bluuebunny/crossref_metadata_2025_split huggingface dataset:
An ecological cost of plant defence: attractiveness of bitter cucumber plants to natural enemies of herbivores
Authors: Agrawal Anurag A. , Janssen Arne , Bruin Jan , Posthumus Maarten A. , Sabelis Maurice W. 
Published: March 2003

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

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

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

AbstractSurface fires in Amazonian forests could contribute as much as 5% of annual carbon emissions from all anthropogenic sources during severe El Niño years. However, these estimates are based on short‐term figures of post‐burn tree mortality, when large thicker barked trees (representing a disproportionate amount of the forest biomass) appear to resist the fires. On the basis of a longer term study, we report that the mortality of large trees increased markedly between 1 and 3 years, more than doubling current estimates of biomass loss and committed carbon emissions from low‐intensity fires in tropical forests.
Green algal extracellular products regulate antialgal toxin production in a cyanobacterium
Authors: Kearns Katherine Dowell , Hunter Mark D. 
Published: March 2003

Many bacterial genes and virulence factors are regulated by interbacterial and/or host–parasite chemical signals. We demonstrate that toxin production by a free‐living freshwater cyanobacterium is regulated in part by the presence of extracellular products of a eukaryotic green alga. In growth experiments, extracellular products made by the cyanobacterium Anabaena flos‐aquae contained both anatoxin and microcystin, and significantly reduced the yield of Chlamydomonas reinhardtii, a green alga. Based on experiments in which we added purified toxins to C. reinhardtii cultures, we believe that microcystin was responsible for the growth reduction. A. flos‐aquae produced anatoxin constitutively when grown alone, but anatoxin concentration increased in the presence of C. reinhardtii elicitors. Microcystin accumulation depended on the growth phase; however, high concentrations of C. reinhardtii extracellular products completely inhibited microcystin accumulation. Our results demonstrate that cyanobacterial toxin production may be regulated by complex growth phase‐dependent and environmental chemical cues, and suggest that secreted chemicals can mediate the outcome of competition between the cyanobacterium A. flos‐aquae and the green alga C. reinhardtii.
Microenvironments and distribution of nitrifying bacteria in a membrane‐bound biofilm
Authors: Schramm Andreas , De Beer Dirk , Gieseke Armin , Amann Rudolf 
Published: March 2003

The distribution of nitrifying bacteria of the genera Nitrosomonas, Nitrosospira, Nitrobacter and Nitrospira was investigated in a membrane‐bound biofilm system with opposed supply of oxygen and ammonium. Gradients of oxygen, pH, nitrite and nitrate were determined by means of microsensors while the nitrifying populations along these gradients were identified and quantified using fluorescence in situ hybridization (FISH) in combination with confocal laser scanning microscopy. The oxic part of the biofilm which was subjected to high ammonium and nitrite concentrations was dominated by Nitrosomonas europaea‐like ammonia oxidizers and by members of the genus Nitrobacter. Cell numbers of Nitrosospira sp. were 1–2 orders of magnitude lower than those of N. europaea. Nitrospira sp. were virtually absent in this part of the biofilm, whereas they were most abundant at the oxic–anoxic interface. In the totally anoxic part of the biofilm, cell numbers of all nitrifiers were relatively low. These observations support the hypothesis that N. europaea and Nitrobacter sp. can out‐compete Nitrosospira and Nitrospira spp. at high substrate and oxygen concentrations. Additionally, they suggest microaerophilic behaviour of yet uncultured Nitrospira sp. as a factor of its environmental competitiveness.
The effects of copper on the microbial community of a coral reef sponge
Authors: Webster Nicole S. , Webb Richard I. , Ridd Michael J. , Hill Russell T. , Negri Andrew P. 
Published: March 2003

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

Summary Aeromonas hydrophila is an opportunistic Gram‐negative pathogen that readily attaches to stainless steel to produce a thin biofilm with a complex 3D structure covering 40–50% of the available surface and producing large microcolonies. As A. hydrophila possesses an N‐acylhomoserine lactone (AHL)‐dependent quorum‐sensing system based on the ahyRI locus, the presence of the AhyI protein and C4‐HSL within the biofilm phase was first established by Western blot and AHL biosensor analysis respectively. The ability of the A. hydrophila AH‐1 N strain to form biofilms in a continuous‐flow chamber was compared with isogenic ahyI and ahyR mutants. The ahyI mutant, which cannot produce C4‐HSL, failed to form a mature biofilm. In addition, the viable count of biofilm, but not planktonic phase ahyI mutants, was significantly lower that the parent or ahyR mutant. This defect in the differentiation of the ahyI mutant biofilm could be partially restored by the addition of exogenous C4‐HSL. A mutation in ahyR increased coverage of the available surface to around 80% with no obvious effect upon biofilm microcolony formation. These data support a role for AHL‐dependent quorum sensing in A. hydrophila biofilm development. Exposure of the A. hydrophila AH‐1N biofilm to N‐(3‐oxodecanoyl)homoserine lactone, which inhibits exoprotease production in planktonic cells, however, had no effect on biofilm formation or architecture within the continuous‐flow chamber.
Analysis of the Pseudomonas aeruginosa oprD gene from clinical and environmental isolates
Authors: Pirnay Jean‐Paul , Vos Daniel De , Mossialos Dimitris , Vanderkelen Alain , Cornelis Pierre , Zizi Martin 
Published: March 2003

SummaryGenomes are constantly evolving. Our report highlights the wide mutational diversity of clinical as well as environmental isolates, compared with the laboratory strain(s), through the systematic genetic analysis of a chromosomal porin gene (oprD) in relation to a specific antibiotic resistance. Mutational inactivation of the oprD gene is associated with carbapenem resistance in Pseudomonas aeruginosa. The sequence of the oprD gene of 55 Pseudomonas aeruginosa natural isolates obtained from across the world – from sources as diverse as patients and rhizospheres – was analysed. A microscale mosaic structure for this gene – resulting from multiple intra‐ and possibly interspecies recombinational events – is reported. An array of independent and seemingly fast‐occurring defective oprD mutations were found, none of which had been described before. A burn wound isolate demonstrated unusually high overall sequence variability typical of mutator strains. We also present evidence for the existence of OprD homologues in other fluorescent pseudomonads.
Enrichment versus biofilm culture: a functional and phylogenetic comparison of polycyclic aromatic hydrocarbon‐degrading microbial communities
Authors: Stach James E. M. , Burns Richard G. 
Published: March 2003

SummaryThe effect that culture methods have on the diversity of degradative microbial communities is not well understood. We compared conventional batch enrichment with a biofilm culture method for the isolation of polycyclic aromatic hydrocarbon (PAH)‐degrading microbial communities from a PAH‐contaminated soil. The two methods were assessed by comparing: (i) the diversity of culturable bacteria; (ii) the diversity of PAH‐catabolic genes in isolated bacteria; (iii) the inter‐ and intraspecific diversity of active PAH‐catabolic gene classes; (iv) the diversity of bacteria present in 16S rRNA gene libraries generated from RNA extracted from the two communities and soil; and (v) the estimated diversity of active bacteria in the soil and culture systems. Single‐strand conformation polymorphism analysis showed that the biofilm culture yielded 36 bacterial and two fungal species compared with 12 bacterial species from the enrichment culture. Application of accumulation and non‐parametric estimators to clone libraries generated from 16S rRNA confirmed that the biofilm community contained greater diversity. Sequencing of clones showed that only species from the Proteobacteria were active in the enrichment culture, and that these species were expressing an identical nahAc‐like naphthalene
dioxygenase. 16S rRNA clones generated from the biofilm community indicated that
species from the Cytophaga/Flavobacterium, high G+C bacteria and Proteobacteria were
active at the time of sampling, expressing cndA‐, nahAc‐ and phnAc‐like naphthalene dioxygenases. The diversity of active species in the biofilm culture system closely matched that in the PAH‐contaminated source soil. The results of this study showed that biofilm culture methods are more appropriate for the study of community‐level interactions in PAH‐degrading microbial communities. The study also indicated that cultivation of microbial communities on solid media might be the primary source of bias in the recovery of diverse species.
Phylogenetic 16S rRNA analysis reveals the presence of complex and partly unknown bacterial communities in Tito Bustillo cave, Spain, and on its Palaeolithic paintings
Authors: Schabereiter‐Gurtner Claudia , Saiz‐Jimenez Cesareo , Piñar Guadalupe , Lubitz Werner , Rölleke Sabine 
Published: March 2003

SummaryTito Bustillo cave (Ribadesella, Spain) contains valuable Palaeolithic paintings, which date back 15 000–20 000 years. Since 1969, the cave has been open to the public. Rock wall surfaces, spelaeothems and soils are covered by apparent biofilms of phototrophic microorganisms, which develop under artificial lighting. In addition, rock surfaces present conspicuous bacterial growth in the form of round colonies of different colours and about 1–2 mm in diameter. Even the famous Paintings Panel shows some evident microbial growth. In the present study, bacterial communities on the paintings and on the rock surfaces near the paintings were analysed by culture‐independent techniques, including polymerase chain reaction (PCR) amplification of bacterial 16S rRNA genes (16S rDNA), phylogenetic sequence analyses and genetic community fingerprinting by denaturing gradient gel electrophoresis (DGGE). DGGE fingerprints showed complex bacterial community patterns. Forty‐one clones matching DGGE bands of the community fingerprints were sequenced, representing about 39% of DNA fragments in the DGGE patterns. Phylogenetic sequence analyses revealed a high number of phylogenetically novel 16S rDNA sequence types and a high diversity of putatively chemotrophic and heterotrophic bacteria. Sequences were phylogenetically most closely related to the Proteobacteria (20 clones), green non‐sulphur bacteria (three clones), Planctomycetales order (one clone), Cytophaga–Flexibacter– Bacteroides division (one clone) and the Actinobacteria (four clones). Furthermore, we report the presence of members of the Acidobacterium division (12 clones) in a karstic hypogean environment. Members of this phylum have not so far been detected in these particular environments.
Characterization of the bacterial consortium associated with black band disease in coral using molecular microbiological techniques
Authors: Cooney Rory P. , Pantos Olga , Tissier Martin D. A. Le , Barer Michael R. , O´Donnell Anthony G. , Bythell John C 
Published: March 2003

SummaryThe bacterial community associated with black band disease (BBD) of the scleractinian corals Diploria strigosa, Montastrea annularis and Colpophyllia natans was examined using culture‐independent techniques. Two complementary molecular screening techniques of 16S rDNA genes [amplified 16S ribosomal DNA restriction analysis (ARDRA) of clone libraries and denaturing gradient gel electrophoresis (DGGE)] were used to give a comprehensive characterization of the community. Findings support previous studies indicating low bacterial abundance and diversity associated with healthy corals. A single cyanobacterial ribotype was present in all the diseased samples, but this was not the same as that identified from Phormidium corallyticum culture isolated from BBD. The study confirms the presence of Desulfovibrio spp. and sulphate‐reducing bacteria that have previously been associated with the BBD consortium. However, the species varied between diseased coral samples. We found no evidence of bacteria from terrestrial, freshwater or human sources in any of the samples. We report the presence of previously unrecognized potential pathogens [a Cytophaga sp. and an α‐proteobacterium identified as the aetiological agent of juvenile oyster disease (JOD)] that were consistently present in all the diseased coral samples. The molecular biological approach described here gives an increasingly comprehensive and more precise picture of the bacterial population associated with BBD. To understand the pathogenesis of BBD, our attention should be focused on the pervasive ribotypes identified in this study (the Cyanobacterium sp., the Cytophaga sp. and the JOD pathogen).
Estimation of methanotroph abundance in a freshwater lake sediment
Authors: Costello Andria M. , Auman Ann J. , Macalady Jennifer L. , Scow Kate M. , Lidstrom Mary E. 
Published: March 2003

AbstractThe numbers of methane‐oxidizing bacteria (methanotrophs) in the sediments of Lake Washington were estimated using three culture‐independent methods. Quantitative slot‐blot hybridizations were performed with type I and type II methanotroph‐specific probes. These data were compared to data from quantitative hybridizations using a pmoA‐specific probe and a eubacterial probe. From the combined hybridi‐zation data, the methanotroph population in Lake Washington was estimated to be 3.6 × 108–7.4 × 108 cells/g dry weight. Methanotroph community structure and number were also investigated using polar lipid fatty acid (PLFA) analysis. Analysis of biomarker PLFAs characteristic of both type I (16:1ω8) and type II (18:1ω8) methanotrophs was used to estimate the abundance of these bacteria in Lake Washington sediments. From the PLFA data, the methanotroph population in Lake Washington was estimated to be 7.1 × 108–9.4 × 109 cells/g dry weight. As a third method of quantitation, we calculated the methanotroph population using the total methane oxidation rate for whole cells in Lake Washington sediment to be 1.3 × 108–1.2 × 109 cells/g dry weight. The three independent estimates of the number of methanotrophs in Lake Washington sediment agree within a two‐ to fourfold range. These data suggest that the three techniques used in this study detect the functionally significant population of methanotrophs in Lake Washington. Furthermore, these techniques will be useful for obtaining estimates of methanotroph abundance in additional environments.
Recovery of novel bacterial diversity from a forested wetland impacted by reject coal
Authors: Brofft Jennifer E. , McArthur J. Vaun , Shimkets Lawrence J. 
Published: March 2003

SummarySulphide mineral mining together with improperly contained sulphur‐rich coal represents a significant environmental problem caused by leaching of toxic material. The Savannah River Site's D‐area harbours a 22‐year‐old exposed reject coal pile (RCP) from which acidic, metal rich, saline runoff has impacted an adjacent forested wetland. In order to assess the bacterial community composition of this region, composite sediment samples were collected at three points along a contamination gradient (high, middle and no contamination) and processed for generation of bacterial and archaeal 16S rDNA clone libraries. Little sequence overlap occurred between the contaminated (RCP samples) and unimpacted sites, indicating that the majority of 16S rDNAs retrieved from the former represent organisms selected by the acidic runoff. Archaeal diversity within the RCP samples consisted mainly of sequences related to the genus Thermoplasma and to sequences of a novel type. Bacterial RCP libraries contained 16S rRNA genes related to isolates (Acidiphilium sp., Acidobacterium capsulatum, Ferromicrobium acidophilium and Leptospirillum ferrooxidans) and environmental clones previously retrieved from acidic habitats, including ones phylogenetically associated with organisms capable of sulphur and iron metabolism. These libraries also exhibited particularly novel 16S rDNA types not retrieved from other acid mine drainage habitats, indicating that significant diversity remains to be detected in acid mine drainage‐type systems.
Holy water fonts are reservoirs of pathogenic bacteria
Authors: Jurado V. , Ortiz‐Martinez A. , Gonzalez‐delValle M. , Hermosin B. , Saiz‐Jimenez C. 
Published: March 2003

SummaryThe holy water fonts from the churches of Seville, Spain have a strong bacterial contamination. Coliforms, Enterobacteriaceae and other pathogenic bacteria are widely represented in the fonts investigated. Thirty out of the 37 different species isolated from holy waters are known human pathogens. The high bacterial contamination is related to human skin transmission and, probably, to misuse of the water.