Bacterial ecology, antibiotics and selection for virulence

The evolution of antibiotic resistance in bacteria is well known. Here I describe possible mechanisms by which an increased rate of re-colonization of vertebrate guts by microbes caused by antibiotic use could lead to selection for increased virulence in currently mutualistic or benign microbes. The importance of understanding both the source and the frequency of colonization in such mutualisms is stressed and the possible importance of pseudo-vertical transmission in the evolution of these systems is discussed. A number of areas requiring experimental investigation are identified.     

Synopsis of scientific results of the sarec sponsored project on the ecology of Lake Kariba

A summary of current research on Lake Kariba is given. Lake Kariba is now a phosphorus limited oligotrophic lake, dependent on annual nutrient input for the maintenance of production. Nitrogen fixation by cyanobacteria has become an important source of nitrogen in the dry season and that fish harvesting is an important phosphorus sink. An up to date plankton composition list has been produced and plankton biomass determined. Diving studies indicate large biomass of bivalves. The aquatic vegetation displays both longitudinal as well as depth gradients, related to light regimes. Only preliminary data are available on mud/water interactions, but the available data indicate considerable fluxes in the river mouth stations and shallow protected littoral areas. The role of predatory birds and crocodiles in the fishery economy of the lake is evaluated and indicates no major conflict between these predators and human fishing interests. The research also draws attention to pesticides in Lake Kariba as indicated by work on fish eating birds and crocodile research. Since the publication of ‘Lake Kariba’ by Balon & Coche (1975) the research project, THE ECOLOGY OF LAKE KARIBA, being undertaken by the University Lake Kariba Research Station constitutes the first multidisciplinary study of the lake, 30 years after the Zambezi river was impounded at Kariba Gorge. It could have offered a unique opportunity of comparing the lake now with what it was soon after impoundment.     

Avian growth and development rates and age-specific mortality: the roles of nest predation and adult mortality

Previous studies have shown that avian growth and development covary with juvenile mortality. Juveniles of birds under strong nest predation pressure grow rapidly, have short incubation and nestling periods, and leave the nest at low body mass. Life-history theory predicts that parental investment increases with adult mortality rate. Thus, developmental traits that depend on the parental effort exerted (pre- and postnatal growth rate) should scale positively with adult mortality, in contrast to those that do not have a direct relationship with parental investment (timing of developmental events, e.g. nest leaving). I tested this prediction on a sample of 84 North American songbirds. Nestling growth rate scaled positively and incubation period duration negatively with annual adult mortality rates even when controlled for nest predation and other covariates, including phylogeny. On the contrary, neither the duration of the nestling period nor body mass at fledging showed any relationship. Proximate mechanisms generating the relationship of pre- and postnatal growth rates to adult mortality may include increased feeding, nest attentiveness during incubation and/or allocation of hormones, and deserve further attention.     

Environmental and ecological factors that shape the gut bacterial communities of fish: a meta-analysis

Symbiotic bacteria often help their hosts acquire nutrients from their diet, showing trends of co-evolution and independent acquisition by hosts from the same trophic levels. While these trends hint at important roles for biotic factors, the effects of the abiotic environment on symbiotic community composition remain comparably understudied. In this investigation, we examined the influence of abiotic and biotic factors on the gut bacterial communities of fish from different taxa, trophic levels and habitats. Phylogenetic and statistical analyses of 25 16S rRNA libraries revealed that salinity, trophic level and possibly host phylogeny shape the composition of fish gut bacteria. When analysed alongside bacterial communities from other environments, fish gut communities typically clustered with gut communities from mammals and insects. Similar consideration of individual phylotypes (vs. communities) revealed evolutionary ties between fish gut microbes and symbionts of animals, as many of the bacteria from the guts of herbivorous fish were closely related to those from mammals. Our results indicate that fish harbour more specialized gut communities than previously recognized. They also highlight a trend of convergent acquisition of similar bacterial communities by fish and mammals, raising the possibility that fish were the first to evolve symbioses resembling those found among extant gut fermenting mammals.     

Altering the balance between bacterial production and protistan bacterivory triggers shifts in freshwater bacterial community composition

Bacterivorous protists are known to induce changes in bacterial community composition (BCC). We hypothesized that changes in BCC could be related quantitatively to a measure of grazing: the ratio of bacterial mortality to growth rate. To test this hypothesis, we analyzed time-course changes in BCC, protistan grazing rate, and bacterial production from 3 in situ studies conducted in a freshwater reservoir and three laboratory studies. In the field experiments, samples were manipulated to yield different levels of protistan bacterivory and incubated in dialysis bags. Laboratory investigations were continuous cultivation studies in which different bacterivorous protists were added to bacterial communities. BCC was assessed using 4–6 different rRNA-targeted oligonucleotide probes for community analysis. Change in BCC (Δ BCC) was estimated as the sum of changes in the proportions of the two phylogenetic groups that showed the largest shifts. Analysis of a set of 22 estimates of shifts in the ratio of grazing to production rate over periods of 48–72 h and Δ BCC showed that Δ BCC was positively and tightly correlated (r ² = 0.784) with shifts in the ratio of grazing mortality to cell production. While the nature of a shift in BCC is unpredictable, the magnitude of the change can be related to changes in the balance between bacterial production and protistan grazing. This revised version was published online in August 2006 with corrections to the Cover Date.     

Influence of nutrient status and grazing pressure on the fate of Francisella tularensis in lake water

The natural reservoir of Francisella tularensis , the causative agent of tularaemia, is yet to be identified. We investigated the possibility that Francisella persists in natural aquatic ecosystems between outbreaks. It was hypothesized that nutrient-rich environments, with strong protozoan predation, favour the occurrence of the tularaemia bacterium. To investigate the differences in adaptation to aquatic environments of the species and subspecies of Francisella , we screened 23 strains for their ability to survive grazing by the ciliate Tetrahymena pyriformis . All the Francisella strains tested were consumed at a low rate, although significant differences between subspecies were found. The survival and virulence of gfp -labelled F. tularensis ssp. holarctica were then studied in a microcosm experiment using natural lake water, with varying food web complexities and nutrient availabilities. High nutrient conditions in combination with high abundances of nanoflagellates were found to favour F. tularensis ssp. holarctica . The bacterium was observed both free-living and within the cells of a nanoflagellate. Francisella tularensis entered a viable but nonculturable state during the microcosm experiment. When studied over a longer period of time, F. tularensis ssp. holarctica survived in the lake water, but loss of virulence was not prevented by either high nutrient availability or the presence of predators.     

Patterns of natural mortality in stream‐living brown trout (Salmo trutta)

1. We tested the hypothesis that lifetime mortality patterns and their corresponding rates and causal factors differ among populations of stream‐living salmonids. To this end, we examined the lifetime mortality patterns of several successive cohorts of two stream‐living brown trout (Salmo trutta) populations in Spain and Denmark. 2. In the southern population, we observed a consistent two‐phase pattern, in which mortality was negligible during the first half of the lifetime and severe during the rest of the lifetime. In contrast, the northern population demonstrated a three‐phase pattern with an earlier phase varying from negligible to severe, followed by a second stage of weak mortality, and lastly by a third life stage of severe mortality. 3. Despite substantial differences in the mortality patterns between the two populations, the combined effect of recruitment (as a proxy of the density‐dependent processes occurring during the lifetime) and mean body mass (as a proxy of growth experienced by individuals in a given cohort) explained c. 89% of the total lifetime mortality rates across cohorts and populations. 4. A comparison with other published data on populations of stream‐living brown trout within its native range highlighted lifetime mortality patterns of one, two, three and four phases, but also suggested that common patterns may occur in populations that experience similar individual growth and population density.     

Parallel changes in the taxonomical structure of bacterial communities exposed to a similar environmental disturbance

Bacterial communities play a central role in ecosystems, by regulating biogeochemical fluxes. Therefore, understanding how multiple functional interactions between species face environmental perturbations is a major concern in conservation biology. Because bacteria can use several strategies, including horizontal gene transfers (HGT), to cope with rapidly changing environmental conditions, potential decoupling between function and taxonomy makes the use of a given species as a general bioindicator problematic. The present work is a first step to characterize the impact of a recent polymetallic gradient over the taxonomical networks of five lacustrine bacterial communities. Given that evolutionary convergence represents one of the best illustration of natural selection, we focused on a system composed of two pairs of impacted and clean lakes in order to test whether similar perturbation exerts a comparable impact on the taxonomical networks of independent bacterial communities. First, we showed that similar environmental stress drove parallel structural changes at the taxonomic level on two independent bacterial communities. Second, we showed that a long-term exposure to contaminant gradients drove significant taxonomic structure changes within three interconnected bacterial communities. Thus, this model lake system is relevant to characterize the strategies, namely acclimation and/or adaptation, of bacterial communities facing environmental perturbations, such as metal contamination.     

Consequences of protist-stimulated bacterial production for estimating protist growth efficiencies

The trophic link between bacteria and bacterivorous protists is a complex interaction that involves feedback of inorganic nutrients and growth substrates that are immeadiately available for prey growth. These interactions were examined in the laboratory and in incubations of concentrated natural assemblages of bacterioplankton. Growth dynamics of estuarine and marine bacterivorous protists were determined in laboratory culture using Vibrio natriegens as prey and were compared to growth of protists on bacterioplankton assemblages concentrated by tangential flow filtration from four northwest Florida Estuaries. Biomass transfers from bacteria to protists were monitored by tracing elemental carbon and nitrogen in particulate fractions of protist added and grazer free controls. Gross growth efficiencies of the protists on naturally occurring bacteria were within the range determined in lab estimates of growth efficiency on cultured bacteria (50%). However, bacterial response to protist excretion products was different in the lab and field incubations, and bacterial growth contributed to the biomass available to protists in the field incubations. As determined by radioisotope-labeled substrate incorporation, a time lag in bacterial reponse to protist excretion products was observed for laboratory batch cultures, allowing accurate estimation of growth efficiency. In incubations with concentrated natural bacterial assemblages, bacterial growth response coincided with protist growth and excretion. The additional bacterial production on protist excretion products reached a maximum of 2–3-fold higher than protist-free controls. In addition, ammonium concentrations increased with protist grazing and growth in lab cultures, but ammonium excreted by protists in concentrates did not accumulate. The C:N values for the bacterial concentrates suggests that these bacteria were nitrogen limited. It is speculated that dissolved organic carbon, concentrated by tangential flow filtration (> 100,000 MW membrane) with the bacterioplankton, was utilized by bacteria when nitrogen was supplied as ammonium and amino acids from protist excretion. Thus, estimates of protist growth efficiency on naturally occurring bacterioplankton, corrected for protist-stimulated bacterial production, were in the range of 13–21%.     

Analysis of the intestinal microflora: a renaissance

The ability of microbial ecologists to analyse the composition of complex bacterial communities has been greatly enhanced by the application of molecular methodologies. The use of these techniques should enable an accurate record of the identity and population dynamics of the inhabitants of the intestinal tract to be obtained, and should promote an improved comprehension of the relationship between the microflora and the human host. This, in turn, will lead to a new concept of the intestinal microflora of humans.     

Growth, production and mortality of two species of Agapetus (Trichoptera: Glossosomatidae) in the Acheron River, south-east Australia

1. Quantitative samples of Agapetus pontona and Agapetus monticolus larvae were taken at two sites on each of three rivers in the catchment of the Acheron River (i.e. Little River, Steavenson River and Acheron River). Both species were univoltine with A. pontona having a 5–6-month life cycle (spring to late summer) and A. monticolus a 10-month life cycle (autumn to early summer). 2. Population densities, biomass (B), growth rates and mortality patterns derived from these field data were used to calculate secondary production (P) and turnover (P/B). At each site, these features were measured for the whole of the A. pontona life cycle, but only for the last 3 months of the A. monticolus life cycle. 3. Growth rates were highest at the sites on the Little River during summer for both species: 1.8–1.9% dry weight day^?1 for A. pontona and 2.0–2.2% dry weight day^?1 for A. monticolus. Turnover ratios (P/B) were also highest at the Little River sites: 3.2–6.3 for A. pontona and 1.6–1.9 for A. monticolus. Production was variable and was not significantly different among rivers for A. pontona (28.4–222.1 mg m^?2 per 6 months) but was for A. monticolus (70.5–123.8 mg m^?2 per 3 months for the Little River compared with 14.8–23.3 mg m^?2 at the other sites). 4. Two of the rivers were subject to higher levels of rock movement during summer than the third (Little River). It was suggested that the higher growth rates (and turnover ratios) in the Little River were caused by the lower levels of rock movement causing less disruption to the feeding of the larvae. 5. Little or no larval mortality of A. pontona was observed at any site. However, mortality occurred between instar 5 and the pupal stage. This varied in a density dependent fashion, suggesting population regulation occurred: the higher the larval density the greater the mortality suffered by the pupae. No such density dependent pattern occurred for the mortality between instar 5 and the pupal stage of A. monticolus. 6. The population of A. pontona was not food limited and larval densities were low. Competition appeared to occur for pupation sites. Low and relatively constant discharges during the late summer when A. pontona pupated appeared to provide more predictable conditions than those experienced by A. monticolus in the spring when discharge was very variable resulting in the stranding (and thus death) of pupae above the water line. Such unpredictable conditions would not foster density dependent population regulation via pupal mortality.     

Density dependent mortality in the springtail species Orchesella cincta due to predation by the carabid beetle Notiophilus biguttatus

Mortality of the collembole species Orchesella cincta (L.), due to predation by the carabid Notiophilus biguttatus F., has been measured in the laboratory at three levels of prey density. Prey densities were chosen such that the predator's consumption at the lowest prey density was a little above the maintenance ration. Between the two lowest prey densities, mortality increased significantly with prey density. We presume that density-dependent search activity by the predator is responsible for the positive density-dependent mortality. A method is proposed to solve the problem of decreasing prey density during the observations.

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Relation positive entre la densité de Orchesella cincta et la mortalité due à la prédation part Nothiophilus biguttarus

Résumé Cet article décrit l'importance de la prédation par le carabe N. biguttatus en fonction de la densité de la proie, O. cincta. Les résultats montrent que, sous l'effet de la prédation, la mortalité de la proie augmente avec sa densité. La quantité minimale de proies qui doit être consommée pour permettre la reproduction du carabe, a été déterminée. La relation entre la fécondité du carabe et l'effectif consommé, montre l'effet stabilisant de la prédation sur les populations de proies.La relation de dépendance de la densité observée avec la mortalité est due à une modification du comportement du carabe en fonction de la densité de sa proie. Nous proposons un modèle permettant de prévoir la régression de la population de proies sous les effets de la prédation.

     

Mortality of marine bacterial strains in seawater

As an approach for assessing the dynamics of bacterial population in seawater, the survival of five isolated marine bacteria strains was assessed by the disappearance of radioactivity in the cold trichloroacetic acid (TCA)-insoluble fraction from a previously³H-labeled culture. Metabolic activity during survival experiments was assessed by the measurement of electron transport system (ETS) activity. Fractionated filtration was used to assess the grazing mortality. The particulate fraction that passed 2.0 m and was retained in 0.2 m was the main cause of mortality.     

Distribution of echinoderms and their larvae in the southwestern Peter the Great Bay, Sea of Japan

Based on results of processing planktonic and benthic samples collected in 1996 and 1997, a spatial distribution of echinoderms in the bottom and of their larvae in the plankton were collated for the water area of the Southern region of the Far Eastern State Biosphere Marine Reserve. Some correlation between distributions of the adult and larval sea star Asterias amurensis in July was revealed. At the same time, there was no correlation between distributions of larvae and adult individuals of the brittle star Ophiura sarsi and sea urchin Echinocardium cordatum, which are most abundant in the area. The size structure of bottom populations of the brittle stars O. sarsi and Amphiodia fissa in the studied area was assessed. The correlation coefficient between the distribution of young-of-the-year and the population density was 0.47 in O. sarsi and 0.74 in A. fissa respectively, which implied a selective settling of larvae of those species in areas inhabited by adult brittle stars. Recruitment of bottom populations from 1996 spawning was 5% in O. sarsi and 3.3% in A. fissa.     

The microbial loop in a humic lake: seasonal and vertical variations in the structure of the different communities

Seasonal and vertical variations of the main microbial communities (heterotrophic bacteria, autotrophic picoplankton, auto- and heterotrophic nanoflagellates, ciliated protozoa and microalgae) and auto- and heterotrophic activities were estimated in a brown-colored humic and moderately acid lake in central France, the lake of Vassivière. The results demonstrated the dominant role of light in the vertical distribution of autotrophic and mixotrophic microorganisms which are confined to the 0–5 m layer during thermal stratification. The bacterial biomass was high throughout the water column probably because of the great availability of dissolved organic matter. Consequently, the predatory microzooplankton and particularly the various trophic groups of ciliated protozoa, were distributed in the water column according to the vertical distribution of the particular food resources (detritus, bacteria, algae). However, despite the great abundance of algae and bacteria, biomass of flagellated and ciliated protozoa was relatively weak. Most of the phytoplanktonic biomass was filamentous (Diatoms) or colonial (Cyanobacteria) and therefore almost probably difficult to ingest for algivorous microzooplankton. Regarding the low abundance of bacterivorous protozoa, the relation with the special physicochemical properties of this lake is discussed.

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Résumé Les variabilités saisonnière et verticale de l'abondance et de la biomasse des principles communautés de la boucle microbienne (bactéries hétérotrophes, picoplancton autotrophe, protozoaires flagellés auto- et hétérotrophes, protozoaires ciliés, microalgues et microcyanobactéries), et des activités auto- et hétérotrophes, ont été étudiées dans un lac à caractère humique et modérément acide du Massif Central Français, le lac de Vassivière.Le dénombrement des communautés de microorganismes a été réalisé en microscopie inversée et à épifluorescence après mise en oeuvre des fixations et des colorations adéquates. Les activités photosynthétique, photo- et chemohétérotrophes ont été mesurées à partir de l'assimilation de NaH¹⁴CO₃ et d'un mélange d'acides aminés tritiés grâce à une technique de double marquage. Les résultats obtenus mettent en évidence le rôle prépondérant du facteur lumineux dans la répartition verticale des microorganismes autotrophes et mixotrophes, dont l'essentiel de la biomasse est confiné dans la zone 0–5 m en période de stratification, alors que la biomasse bactérienne est élevée sur l'ensemble de la colonne d'eau en raison, sans doute, de la grande disponibilité en matiére organique dissoute. Consécutivement, le microzooplancton prédateur, et notamment les différents types trophiques de protozoaires ciliés, se répartit dans la colonne d'eau selon la distribution verticale des ressources nutritives particularies. Cependant, compte-tenu de l'abondance bactérienne et algae, la biomasse des protozoaires flagellés et ciliésest relativement peu importante. Concernant les espèces algivores, l'essentiel de la biomasse phytoplanctonique est de nature filamenteuse (Diatomées) ou coloniale (Cyanobactéries) est est donc sans doute difficilement ingérable pour le microzooplancton. Enfin, les relations entre les caractéristiques physico-chimiques spécifiques de ce lac et le faible développement des protozoaires bactérivores sont discutées.

     

Honeybees and bumblebees share similar bacterial symbionts

Associations with symbiotic microorganisms are a major source for evolutionary innovation in eukaryotes. Arthropods have long served as model systems to study such associations, especially since Paul Buchner’s (1965) seminal work that beautifully illustrated the enormous diversity of microorganisms associated with insects. Particularly high taxonomic and functional diversities of microbial symbionts have been found in the guts and gut‐associated organs of insects. These microorganisms play important roles in the digestion, nutrition and defence of the host. However, most studies of gut microorganisms have focused on single host taxa, limiting the ability to draw general conclusions on composition and functional roles of the insect gut microbiota. This is especially true for the diverse and important insect order Hymenoptera that comprises the bees, wasps and ants. Recently, Russell et al. (2009) analysed the bacterial community associated with diverse ant species and found evidence for changes in the microbial gut community coinciding with the evolution of herbivory. In this issue of Molecular Ecology, Martinson et al. (2011) provide the first broad‐scale bacterial survey for bees. Their findings substantiate earlier evidence for a surprisingly simple gut microbiota in honeybees (Apis mellifera) that is composed of only six to ten major phylotypes. Importantly, Martinson et al. demonstrate for the first time that the same bacterial phylotypes are major constituents of other Apis as well as Bombus species, but not of any other bees and wasps outside of the corbiculate bees, a clade of four tribes within the subfamily Apinae. These results indicate that corbiculate bees harbour a specific and possibly co‐evolved bacterial community in their digestive tract. Furthermore, the comparison with other bees and wasps suggests that changes in social lifestyle may have had a stronger effect on the evolution of the gut microbiota than the dietary shift from predatory ancestors to pollen‐feeding (i.e. herbivorous) species. These findings have far‐reaching implications for research on the microbial symbionts of insects as well as on the nutritional physiology of the ecologically and economically important group of corbiculate bees.     

Pattern and mortality in Colorado Desert plants

Summary We tested for intraspecific interference among Colorado Desert shrubs using an integrated analysis of spatial pattern and juvenile mortality. The data set included 7,000 woody perennials of 24 species in a mapped hectare of Joshua Tree National Monument, California. The site is dominated by Ambrosia dumosa (62.0% of the stems), with Larre tridentata a conspicuous secondary species (2.3% of the stems). Analyses of static pattern for common species showed: (1) aggregated adults and juveniles for Ambrosia dumosa, Erigonum fasciculatum, Mirabilis bigelovii, and Sphaeralcea ambigua, with more aggregation among juveniles than adults; (2) randomly distributed adults and juveniles for Krameria grayi, Opuntia rasmosissima, Simondsia chinensis, and Yucca schidigera. The summed volumes and distances between nearest conspecific neighbors were positively correlated for Ambrosia dumosa and Larrea tridentata, but not significantly correlated for eight remaining species with 100 individuals. Static pattern suggests only weak evidence for negative interactions in Ambrosia and Larrea, and little evidence for other species. Alternative mechanisms other than negative interaction that could give rise to these static patterns are discussed. Juvenile mortality was documented for four common species (Ambrosia dumosa, Eriogonum fasciculatum, Mirabilis bigelovii, and Sphaeralcea ambigua) that experienced substantial mortality. Analyses show: (1) the proportion of individuals that died was independent of the initial density of conspecifics; (2) distance to conspecific adults did not differ for juveniles that died versus those that survived; and (3) death was no more likely for juveniles that contacted other plants than for those that were isolated. The exception was a vine, Mirabilis bigelovii, whose juveniles survived better in contact with other plants. In sum, neither spatial pattern nor patterns of mortality showed clear evidence of negative intraspecific interference.     

Seed transfer among bird-dispersed trees and its consequences for post-dispersal seed fate

We investigated seed transfer, i.e. the seed movement away from a source canopy to areas beneath heterospecific canopies, among the ornithochorous tree species Taxus baccata, Ilex aquifolium and Crataegus monogyna in temperate secondary forests in NW Spain, by analysing the composition of multispecific seed rain beneath the canopy of each species, at four sites and for 2 years. To evaluate the consequences on seed fate, we estimated predation by rodents in manipulated seed rains, representing variable levels of relative proportion and total density for combinations of a preferred species paired with a less-preferred species. Seed rain under Taxus canopies was dominated by Taxus seeds, which occurred in low proportion under heterospecific canopies. Ilex seeds dominated the areas under Ilex but accounted for 20–40% of seeds under heterospecific trees. Crataegus seeds were not dominant in any of the microhabitats. The probability of being deposited beneath a heterospecific canopy was much higher for Ilex and Crataegus than for Taxus. The effects of seed rain composition on post-dispersal seed predation were species-specific. Taxus seeds experienced lower predation when occurring in a background of seeds dominated by heterospecific, Ilex or Crataegus, seeds. Crataegus seeds escaped predation more successfully in high-density patches, independently of seed clump composition. Predation on Ilex seeds was independent to both the density and the composition of seed clump. Seed transfer among heterospecific tree species may contribute to shape the template of propagule abundances from which forest will develop, by generating seed combinations favourable to escape from predation.