Linking genetic change to community evolution: insights from studies of bacteria and bacteriophage

A major goal of community ecology is to link biological processes at lower scales with community patterns. Microbial communities are especially powerful model systems for making these links. In this article, we review recent studies of laboratory communities of bacteria and bacteriophage (viruses that infect bacteria). We focus on the ecology and evolution of bacteriophage-resistance as a case study demonstrating the relationship between specific genes, individual interactions, population dynamics, community structure, and evolutionary change. In laboratory communities of bacteria and bacteriophage, bacteria rapidly evolve resistance to bacteriophage infection. Different resistance mutations produce distinct resistance phenotypes, differing, for example, in whether resistance is partial or complete, in the magnitude of the physiological cost associated with resistance, and in whether the mutation can be countered by a host-range mutation in the bacteriophage. These differences determine whether a mutant can invade, the effect its invasion has on the population dynamics of sensitive bacteria and phage, and the resulting structure of the community. All of these effects, in turn, govern the community's response to environmental change and its subsequent evolution.     

The use of species abundance estimates in marine benthic studies

The application of species abundance estimates, commonly used in terrestrial plant ecology, to marine benthic dredge data is advocated. Two possible scales were tested for their ability to measure adequately the structure of an assemblage by computing measures of evenness diversity McNaughton's dominance index, and Morisita's index of dispersion using both real counts obtained from grab samples and these counts transformed into the two respective abundance estimates. It is concluded that species abundance estimators, when applied to grab or dredge data result in significant savings in sample processing time with only a minimal loss of information about assemblage structure.     

Dynamics of microbial communities on marine snow aggregates: colonization,growth, detachment,and grazing mortality of attached bacteria

We studied the dynamics of microbial communities attached to model aggregates (4-mm-diameter agar spheres) and the component processes of colonization, detachment, growth, and grazing mortality. Agar spheres incubated in raw seawater were rapidly colonized by bacteria, followed by flagellates and ciliates. Colonization can be described as a diffusion process, and encounter volume rates were estimated at about 0.01 and 0.1 cm(3) h(-1) for bacteria and flagellates, respectively. After initial colonization, the abundances of flagellates and ciliates remained approximately constant at 10(3) to 10(4) and approximately 10(2) cells sphere(-1), respectively, whereas bacterial populations increased at a declining rate to >10(7) cells sphere(-1). Attached microorganisms initially detached at high specific rates of approximately 10(-2) min(-1), but the bacteria gradually became irreversibly attached to the spheres. Bacterial growth (0 to 2 day(-1)) was density dependent and declined hyperbolically when cell density exceeded a threshold. Bacterivorous flagellates grazed on the sphere surface at an average saturated rate of 15 bacteria flagellate(-1) h(-1). At low bacterial densities, the flagellate surface clearance rate was approximately 5 x 10(-7) cm(2) min(-1), but it declined hyperbolically with increasing bacterial density. Using the experimentally estimated process rates and integrating the component processes in a simple model reproduces the main features of the observed microbial population dynamics. Differences between observed and predicted population dynamics suggest, however, that other factors, e.g., antagonistic interactions between bacteria, are of importance in shaping marine snow microbial communities.     

Salinity effect on the maximal growth temperature of some bacteria isolated from marine enviroments

Salinity of the growth medium was found to have a marked effect on the maximal growth temperature of four bacteria isolated from marine sources. Vibrio marinus MP-1 had a maximal growth temperature of 21.2 C at a salinity of 35% and a maximal growth temperature of 10.5 C at a salinity of 7%, the lowest salinity at which it would grow. This effect was shown to be due to the presence of various cations in the medium. The order of effectiveness of cations in restoring the normal maximal growth temperature, when added to dilute seawater, was Na(+) > Li(+) > Mg(++) > K(+) > Rb(+) > NH(4) (+). The anions tested, with the exception of SO(4)=, had no marked effect on the maximal growth temperature response. In a completely defined medium, the highest maximal growth temperature was 20.0 C at 0.40 m NaCl. A decrease in the maximal growth temperature was observed at both low and high concentrations of NaCl.     

The hydrodynamic resistance of hyaluronic acid: estimates from sedimentation studies

The problem of estimating the permeability of hyaluronic acid as a function of concentration has been examined. A previously known method of obtaining permeability from sedimentation studies has been employed, and the results have been compared to those obtained from convection studies, in which solvent is forced through the hyaluronic acid. The two sets of results were seen to be at variance, which could be explained by a flow-induced polarization of the hyaluronic acid in the convection studies. The polarization phenomenon was described in terms of a convection-associated compaction balancing the hyaluronic acid's intrinsic resistance to compression. Based on these results and other arguments, it was suggested that data from sedimentation studies provide a more accurate estimate of hyaluronic acid permeability than do convection experiments. The implications of this finding in a physiological context were briefly discussed.     

Microcalorimetric studies of the growth of sulfate-reducing bacteria: energetics of Desulfovibrio vulgaris growth.

The metabolism of Desulfovibrio vulgaris Hildenborough grown on medium containing lactate or pyruvate plus a high concentration of sulfate (36 mM) was studied. Molecular growth yields were 6.7 +/- 1.3 and 10.1 +/- 1.7 g/mol for lactate and pyruvate, respectively. Under conditions in which the energy source was the sole growth-limiting factor, we observed the formation of 0.5 mol of hydrogen per mol of lactate and 0.1 mol of hydrogen per mol of pyruvate. The determination of metabolic end products revealed that D. vulgaris produced, in addition to normal end products (acetic acid, carbon dioxide, hydrogen sulfide) and molecular hydrogen, 2 and 5% of ethanol per mol of lactate and pyruvate, respectively. Power-time curves of growth of D. vulgaris on lactate and pyruvate were obtained, by the microcalorimetric Tian-Calvet apparatus. The enthalpies (delta Hmet) associated with the oxidation of these substrates and calculated from growth thermograms were -36.36 +/- 5 and -70.22 +/- 3 kJ/mol of lactate and pyruvate, respectively. These experimental values were in agreement with the homologous values assessed from the theoretical equations of D. vulgaris metabolism of both lactate and pyruvate. The hydrogen production by this sulfate reducer constitutes an efficient regulatory system of electrons, from energy source through the pathway of sulfate reduction. This hydrogen value may thus facilitate interactions between this strain and other environmental microflora, especially metagenic bacteria.     

Alternative spatial sampling in studies of plant demography: consequences for estimates of population growth rate

Ecologists commonly use matrix models to study the population dynamics of plants. Most studies of plant demography use plot-based methods to collect data, in part, because mapped individuals are easier to relocate in subsequent surveys and survey methods can be standardized among sites. However, there is tremendous variation among studies, both in terms of plot arrangement and the total area sampled. In addition, there has been little discussion of how alternative sampling arrangements influence estimates of population growth rates (λ) calculated with matrix models. We surveyed the literature to determine what sampling designs are most used in studies of plant demography using matrix models. We then used simulations of three common sampling techniques—using a single randomly placed plot, multiple randomly placed plots, and systematically distributed plots—to evaluate how these alternative strategies influenced the precision of estimates of λ. These simulations were based on long-term demographic data collected on 13 populations of the Amazonian understory herb Heliconia acuminate (Heliconiaceae). We found that the method used to collect data did not affect the bias or precision of estimates in our system—a surprising result, since the advantage in efficiency that is gained from systematic sampling is a well-known result from sampling theory. Because the statistical advantage of systematic sampling is most evident when there is spatial structure in demographic vital rates, we attribute this result to the lack of spatially structured vital rates in our focal populations. Given the likelihood of spatial autocorrelation in most ecological systems, we advocate sampling with a systematic grid of plots in each study site, as well as that researchers ensure that enough area is sampled—both within and across sites—to encompass the range of spatial variation in plant survival, growth, and reproduction.     

VIS-O-BAC: exploratory visualization of functional genome studies from bacteria

SUMMARY: The visualization-aided exploration of complex datasets will allow the research community to formulate novel functional hypotheses leading to a better understanding of biological processes at all levels. Therefore, we have developed a web resource termed VIS-O-BAC designed for the functional investigation of expression data for model systems, such as bacterial pathogens based on a graphical display. Genome-scale datasets derived from typical 'omic' approaches can directly be explored with respect to three biologically relevant aspects, the genome structure (operon organization), the organization of genes in pathways (KEGG) and the gene function with Gene Ontology (GO) terms. The integrated viewers can be used in parallel and combine expression data and functional annotations from different external data repositories. The graphical visualizations evidently accelerate both the validation of regulatory information and the detection of affected biological processes. AVAILABILITY: http://leger2.gbf.de/cgi-bin/vis-o-bac.pl. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.     

Water and temperature relations of softrot bacteria: growth and disease development

The effect of water availability and the temperature of the growth substrate on growth and disease development of softrot bacteria were studied using artificial media and plant material. Water availability was measured as the osmotic potential of a solution (ψ_osm) and was assessed for solutions of PEG4000 and KNO₃ as artificial osmotica and for plant tissue of chicory heads. Growth of softrot bacteria was found at water potentials from ψ= -0.12 MPa to ψ= -8.0 MPa but the lag phase of the growth curve increased with decreasing water potential. The relative growth rates of the three softrot pathogens showed a sigmoidal relationship with water potential, the relative growth rates decreasing rapidly at water potentials lower than ψ= -1.5 MPa. The water potential of harvested chicory heads decreased with storage time of the harvested crop but was still within the growth limits for softrot bacteria. In relation to temperature, the relative growth rate of Erwinia carotovora subsp. carotovora (Ecc) was highest at 10°C, of Erwinia carotovora subsp. atroseptica (Eca) at 15°C and of Pseudomonas marginalis (Pm) at 5°C. Chicory heads of two cultivars, Rumba and Salsa, inoculated with Ecc, had a significantly higher disease severity at 30°C (0.72 for Rumba and 0.47 for Salsa) than at lower or higher temperatures. In conclusion, temperature and water availability during forcing of chicory were not factors limiting populations of softrot bacteria. Possibilities for crop protection thus only avail during chicory root storage. During storage a high death rate combined with a low growth rate of the softrot bacteria may result in a decrease of bacterial populations below the minimum densities needed for infection during the forcing of chicory heads.     

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.     

Possible quorum sensing in marine snow bacteria: production of acylated homoserine lactones by Roseobacter strains isolated from marine snow

We report here, for the first time, that bacteria associated with marine snow produce communication signals involved in quorum sensing in gram-negative bacteria. Four of 43 marine microorganisms isolated from marine snow were found to produce acylated homoserine lactones (AHLs) in well diffusion and thin-layer chromatographic assays based on the Agrobacterium tumefaciens reporter system. Three of the AHL-producing strains were identified by 16S ribosomal DNA gene sequence analysis as Roseobacter spp., and this is the first report of AHL production by these alpha-PROTEOBACTERIA: It is likely that AHLs in Roseobacter species and other marine snow bacteria govern phenotypic traits (biofilm formation, exoenzyme production, and antibiotic production) which are required mainly when the population reaches high densities, e.g., in the marine snow community.     

Uncertainty in population growth rates: determining confidence intervals from point estimates of parameters

Background

Demographic models are widely used in conservation and management, and their parameterisation often relies on data collected for other purposes. When underlying data lack clear indications of associated uncertainty, modellers often fail to account for that uncertainty in model outputs, such as estimates of population growth.

Methodology/Principal Findings

We applied a likelihood approach to infer uncertainty retrospectively from point estimates of vital rates. Combining this with resampling techniques and projection modelling, we show that confidence intervals for population growth estimates are easy to derive. We used similar techniques to examine the effects of sample size on uncertainty. Our approach is illustrated using data on the red fox, Vulpes vulpes, a predator of ecological and cultural importance, and the most widespread extant terrestrial mammal. We show that uncertainty surrounding estimated population growth rates can be high, even for relatively well-studied populations. Halving that uncertainty typically requires a quadrupling of sampling effort.

Conclusions/Significance

Our results compel caution when comparing demographic trends between populations without accounting for uncertainty. Our methods will be widely applicable to demographic studies of many species.     

Effect of dissolved aromatic hydrocarbons on the growth of marine bacteria in batch culture.

Dissolved aromatic hydrocarbons were found to decrease growth rate and maximum cell density of marine bacteria in batch cultures. The magnitude of the decrement was observed to be a function of concentration of the hydrocarbon and inherent toxicity. The inherent toxicity was observed to increase inversely with solubility such that naphthalene at 100 muM concentration demonstrated a toxic effect similar to benzopyrene at 0.02 muM. A partial oxidation product of naphthalene was found to be more effective in decreasing growth parameters than naphthalene at equivalent concentrations and to cause complete cessation of growth at the higher concentrations permitted by its polar structure.     

Extreme longevity in freshwater mussels revisited: sources of bias in age estimates derived from mark–recapture experiments

1. There may be bias associated with mark–recapture experiments used to estimate age and growth of freshwater mussels. Using subsets of a mark–recapture dataset for Quadrula pustulosa, I examined how age and growth parameter estimates are affected by (i) the range and skew of the data and (ii) growth reduction due to handling. I compared predictions from von Bertalanffy growth models based on mark–recapture data with direct observation of mussel age and growth inferred from validated shell rings. 2. Growth models based on a dataset that included observations from a wide range of length classes (spanning ≥ the upper 50% of the population length range) produced only slightly biased age estimates for small and medium‐sized individuals (overestimated by 1–2 years relative to estimates from validated shell rings) but estimates became increasingly biased for larger individuals. Growth models using data that included only observations of larger animals (< the upper 50% of length range) overestimated age for all length classes, and estimated maximum age was two to six times greater than the maximum age observed in the population (47 years). Similarly, growth models using a left‐skewed dataset overestimated age. 3. Reductions of growth due to repeated handling also resulted in overestimates of age. The estimated age of mussels that were handled in two consecutive years was as much as twice that of mussels that were handled only once over the same period. Assuming a constant reduction in the annual rate of growth, handling an individual for five consecutive years could result in an estimated age that is five times too high. 4. These findings show that mark–recapture methods have serious limitations for estimating mussel age and growth. A previous paper (Freshwater Biology, 46, 2001, 1349) presented longevity estimates for three mussel species that were an order of magnitude higher than estimates inferred from shell rings. Because those estimates of extreme longevity were based on mark–recapture methods and subject to multiple, additive sources of bias, they cannot be considered accurate representations of life span and cannot be used to conclude that traditional methods of bivalve ageing by interpretation of shell rings are flawed.