The myth of bacterial species and speciation

The Tree of Life hypothesis frames the evolutionary process as a series of events whereby lineages diverge from one another, thus creating the diversity of life as descendent lineages modify properties from their ancestors. This hypothesis is under scrutiny due to the strong evidence for lateral gene transfer between distantly related bacterial taxa, thereby providing extant taxa with more than one parent. As a result, one argues, the Tree of Life becomes confounded as the original branching structure is gradually superseded by reticulation, ultimately losing its ability to serve as a model for bacterial evolution. Here we address a more fundamental issue: is there a Tree of Life that results from bacterial evolution without considering such lateral gene transfers? Unlike eukaryotic speciation events, lineage separation in bacteria is a gradual process that occurs over tens of millions of years, whereby genetic isolation is established on a gene-by-gene basis. As a result, groups of closely related bacteria, while showing robust genetic isolation as extant lineages, were not created by an unambiguous series of lineage-splitting events. Rather, a temporal fragmentation of the speciation process results in cognate genes showing different genetic relationships. We argue that lineage divergence in bacteria does not produce a tree-like framework, and inferences drawn from such a framework have the potential to be incorrect and misleading. Therefore, the Tree of Life is an inappropriate paradigm for bacterial evolution regardless of the extent of gene transfer between distantly related taxa.     

Catalyzing bacterial speciation: correlating lateral transfer with genetic headroom

Unlike crown eukaryotic species, microbial species are created by continual processes of gene loss and acquisition promoted by horizontal genetic transfer. The amounts of foreign DNA in bacterial genomes, and the rate at which this is acquired, are consistent with gene transfer as the primary catalyst for microbial differentiation. However, the rate of successful gene transfer varies among bacterial lineages. The heterogeneity in foreign DNA content is directly correlated with amount of genetic headroom intrinsic to a bacterial species. Genetic headroom reflects the amount of potentially dispensable information--reflected in codon usage bias and codon context bias--that can be transiently sacrificed to allow experimentation with functions introduced by gene transfer. In this way, genetic headroom offers a potential metric for assessing the propensity of a lineage to speciate.     

Modelling within-host spatiotemporal dynamics of invasive bacterial disease

Mechanistic determinants of bacterial growth, death, and spread within mammalian hosts cannot be fully resolved studying a single bacterial population. They are also currently poorly understood. Here, we report on the application of sophisticated experimental approaches to map spatiotemporal population dynamics of bacteria during an infection. We analyzed heterogeneous traits of simultaneous infections with tagged Salmonella enterica populations (wild-type isogenic tagged strains [WITS]) in wild-type and gene-targeted mice. WITS are phenotypically identical but can be distinguished and enumerated by quantitative PCR, making it possible, using probabilistic models, to estimate bacterial death rate based on the disappearance of strains through time. This multidisciplinary approach allowed us to establish the timing, relative occurrence, and immune control of key infection parameters in a true host–pathogen combination. Our analyses support a model in which shortly after infection, concomitant death and rapid bacterial replication lead to the establishment of independent bacterial subpopulations in different organs, a process controlled by host antimicrobial mechanisms. Later, decreased microbial mortality leads to an exponential increase in the number of bacteria that spread locally, with subsequent mixing of bacteria between organs via bacteraemia and further stochastic selection. This approach provides us with an unprecedented outlook on the pathogenesis of S. enterica infections, illustrating the complex spatial and stochastic effects that drive an infectious disease. The application of the novel method that we present in appropriate and diverse host–pathogen combinations, together with modelling of the data that result, will facilitate a comprehensive view of the spatial and stochastic nature of within-host dynamics.     

Modelling the bacterial growth/no growth interface

A logistic regression model is proposed which enables one to model the boundary between growth and no growth for bacterial strains in the presence of one or more growth controlling factors such as temperature, pH and additives such as salt and sodium nitrite. The form of the expression containing the growth limiting factors may be suggested by a kinetic model, while the response at a given combination of factors may either be presence/absence (i.e. growth/no growth) or probabilistic (i.e. r successes in n trials). The approach described represents an integration of the probability and kinetic aspects of predictive microbiology, and a unification of predictive microbiology and the hurdle concept. The model is illustrated using data for Shigella flexneri.     

Modelling bacterial transmission in human allergen-specific IgE sensitization

Aims: The impact of bacterial transmission from mother to child on human allergy development is poorly understood. The aim of the present work was therefore to use a temporal collected dataset of 117 mothers and their children to model the potential effect of mother‐to‐child bacterial transmission on allergy (IgE) sensitization. Methods and Results: We have recently shown a negative IgE correlation to high Escherichia coli levels until the age of 1 year, with a shift to positive correlation to high Bacteroides fragilis levels at the age of 2. In the present work, we used the previous published data to model the persistence and interaction effects of E. coli and B. fragilis with respect to IgE sensitization. Temporal modelling was made by first defining a stochastic model for sensitization state based on Markov chains and regression tree analyses. Subsequent simulations were used to determine the impact of mother‐to‐infant bacterial transmission. The regression tree analyses showed that E. coli colonization within 4 days was negatively correlated to sensitization, while lack of E. coli colonization at day 4 combined with B. fragilis colonization after 4 months was positively correlated. With Markov chain analyses, we found that E. coli was highly persistent in infants until the age of 4 months, while the persistence of B. fragilis increased with age. Conclusions: Simulations showed that the mother’s bacterial composition correlated significantly to the child’s IgE sensitization state at the age of 2 years. High E. coli and low B. fragilis levels in the mother were negatively correlated, while low E. coli and high B. fragilis were positively correlated to IgE. Significance and Impact of the Study: Our results support that allergy could partly be communicable, being transferred from mother to infant through the gut microbiota.     

Gene transfer, speciation, and the evolution of bacterial genomes.

Studies in microbial evolution have focused on the origin and vertical transmission of genetic variation within populations experiencing limited recombination. Genomic analyses have highlighted the importance of horizontal genetic transfer in shaping the composition of microbial genomes, providing novel metabolic capabilities, and catalyzing the diversification of bacterial lineages.     

Modelling sympatric speciation by means of biologically plausible mechanistic processes as exemplified by threespine stickleback species pairs

We investigate the plausibility of sympatric speciation through a modelling study. We built up a series of models with increasing complexity while focussing on questioning the realism of model assumptions by checking them critically against a particular biological system, namely the sympatric benthic and limnetic species of threespine stickleback in British Columbia, Canada. These are morphologically adapted to their feeding habits: each performs better in its respective habitat than do hybrids with intermediate morphology. Ecological character displacement through disruptive selection and competition, and reinforcement through mating preferences may have caused their divergence. Our model assumptions include continuous morphological trait(s) instead of a dimorphic trait, and mating preferences based on the same trait(s) as selected for in food competition. Initially, morphology is intermediate. We apply disruptive selection against intermediates, frequency-dependent resource competition, and one of two alternative mating preference mechanisms. Firstly, preference is based on similarity where mating preference may result from “imprinting” on conspecifics encountered in their preferred foraging habitat. Here, speciation occurs easily—ecological hybrid inferiority is not necessary. Hybrid inferiority reinforces the stringency of assortative mating. Secondly, individual preferences exist for different trait values. Here, speciation occurs when linkage disequilibrium between trait and preference develops, and some hybrid inferiority is required. Finally, if the morphology subject to disruptive selection, frequency-dependent competition, and mate choice, is coded for by two loci, linkage disequilibrium between the two loci is required for speciation. Speciation and reinforcement of stringency of choosiness are possible in this case too, but rarely. Results demonstrate the contingency of speciation, with the same starting point not necessarily producing the same outcome. The study resulted in flagging issues where models often lack in biological realism and issues where more empirical studies could inform on whether assumptions are likely valid.     

Pleistocene speciation is not refuge speciation

A number of researchers working on the origin of extant Neotropical biodiversity implicitly and without appropriate proofs assume that Pleistocene speciation should necessarily follow the rules of the refuge hypothesis. A recent example is provided by a study of Neotropical butterflies. Although the analysis showed that these groups experienced their main diversification burst during the last 2.6 million years, coinciding with the Pleistocene glacial cycles (Garzón‐Orduña et al., 2014, Journal of Biogeography, 41 , 1631–1638), a causal link between the speciation chronology and the evolutionary mechanisms proposed by the refuge hypothesis is not provided. Without more detailed studies on the environmental drivers, geographical patterns and speciation modes, establishing a causal link between speciation chronology and a particular speciation model – of which the refuge hypothesis is only one among many possibilities – is too speculative. Here I provide a six‐step conceptual framework for linking the speciation chronology with the environmental drivers and the ecological and evolutionary mechanisms potentially involved.     

Symbiont-induced speciation

Speciation induced by parasitic or mutualistic symbionts has been suggested for taxa ranging from plants to insects to monkeys. Previous models for symbiont-induced speciation have been based upon hybrid inferiority and selection for reinforcement genes. Taken on their own, however, such models have severe theoretical limitations and little empirical support. Two conditions that may favour symbiont-induced speciation are presented here: (1) interaction norms in which the outcomes of host/symbiont interactions differ between environments and (2) differential coadaptation of host and symbiont populations between environments or along an environmental gradient. Symbiont-induced speciation can be considered as one form of 'mixed-process coevolution': reciprocal evolution in which adaptation of a population of one species to a population of a second species (or coadaptation of the populations) causes the population of the second species to become reproductively isolated from other populations.     

Ecological speciation

Ecological processes are central to the formation of new species when barriers to gene flow (reproductive isolation) evolve between populations as a result of ecologically‐based divergent selection. Although laboratory and field studies provide evidence that ‘ecological speciation’ can occur, our understanding of the details of the process is incomplete. Here we review ecological speciation by considering its constituent components: an ecological source of divergent selection, a form of reproductive isolation, and a genetic mechanism linking the two. Sources of divergent selection include differences in environment or niche, certain forms of sexual selection, and the ecological interaction of populations. We explore the evidence for the contribution of each to ecological speciation. Forms of reproductive isolation are diverse and we discuss the likelihood that each may be involved in ecological speciation. Divergent selection on genes affecting ecological traits can be transmitted directly (via pleiotropy) or indirectly (via linkage disequilibrium) to genes causing reproductive isolation and we explore the consequences of both. Along with these components, we also discuss the geography and the genetic basis of ecological speciation. Throughout, we provide examples from nature, critically evaluate their quality, and highlight areas where more work is required.     

Competitive speciation

A new mode of speciation, competitive speciation, is suggested. It assumes that fitness is depressed by the density of a phenotype's competitors, and that the adaptive landscape of phenotypes is complex. From this it follows that some intermediate forms may be fit if and only if some extreme forms are rare or absent. Subsequent to the evolution and population growth of both extreme forms, the intermediate may disappear and homogamy evolve among each of the extremes because of disruptive selection If so, sympatric speciation has occurred and niche space has been rendered into discrete segments.
The limitations of the forces leading to competitive speciation are explored. Competitive speciation is discussed in relation to stasipatric speciation and host race formation. It may be responsible for both. Finally the rates of geographical speciation and polyploidy are compared to those of competitive speciation. The latter should be almost as fast as polyploidy and may be at the root of adaptive radiation. Unlike either polyploidy or geographical speciation, competitive speciation accelerates when species diversity declines.     

Modelling bacterial spoilage in cold-filled ready to drink beverages by Acinetobacter calcoaceticus and Gluconobacter oxydans

AIMS: Characterization of a bacterial isolate (strain MAE2) from intertidal beach sediment capable of degrading linear and branched alkanes. METHODS AND RESULTS: A Gram-positive, aerobic, heterotrophic bacterium (strain MAE2), that was capable of extensive degradation of alkanes in crude oil but had a limited capacity for the utilization of other organic compounds, was isolated from intertidal beach sediment. MAE2 had an obligate requirement for NaCl but could not tolerate high salt concentrations. It was capable of degrading branched and n-alkanes in crude oil from C11 to C33, but was unable to degrade aromatic hydrocarbons. Comparative 16S rRNA sequence analysis placed the isolate with members of the genus Planococcus. That finding was corroborated by chemotaxonomic and physiological data. The fatty acid composition of strain MAE2 was very similar to the type species of the genus Planococcus, P. citreus (NCIMB 1493T) and P. kocurii (NCIMB 629T), and was dominated by branched acids, mainly a15:0. However, the 16S rRNA of strain MAE2 had less than 97% sequence identity with the type strains of P. citreus (NCIMB 1439T), P. kocurii (NCIMB 629T) and two Planococcus spp. (strain MB6-16 and strain ICO24) isolated from Antarctic sea ice. This indicated that strain MAE2 represented a separate species from these planococci. Morphologically, the isolate resembled P. okeanokoites (NCIMB 561T) and P. mcmeekinii S23F2 (ATCC 700539T). The cellular fatty acid composition of P. okeanokoites and P. mcmeekinii was considerably different from strain MAE2, and the mol % G + C content of P. mcmeekinii was far lower than that of MAE2. CONCLUSION: On the basis of phenotypic and genotypic data, it is proposed that strain MAE2 is a new species of Planococcus, Planococcus alkanoclasticus sp. nov., for which the type strain is P. alkanoclasticus MAE2 (NCIMB 13489T). SIGNIFICANCE AND IMPACT OF THE STUDY: Planococcus species are abundant members of the bacterial community in a variety of marine environments, including some in sensitive Antarctic ecosystems. The occurrence of hydrocarbon-degrading Planococcus spp. is potentially of importance in controlling the impact of hydrocarbon contamination in sensitive marine environments.     

Ciprofloxacin interactions with bacterial protein OmpF: Modelling of FRET from a multi-tryptophan protein trimer

The outer membrane protein F (OmpF) is known to play an important role in the uptake of fluoroquinolone antibiotics by bacteria. In this study, the degree of binding of the fluoroquinolone antibiotic ciprofloxacin to OmpF in a lipid membrane environment is quantified using a methodology based on Förster resonance energy transfer (FRET). Analysis of the fluorescence quenching of OmpF is complex as each OmpF monomer presents two tryptophans at different positions, thus sensing two different distributions of acceptors in the bilayer plane. Specific FRET formalisms were derived accounting for the different energy transfer contributions to quenching of each type of tryptophan of OmpF, allowing the recovery of upper and lower boundaries for the ciprofloxacin-OmpF binding constant (K_B). log (K_B) was found to lie in the range 3.15-3.62 or 3.58-4.00 depending on the location for the ciprofloxacin binding site assumed in the FRET modelling, closer to the centre or to the periphery of the OmpF trimer, respectively. This methodology is suitable for the analysis of FRET data obtained with similar protein systems and can be readily adapted to different geometries.     

Modelling the importance of sediment bacterial carbon for profundal macroinvertebrates along a lake nutrient gradient

In dimictic, temperate lakes little is known about the quantitative importance of trophic coupling between pelagic and profundal communities. Although it is a generally accepted paradigm that profundal secondary production is dependent on autochthonous pelagic production (primarily diatoms), the importance of interactions between phytodetrital inputs, sediment bacteria, and macroinvertebrates are still not well understood. In this study, we used theoretical models to estimate macroinvertebrate carbon requirement (production + respiration) and bacterial production for lakes of different trophic categories. Comparisons of estimates show that the importance of bacterial production as a carbon source for benthic macroinvertebrates is inversely related to lake trophic state. Assuming that infauna assimilates 50% of ingested bacterial carbon, this food source could account for between 47% (oligotrophic lakes) and 2% (hypertrophic lakes) of their carbon demand. These calculations indicate that bacterial carbon should not be an important C-resource for profundal macroinvertebrates of eutrophic and hypertrophic lakes.     

Modelling of crowded polymers elucidate effects of double-strand breaks in topological domains of bacterial chromosomes

Using numerical simulations of pairs of long polymeric chains confined in microscopic cylinders, we investigate consequences of double-strand DNA breaks occurring in independent topological domains, such as these constituting bacterial chromosomes. Our simulations show a transition between segregated and mixed state upon linearization of one of the modelled topological domains. Our results explain how chromosomal organization into topological domains can fulfil two opposite conditions: (i) effectively repulse various loops from each other thus promoting chromosome separation and (ii) permit local DNA intermingling when one or more loops are broken and need to be repaired in a process that requires homology search between broken ends and their homologous sequences in closely positioned sister chromatid.     

Speedy speciation in a bacterial microcosm: new species can arise as frequently as adaptations within a species

Microbiologists are challenged to explain the origins of enormous numbers of bacterial species worldwide. Contributing to this extreme diversity may be a simpler process of speciation in bacteria than in animals and plants, requiring neither sexual nor geographical isolation between nascent species. Here, we propose and test a novel hypothesis for the extreme diversity of bacterial species—that splitting of one population into multiple ecologically distinct populations (cladogenesis) may be as frequent as adaptive improvements within a single population''s lineage (anagenesis). We employed a set of experimental microcosms to address the relative rates of adaptive cladogenesis and anagenesis among the descendants of a Bacillus subtilis clone, in the absence of competing species. Analysis of the evolutionary trajectories of genetic markers indicated that in at least 7 of 10 replicate microcosm communities, the original population founded one or more new, ecologically distinct populations (ecotypes) before a single anagenetic event occurred within the original population. We were able to support this inference by identifying putative ecotypes formed in these communities through differences in genetic marker association, colony morphology and microhabitat association; we then confirmed the ecological distinctness of these putative ecotypes in competition experiments. Adaptive mutations leading to new ecotypes appeared to be about as common as those improving fitness within an existing ecotype. These results suggest near parity of anagenesis and cladogenesis rates in natural populations that are depauperate of bacterial diversity.     

Assessment of lead speciation by organic ligands using speciation models

Abstract

The biogeochemical behaviour of lead (Pb) in ecosystems greatly depends on its chemical species. Organic ligands strongly influence Pb species and mobility in soil solution. In the present study, two metal speciation models, Windermere Humic Aqueous Model (WHAM) and Visual Minteq are used to compute Pb speciation in nutrient solution in the presence and absence of organic ligands. The three organic ligands used include ethylenediamine tetraacetic acid (EDTA), citric acid (CA) and fulvic acid (FA). The results show that in the absence of organic ligands, Pb²⁺ is the dominant form under acidic conditions and Pb–OH under alkaline conditions. The presence of organic ligands strongly influences Pb speciation. EDTA is more effective than are CA and FA concerning its influence on Pb speciation due to high Pb binding capacity. The results also indicate that Pb binding capacity of organic ligands varies with solution pH.     

Hybridization and speciation

Hybridization has many and varied impacts on the process of speciation. Hybridization may slow or reverse differentiation by allowing gene flow and recombination. It may accelerate speciation via adaptive introgression or cause near‐instantaneous speciation by allopolyploidization. It may have multiple effects at different stages and in different spatial contexts within a single speciation event. We offer a perspective on the context and evolutionary significance of hybridization during speciation, highlighting issues of current interest and debate. In secondary contact zones, it is uncertain if barriers to gene flow will be strengthened or broken down due to recombination and gene flow. Theory and empirical evidence suggest the latter is more likely, except within and around strongly selected genomic regions. Hybridization may contribute to speciation through the formation of new hybrid taxa, whereas introgression of a few loci may promote adaptive divergence and so facilitate speciation. Gene regulatory networks, epigenetic effects and the evolution of selfish genetic material in the genome suggest that the Dobzhansky–Muller model of hybrid incompatibilities requires a broader interpretation. Finally, although the incidence of reinforcement remains uncertain, this and other interactions in areas of sympatry may have knock‐on effects on speciation both within and outside regions of hybridization.