Evolutionary dynamics of pathogen resistance and tolerance

Abstract.— Host organisms can respond to the threat of disease either through resistance defenses (which inhibit or limit infection) or through tolerance strategies (which do not limit infection, but reduce or offset its fitness consequences). Here we show that resistance and tolerance can have fundamentally different evolutionary outcomes, even when they have equivalent short-term benefit for the host. As a gene conferring disease resistance spreads through a population, the incidence of infection declines, reducing the fitness advantage of carrying the resistance gene. Thus genes conferring complete resistance cannot become fixed (i.e., universal) by selection in a host population, and diseases cannot be eliminated solely by natural selection for host resistance. By contrast, as a gene conferring disease tolerance spreads through a population, disease incidence rises, increasing the evolutionary advantage of carrying the tolerance gene. Therefore, any tolerance gene that can invade a host population will tend to be driven to fixation by selection. As predicted, field studies of diverse plant species infected by rust fungi confirm that resistance traits tend to be polymorphic and tolerance traits tend to be fixed. These observations suggest a new mechanism for the evolution of mutualism from parasitism, and they help to explain the ubiquity of disease.     

Neotropical bats in the canopy: diversity,community structure,and implications for conservation

We compare results of parallel ground and canopy netting of bats (Microchiroptera) in three adjacent forest sites near Belém, Brazil, to document possible differences in vertical distribution of species. We caught 1871 individuals representing 49 species of three families (Emballonuridae, Phyllostomidae, Vespertilionidae). Capture effort, totaling 1955.5 mistnet hours in several cycles over a two-year period, was similar for ground and canopy nets. The canopy rigs yielded more species (n = 41) than the ground nets (n = 35), but both samples were characterized by rank abundance curves with similar shape and with a dominance of frugivores (Phyllostomidae). Nearly half (n = 24) of the species were captured in numbers too small (n < 6) to allow firm classification, but differences in capture frequencies of some of the better-sampled species in high and low nets reveal vertical stratification. Species-specific differences in diet, foraging strategies, roost sites, and sampling bias contribute to this pattern. As a result of the differential use of space among bats, alterations of forest structure are likely to result in changes in structure and function of local bat communities, but our limited knowledge of natural history and ecology of many species limits definition of changes. We see a critical need for further research into the extent to which habitat complexity influences species richness and abundance of bats. This information is especially important in view of the need to develop and apply conservation-oriented programs to maintain biodiversity. A review of recent improvements in techniques for inventorying bats shows that a combination of methods, including mistnetting and acoustic monitoring, is mandatory for such studies.     

Bacterial community dynamics during the ensilage of wilted grass

Aims:  Grass silage is the product formed by a natural lactic acid bacterial fermentation when grass is stored under anaerobic conditions, and represents an important ruminant feedstuff on farms during winter. Of the two commonly employed methods of ensiling forage, baled silage composition frequently differs from that of comparable precision-chop silage reflecting a different ensiling environment. The aim of this study was to investigate the dynamics of the silage fermentation in wilted grass and between ensiling systems.
Methods and Results:  Fermentation dynamics were examined using traditional methods of silage analyses, including microbial enumeration and analysis of fermentation products, and culture-independent terminal restriction fragment length polymorphism (T-RFLP). A successful fermentation was achieved in both systems, with the fermentation (increase in lactic acid bacteria and lactic acid concentration, decrease in pH) proceeding rapidly once the herbage was ensiled.
Conclusions:  Under controlled conditions, little difference in silage quality and microbial composition were observed between ensiling systems and this was further reflected in the T-RFLP community analysis.
Significance and Impact of the Study:  T-RFLP proved a potentially useful tool to study the ensilage process and could provide valid support to traditional methods, or a viable alternative to these methods, for investigating the dynamics of the bacterial community over the course of the fermentation.     

Bacterial community dynamics during the winter-spring transition in the North Sea

Bacterioplankton dynamics at Helgoland Roads (54 degrees 11.3'N, 7 degrees 54.0'E) in the North Sea over the winter-spring transition were investigated. The bacterial community was analyzed and correlated with phytoplankton community data and abiotic parameters. The community structure was analyzed by ribosomal intergenic spacer analysis (RISA) and by denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes followed by DNA sequence analysis. The linkage of abiotic and biotic environmental factors and bacterial community as well as phylotypes (sequenced DGGE bands) was analyzed by the ordination technique of canonical correspondence analysis (CCA). Generally, an influence of temperature and phytoplankton on the bacterial community during the sampling period was observed. Additionally, multivariate analysis by factors revealed an influence on specific bacterial phylotypes of these factors. Overall, results indicate that changes in the bacterial community were caused not only by abiotic factors but also by the phytoplankton community.     

Bacterial community dynamics during bioremediation of phenanthrene- and fluoranthene-amended soil

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous environmental contaminants that enter the environment via incomplete combustion of fossil fuels and accidental leakage of petroleum products, and as components of products such as creosote. Bacterial community dynamics were examined in soils amended with two PAHs, phenanthrene or fluoranthene, and treated with fertiliser or aerated to stimulate the indigenous microbial population. Profiles of the bacterial communities present under a range of experimental conditions were generated using terminal restriction fragment length polymorphism (TRFLP) and the results were interpreted using sophisticated multivariate statistical analysis. Results indicated a distinct separation between community compositions based on time in phenanthrene-contaminated soil and a similar but less significant effect observed in fluoranthene-contaminated soil. High concentrations of fluoranthene had a positive effect on the abundance of some of the most dominant ribotypes. Aeration provided the most rapid treatment and resulted in almost complete removal of phenanthrene after 28 days.     

Multi-scale regulated plant community dynamics: mechanisms and implications

Plant competition is not a direct interaction, but operates via environmental feedback loops, which interconnect population densities and environmental regulating variables. It is suggested that due to scale dependent elements of these feedback loops, competition may occur eventually on very different scales, necessitating a cross-scale extension of plant competition theory. After introducing the concept of cross-scale competition, we incorporate its elements into a metacommunity model and study its implications on community organization. It is found that both the equilibrium community composition, regarding coexisting functional types, and its stability depend on scale dependent attributes of environmental feedback loops and disturbance regimes. We argue that plant communities are likely to exhibit properties, which are in line with the hierarchical ecosystem concept. Environmental feedback loops on different scales act as distinct organizational levels, what can be affected by disturbances of corresponding spatial extent.     

Bacterial community dynamics in the hyporheic zone of an intermittent stream

The dynamics of in situ bacterial communities in the hyporheic zone of an intermittent stream were described in high spatiotemporal detail. We assessed community dynamics in stream sediments and interstitial pore water over a two-year period using terminal-restriction fragment length polymorphism. Here, we show that sediments remained saturated despite months of drought and limited hydrologic connectivity. The intermittency of stream surface water affected interstitial pore water communities more than hyporheic sediment communities. Seasonal changes in bacterial community composition was significantly associated with water intermittency, phosphate concentrations, temperature, nitrate and dissolved organic carbon (DOC) concentrations. During periods of low- to no-surface water, communities changed from being rich in operational taxonomic units (OTUs) in isolated surface pools, to a few OTUs overall, including an overall decline in both common and rare taxa. Individual OTUs were compared between porewater and sediments. A total of 19% of identified OTUs existed in both porewater and sediment samples, suggesting that bacteria use hyporheic sediments as a type of refuge from dessication, transported through hydrologically connected pore spaces. Stream intermittency impacted bacterial diversity on rapid timescales (that is, within days), below-ground and in the hyporheic zone. Owing to the coupling of intermittent streams to the surrounding watershed, we stress the importance of understanding connectivity at the pore scale, consequences for below-ground and above-ground biodiversity and nutrient processing, and across both short- and long-time periods (that is, days to months to years).     

Bacterial genomics and pathogen evolution

The availability of hundreds of bacterial genome sequences has altered the study of bacterial pathogenesis, affecting both design of experiments and analysis of results. Comparative genomics and genomic tools have been used to identify virulence factors and genes involved in environmental persistence of pathogens. However, a major stumbling block in the genomics revolution has been the large number of genes with unknown function that have been identified in every organism sequenced to date.     

The impact and implications of climate change for bats

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Bacterial community dynamics following antibiotic exposure in a trematode parasite

Parasites harbour rich microbial communities that may play a role in host-parasite interactions, from influencing the parasite’s infectivity to modulating its virulence. Experimental manipulation of a parasite’s microbes would be essential, however, in order to establish their causal role. Here, we tested whether indirect exposure of a trematode parasite within its snail intermediate host to a variety of antibiotics could alter its bacterial community. Based on sequencing the prokaryotic 16S ssrRNA gene, we characterised and compared the bacterial community of the trematode Philophthalmus attenuatus before, shortly after, and weeks after exposure to different antibiotics (penicillin, colistin, gentamicin) with distinct activity spectra. Our findings revealed that indirectly treating the parasites by exposing their snail host to antibiotics resulted in changes to their bacterial communities, measured as their diversity, taxonomic composition, and/or the relative abundance of certain taxa. However, alterations to the parasite’s bacterial community were not always as predicted from the activity spectrum of the antibiotic used. Furthermore, the bacterial communities of the parasites followed significantly divergent trajectories in the days post-exposure to antibiotics, but later converged toward a new state, i.e. a new bacterial community structure different from that pre-exposure. Our results confirm that a trematode’s microbial community can be experimentally altered by antibiotic exposure while within its snail host, with the dynamic nature of the bacterial assemblage driving it to a new state over time after the perturbation. This research opens new possibilities for future experimental investigations of the functional roles of microbes in host-parasite interactions.     

Bacterial cheating drives the population dynamics of cooperative antibiotic resistance plasmids

Inactivation of β ‐lactam antibiotics by resistant bacteria is a ‘cooperative’ behavior that may allow sensitive bacteria to survive antibiotic treatment. However, the factors that determine the fraction of resistant cells in the bacterial population remain unclear, indicating a fundamental gap in our understanding of how antibiotic resistance evolves. Here, we experimentally track the spread of a plasmid that encodes a β ‐lactamase enzyme through the bacterial population. We find that independent of the initial fraction of resistant cells, the population settles to an equilibrium fraction proportional to the antibiotic concentration divided by the cell density. A simple model explains this behavior, successfully predicting a data collapse over two orders of magnitude in antibiotic concentration. This model also successfully predicts that adding a commonly used β ‐lactamase inhibitor will lead to the spread of resistance, highlighting the need to incorporate social dynamics into the study of antibiotic resistance.     

Bacterial larvicides for vector control: mode of action of toxins and implications for resistance

Vector control can be an effective strategy to interrupt disease transmission and biolarvicides based on the entomopathogenic bacteria Bacillus sphaericus, and Bacillus thuringiensis serovar israelensis (Bti) have been successfully used to control species of public health relevance from the genera Aedes, Culex, Anopheles and Simulium. The most important feature of these agents is their ability to produce insecticidal proteins with selective action on the larval midgut. These protoxins are produced as crystals that, once ingested by larvae, are processed into active toxins, interact with receptors in the midgut epithelium and trigger cytopathological effects leading to larval death. B. sphaericus and Bti toxins share the initial steps of the mode of action; however, they interact with different midgut molecules. B. sphaericus presents a single larvicidal factor, the binary (Bin) toxin, whose action relies on the binding to one class of midgut receptors, while Bti crystals contain four protoxins (Cry4Aa, Cry4Ba, Cry11Aa and Cyt1Aa), which display interactions with multiple midgut receptors. The mode of action of B. sphaericus displays a greater potential for resistance selection, compared to Bti, and, to date, there is no record of insect resistance to the latter, contrarily to B. sphaericus. The set of mosquitocidal toxins and their interaction with midgut target sites are described in this review, as well as the implications for the potential to select resistance amongst exposed populations. These biolarvicides have specific mode of action that rely on unique interactions and make them the most selective agents to control Diptera insects actually available.     

Bacterial community dynamics and product distribution during pH-adjusted fermentation of vegetable wastes

AIMS: To estimate the effect of pH on the structures of bacterial community during fermentation of vegetable wastes and to investigate the relationship between bacterial community dynamics and product distribution. METHODS AND RESULTS: The bacterial communities in five batch tests controlled at different pH values [uncontrolled (about pH 4), 5, 6, 7 and 8] were monitored by denaturing gradient gel electrophoresis (DGGE) and single-strand conformation polymorphism (SSCP). The two fingerprinting methods provided consistent results and principal component analysis indicated a close similarity of bacterial community at pH 7 and 8 in addition to those at pH 4-6. This clustering also corresponded to dominant metabolic pathway. Thus, pH 7-8 shifted from alcohol-forming to acid-forming, especially butyric acid, whereas both alcohol-forming and acid-forming dominated at pH 5-6, and at pH 4, fermentation was inhibited. Shannon-weaver index was calculated to analyse the DGGE profiles, which revealed that the bacterial diversities at pH 7 and 8 were the highest while those at pH 5 and 4 (uncontrolled) were the lowest. According to sequencing results of the bands excised from DGGE gels, lactic acid bacteria and Clostridium sp. were predominant at all pH values, but varieties in species were observed as pH changed and time prolonged. CONCLUSIONS: The bacterial community during fermentation was materially influenced by pH and the diverse product distribution was related to the shift of different bacterial population. SIGNIFICANCE AND IMPACT OF THE STUDY: The study reveals that the impact of pH on fermentation product distribution is implemented primarily by changes of bacterial community. It also provides information about the comparison of two fingerprinting methods, DGGE and SSCP.     

Bacterial community dynamics in a functionally stable pilot-scale wastewater treatment plant

To determine whether functional stability was correlated with a stable microbial community structure in a functionally stable pilot-scale wastewater treatment plant, bacterial communities in the system were monitored over a one-year period. Bacterial community dynamics was characterized by the terminal restriction fragment length polymorphism (T-RFLP) of 16S rRNA genes. During the study period, the effluent BOD concentrations were very stable, with the average BOD concentration below 10 mg/L. The effluent TN concentrations were always below 20 mg/L, except for the first 40 days. T-RFLP results showed that, during the test period, the bacterial community structures were not stable, with an average change rate (every 15 days) of 20.4% ± 11.2%. Based on Lorenz distribution curves, it was observed that 20% of the species corresponded with 40-77% of cumulative relative abundances. Results clearly revealed that, in the pilot-scale wastewater treatment plant, functional stability did not correlate with stable bacterial communities.     

Neopolyploidy and pathogen resistance

Despite the well-documented historical importance of polyploidy, the mechanisms responsible for the establishment and evolutionary success of novel polyploid lineages remain unresolved. One possibility, which has not been previously evaluated theoretically, is that novel polyploid lineages are initially more resistant to pathogens than the diploid progenitor species. Here, we explore this possibility by developing and analysing mathematical models of interactions between newly formed polyploid lineages and their pathogens. We find that for the genetic mechanisms of pathogen resistance with the best empirical support, newly formed polyploid populations of hosts are expected to be more resistant than their diploid progenitors. This effect can be quite strong and, in the case of perennial species with recurrent polyploid formation, may last indefinitely, potentially providing a general explanation for the successful establishment of novel polyploid lineages.     

Tree structure and cavity microclimate: implications for bats and birds

It is widely assumed that tree cavity structure and microclimate affect cavity selection and use in cavity-dwelling bats and birds. Despite the interest in tree structure and microclimate, the relationship between the two has rarely been quantified. Currently available data often comes from artificial structures that may not accurately represent conditions in natural cavities. We collected data on tree cavity structure and microclimate from 45 trees in five cypress-gum swamps in the Coastal Plain of Georgia in the United States in 2008. We used hierarchical linear models to predict cavity microclimate from tree structure and ambient temperature and humidity, and used Aikaike’s information criterion to select the most parsimonious models. We found large differences in microclimate among trees, but tree structure variables explained <28 % of the variation, while ambient conditions explained >80 % of variation common to all trees. We argue that the determinants of microclimate are complex and multidimensional, and therefore cavity microclimate cannot be deduced easily from simple tree structures. Furthermore, we found that daily fluctuations in ambient conditions strongly affect microclimate, indicating that greater weather fluctuations will cause greater differences among tree cavities.