ecology and infectious disease.
Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440
Authors: Jiménez José Ignacio , Miñambres Baltasar , García José Luis , Díaz Eduardo
Published: March 2003

Analysis of the catabolic potential of Pseudomonas putida KT2440 against a wide range of natural aromatic compounds and sequence comparisons with the entire genome of this microorganism predicted the existence of at least four main pathways for the catabolism of central aromatic intermediates, that is, the protocatechuate (pca genes) and catechol (cat genes) branches of the β‐ketoadipate pathway, the homogentisate pathway (hmg/fah/mai genes) and the phenylacetate pathway (pha genes). Two additional gene clusters that might be involved in the catabolism of N‐heterocyclic aromatic compounds (nic cluster) and in a central meta‐cleavage pathway (pcm genes) were also identified. Furthermore, the genes encoding the peripheral pathways for the catabolism of p‐hydroxybenzoate (pob), benzoate (ben), quinate (qui), phenylpropenoid compounds (fcs, ech, vdh, cal, van, acd and acs), phenylalanine and tyrosine (phh, hpd) and n‐phenylalkanoic acids (fad) were mapped in the chromosome of P. putida KT2440. Although a repetitive extragenic palindromic (REP) element is usually associated with the gene clusters, a supraoperonic clustering of catabolic genes that channel different aromatic compounds into a common central pathway (catabolic island) was not observed in P. putida KT2440. The global view on the mineralization of aromatic compounds by P. putida KT2440 will facilitate the rational manipulation of this strain for improving biodegradation/biotransformation processes, and reveals this bacterium as a useful model system for studying biochemical, genetic, evolutionary and ecological aspects of the catabolism of aromatic compounds.
Testing the limits of biological tolerance to arsenic in a fungus isolated from the River Tinto
Authors: Cánovas David , Durán Consuelo , Rodríguez Nuria , Amils Ricardo , De Lorenzo Víctor
Published: March 2003

The Tinto river in Spain, with its high acidity and heavy metal concentrations (As, Cu, Cr, Zn), is an example of an environment hostile to life. Yet despite these extreme conditions, the site possesses a great diversity of eukaryotic life forms. We report the isolation of a filamentous fungus able to grow at 200 mM arsenic (∼15 000 p.p.m.), i.e. a concentration 20‐fold above that withstood by the reference microorganismsEscherichia coli,Saccharomyces cerevisiaeandAspergillus nidulans, and 200 times greater than that tolerated byAspergillus niger. Based on morphological, physiological and genotypic criteria, the strain belongs to the genusAspergillus. High concentrations of the metalloid induced vacuolation, suggesting that this organelle is someway connected to arsenic tolerance. Concentrations that are lethal to other organisms do not stressAspergillussp. P37. The fungus was capable of removing arsenic from culture media. In addition to arsenic hyper‐resistance, it also displayed a polyresistant phenotype to copper and chromium.
Cloning of Baeyer‐Villiger monooxygenases from Comamonas, Xanthobacter and Rhodococcus using polymerase chain reaction with highly degenerate primers
Authors: Van Beilen Jan B. , Mourlane Frédéric , Seeger Markus A. , Kovac Jasminka , Li Zhi , Smits Theo H. M. , Fritsche Urban , Witholt Bernard
Published: March 2003

To clone novel type 1 Baeyer‐Villiger monooxygenase (BVMO) genes, we isolated or collected 25 bacterial strains able to grow on alicyclic compounds. Twelve of the bacterial strains yielded polymerase chain reaction (PCR) fragments with highly degenerate primers based on the sequences of known and putative BVMOs. All these fragments were found to encode peptides homologous to published BVMO sequences. The complete BVMO genes and flanking DNA were cloned from a Comamonas, a Xanthobacter and a Rhodococcus strain using the PCR fragments as probes. BVMO genes cloned from the first two strains could be expressed to high levels in Escherichia coli using standard expression vectors, and the recombinants converted cyclopentanone and cyclohexanone to the corresponding lactones. The Rhodococcus BVMO, a putative steroid monooxygenase, could be expressed after modification of the N‐terminal sequence. However, recombinants expressing this protein did not show activity towards progesterone. An esterase homologue located directly upstream of the Xanthobacter BVMO gene and a dehydrogenase homologue encoded directly downstream of the Comamonas sp. NCIMB 9872 BVMO gene were also expressed in E. coli and shown to specify lactone hydrolase and cyclohexanol dehydrogenase activity respectively.
Confirmation of complete colonoscopy without intubation of the ileum
Authors: Clark  , Rocker  , Reddy  , Aslam  , Owen
Published: March 2003

Objectives

To establish whether biopsy of the ileocaecal valve from the caecum provides an alternative to the more technically demanding procedure of terminal ileal intubation and biopsy to document completion of colonoscopy.

Subjects and methods

Fifty‐three patients underwent colonoscopy at which the terminal ileum was intubated and biopsied and, after withdrawal of the endoscope tip into the caecum, the ileocaecal valve was then biopsied. To replicate the situation in which the ileum is not intubated, another group of 30 patients had ileocaecal valve biopsies taken from the caecum before ileal intubation was attempted.

Results

All of the terminal ileal biopsies obtained before ileocaecal valve biopsy showed small bowel mucosa, as did 51 (96%) of the ileocaecal valve specimens from this group. When ileocaecal valve biopsy was obtained first, 16 (53%) specimens contained small bowel mucosa.

Conclusion

Ileocaecal valve biopsies were significantly more likely to yield small bowel mucosa if taken after ileal intubation (P < 0.001, Fisher’s exact test). Nevertheless, about half of ileocaecal valve biopsies taken without ileal intubation contained small bowel mucosa, providing evidence of complete colonoscopy in these cases. Terminal ileal intubation and biopsy, however, remains the only reliable way to document complete colonoscopy.