Heterogeneous selection in a spatially structured environment affects fitness tradeoffs of plasmid carriage in pseudomonads

Persisting uropathogenic Escherichia coli lineages show signatures of niche-specific within-host adaptation mediated by mobile genetic elements

Large-scale genomic studies have identified within-host adaptation as a hallmark of bacterial infections. However, the impact of physiological, metabolic, and immunological differences between distinct niches on the pathoadaptation of opportunistic pathogens remains elusive. Here, we profile the within-host adaptation and evolutionary trajectories of 976 isolates representing 119 lineages of uropathogenic Escherichia coli (UPEC) sampled longitudinally from both the gastrointestinal and urinary tracts of 123 patients with urinary tract infections. We show that lineages persisting in both niches within a patient exhibit increased allelic diversity. Habitat-specific selection results in niche-specific adaptive mutations and genes, putatively mediating fitness in either environment. Within-lineage inter-habitat genomic plasticity mediated by mobile genetic elements (MGEs) provides the opportunistic pathogen with a mechanism to adapt to the physiological conditions of either habitat, and reduced MGE richness is associated with recurrence in gut-adapted UPEC lineages. Collectively, our results establish niche-specific adaptation as a driver of UPEC within-host evolution.

Why are rhizobial symbiosis genes mobile?

Rhizobia are one of the most important and best studied groups of bacterial symbionts. They are defined by their ability to establish nitrogen-fixing intracellular infections within plant hosts. One surprising feature of this symbiosis is that the bacterial genes required for this complex trait are not fixed within the chromosome, but are encoded on mobile genetic elements (MGEs), namely plasmids or integrative and conjugative elements. Evidence suggests that many of these elements are actively mobilizing within rhizobial populations, suggesting that regular symbiosis gene transfer is part of the ecology of rhizobial symbionts. At first glance, this is counterintuitive. The symbiosis trait is highly complex, multipartite and tightly coevolved with the legume hosts, while transfer of genes can be costly and disrupt coadaptation between the chromosome and the symbiosis genes. However, horizontal gene transfer is a process driven not only by the interests of the host bacterium, but also, and perhaps predominantly, by the interests of the MGEs that facilitate it. Thus understanding the role of horizontal gene transfer in the rhizobium-legume symbiosis requires a 'mobile genetic element's-eye view' on the ecology and evolution of this important symbiosis. This article is part of the theme issue 'The secret lives of microbial mobile genetic elements'.

Indirect Fitness Benefits Enable the Spread of Host Genes Promoting Costly Transfer of Beneficial Plasmids

Bacterial genes that confer crucial phenotypes, such as antibiotic resistance, can spread horizontally by residing on mobile genetic elements (MGEs). Although many mobile genes provide strong benefits to their hosts, the fitness consequences of the process of transfer itself are less clear. In previous studies, transfer has been interpreted as a parasitic trait of the MGEs because of its costs to the host but also as a trait benefiting host populations through the sharing of a common gene pool. Here, we show that costly donation is an altruistic act when it spreads beneficial MGEs favoured when it increases the inclusive fitness of donor ability alleles. We show mathematically that donor ability can be selected when relatedness at the locus modulating transfer is sufficiently high between donor and recipients, ensuring high frequency of transfer between cells sharing donor alleles. We further experimentally demonstrate that either population structure or discrimination in transfer can increase relatedness to a level selecting for chromosomal transfer alleles. Both mechanisms are likely to occur in natural environments. The simple process of strong dilution can create sufficient population structure to select for donor ability. Another mechanism observed in natural isolates, discrimination in transfer, can emerge through coselection of transfer and discrimination alleles. Our work shows that horizontal gene transfer in bacteria can be promoted by bacterial hosts themselves and not only by MGEs. In the longer term, the success of cells bearing beneficial MGEs combined with biased transfer leads to an association between high donor ability, discrimination, and mobile beneficial genes. However, in conditions that do not select for altruism, host bacteria promoting transfer are outcompeted by hosts with lower transfer rate, an aspect that could be relevant in the fight against the spread of antibiotic resistance.

Altruistic host bacteria can preferentially enhance the horizontal transfer of beneficial plasmids (such as those conferring antibiotic resistance or virulence) to others of their kind.

In bacteria, genes can move between cells, sometimes with the donor host cell actively involved in the gene transfer mechanisms. This movement of genes is called horizontal gene transfer, and it increases the prevalence of mobile genes in bacterial populations. However, it is not clear if donor host cells benefit from gene spread, or are simply exploited by selfish genes. Here, we show with both modelling and experiments that for the donor host, investing in the transfer of beneficial genes—such as those conferring antibiotic resistance—can be understood as an altruistic behaviour. This behaviour is costly to the donor but beneficial to recipients and can be selected for if a sufficient proportion of recipient cells share the donors’ transfer allele. Preferential transfer from donors towards recipients that share this allele occurs when dispersal is limited or if discrimination mechanisms are present. Our work suggests that both processes are likely to be widespread in nature, promoting horizontal gene spread by host donor cells. As many antimicrobial resistance and virulence genes are mobile, our work further implies that the spread of harmful traits among human pathogens may be modulated by host bacteria in a direction that depends on the bacterial ability to transfer the traits specifically to their kind.

Effect of the IncP-1β plasmid pHB44 on the population dynamics of Burkholderia terrae BS001 in the Lyophyllum sp. strain Karsten mycosphere under different iron conditions

Burkholderia terrae strain BS001 is a well-described inhabitant of the mycosphere of diverse fungi. In the interaction between this bacterium and its fungal host in soil, competition for iron might be a key process. Here, we address the capacity of the broad-host-range IncP-1β plasmid pHB44, originally isolated in Variovorax paradoxus HB44, to enhance or modulate the competitiveness of B. terrae BS001 under different soil iron levels when confronted with (young versus ageing) mycelia of Lyophyllum sp. strain Karsten in microcosms. The data revealed that, in most cases, plasmid pHB44 reduced the fitness of its host in the mycosphere, possibly due to a metabolic burden effect. However, an opposite effect was found under low-iron conditions at the extreme tips of the soil-exploring Lyophyllum sp. strain Karsten mycelium. The negative effect of plasmid pHB44 on strain BS001 population sizes was clearly offset by fitness enhancement under these conditions. Moreover, as evidenced by using plasmid pSUP104 as a tracer, plasmid pHB44 was transferred from the B. terrae BS001 host into V. paradoxus BS64 in the ageing mycosphere, but not in bulk soil. Strikingly, successful plasmid establishment in the new host was more prominent in the iron-limited than in the 'high-iron' mycosphere habitat, indicating plasmid pHB44 was required in the V. paradoxus host as a fitness stimulator in the iron-limited condition. Taken together, the data suggest that efficiency of iron acquisition only served as the selective mechanism under certain conditions of iron availability in the soil, specifically promoting the fitness of V. paradoxus transconjugants. Not only is the mycosphere to be regarded as a selective arena in which horizontal gene transfer across the bacterial inhabitants is spurred, but the outcome of the adaptive processes is strongly shaped by competitive events among the local organisms.

Making pathogens sociable: the [corrected] emergence of high relatedness through limited host invasibility

Cooperation depends upon high relatedness, the high genetic similarity of interacting partners relative to the wider population. For pathogenic bacteria, which show diverse cooperative traits, the population processes that determine relatedness are poorly understood. Here, we explore whether within-host dynamics can produce high relatedness in the insect pathogen Bacillus thuringiensis. We study the effects of host/pathogen interactions on relatedness via a model of host invasion and fit parameters to competition experiments with marked strains. We show that invasibility is a key parameter for determining relatedness and experimentally demonstrate the emergence of high relatedness from well-mixed inocula. We find that a single infection cycle results in a bottleneck with a similar level of relatedness to those previously reported in the field. The bottlenecks that are a product of widespread barriers to infection can therefore produce the population structure required for the evolution of cooperative virulence.

Environmentally co-occurring mercury resistance plasmids are genetically and phenotypically diverse and confer variable context-dependent fitness effects

Plasmids are important mobile elements that can facilitate genetic exchange and local adaptation within microbial communities. We compared the sequences of four co‐occurring pQBR family environmental mercury resistance plasmids and measured their effects on competitive fitness of a Pseudomonas fluorescens  SBW25 host, which was isolated at the same field site. Fitness effects of carriage differed between plasmids and were strongly context dependent, varying with medium, plasmid status of competitor and levels of environmental mercury. The plasmids also varied widely in their rates of conjugation and segregational loss. We found that few of the plasmid‐borne accessory genes could be ascribed functions, although we identified a putative chemotaxis operon, a type IV pilus‐encoding cluster and a region encoding putative arylsulfatase enzymes, which were conserved across geographically distant isolates. One plasmid, pQBR55, conferred the ability to catabolize sucrose. Transposons, including the mercury resistance Tn5042, appeared to have been acquired by different pQBR plasmids by recombination, indicating an important role for horizontal gene transfer in the recent evolution of pQBR plasmids. Our findings demonstrate extensive genetic and phenotypic diversity among co‐occurring members of a plasmid community and suggest a role for environmental heterogeneity in the maintenance of plasmid diversity.

Non-invasive determination of conjugative transfer of plasmids bearing antibiotic-resistance genes in biofilm-bound bacteria: effects of substrate loading and antibiotic selection

Biofilms cause much of all human microbial infections. Attempts to eradicate biofilm-based infections rely on disinfectants and antibiotics. Unfortunately, biofilm bacteria are significantly less responsive to antibiotic stressors than their planktonic counterparts. Sublethal doses of antibiotics can actually enhance biofilm formation. Here, we have developed a non-invasive microscopic image analyses to quantify plasmid conjugation within a developing biofilm. Corroborating destructive samples were analyzed by a cultivation-independent flow cytometry analysis and a selective plate count method to cultivate transconjugants. Increases in substrate loading altered biofilm 3-D architecture and subsequently affected the frequency of plasmid conjugation (decreases at least two times) in the absence of any antibiotic selective pressure. More importantly, donor populations in biofilms exposed to a sublethal dose of kanamycin exhibited enhanced transfer efficiency of plasmids containing the kanamycin resistance gene, up to tenfold. However, when stressed with a different antibiotic, imipenem, transfer of plasmids containing the kan(R+) gene was not enhanced. These preliminary results suggest biofilm bacteria "sense" antibiotics to which they are resistant, which enhances the spread of that resistance. Confocal scanning microscopy coupled with our non-invasive image analysis was able to estimate plasmid conjugative transfer efficiency either averaged over the entire biofilm landscape or locally with individual biofilm clusters.

Determining the effects of a spatially heterogeneous selection pressure on bacterial population structure at the sub-millimetre scale

A key interest of microbial ecology is to understand the role of environmental heterogeneity in shaping bacterial diversity and fitness. However, quantifying relevant selection pressures and their effects is challenging due to the number of parameters that must be considered and the multiple scales over which they act. In the current study, a model system was employed to investigate the effects of a spatially heterogeneous mercuric ion (Hg(2+)) selection pressure on a population comprising Hg-sensitive and Hg-resistant pseudomonads. The Hg-sensitive bacteria were Pseudomonas fluorescens SBW25::rfp and Hg-resistant bacteria were P. fluorescens SBW25 carrying a gfp-labelled, Hg resistance plasmid. In the absence of Hg, the plasmid confers a considerable fitness cost on the host, with µ(max) for plasmid-carrying cells relative to plasmid-free cells of only 0.66. Two image analysis techniques were developed to investigate the structure that developed in biofilms about foci of Hg (cellulose fibres imbued with HgCl(2)). Both techniques indicated selection for the resistant phenotype occurred only in small areas of approximately 178-353 μm (manually defined contour region analysis) or 275-350 μm (daime analysis) from foci. Hg also elicited toxic effects that reduced the growth of both Hg-sensitive and Hg-resistant bacteria up to 250 μm from foci. Selection for the Hg resistance phenotype was therefore highly localised when Hg was spatially heterogeneous. As such, for this model system, we define here the spatial scale over which selection operates. The ability to quantify changes in the strength of selection for particular phenotypes over sub-millimetre scales is useful for understanding the scale over which environmental variables affect bacterial populations.

Heterogeneous selection on a heritable temperament trait in a variable environment

1. Temperament traits increasingly provide a focus for investigating the evolutionary ecology of behavioural variation. Here, we examine the underlying causes and selective consequences of individual variation in the temperament trait 'exploration behaviour in a novel environment' (EB, based on an 8-min assay) in a free-ranging population of a passerine bird, the great tit Parus major. 2. First, we conducted a quantitative genetic analysis on EB using a restricted maximum likelihood-based animal model with a long-term pedigree. Although repeatability was relatively high, EB was only moderately heritable and permanent environment (V(PE)) effects contributed as much to phenotypic variance as additive genetic effects. 3. We then asked whether heterogeneous selection acted on EB at various temporal and spatial scales. Using estimates of lifetime reproductive success, we found evidence of weak negative directional selection acting on EB amongst females which was driven by selection through recruitment, but not fecundity, in one of the four breeding years. There was no evidence of any selection on EB through survival. 4. Heterogeneous selection on EB within seasons was also observed amongst males through fecundity along two fine-scale environmental gradients--local breeding density and habitat quality; we are unaware of any previous equivalent demonstrations. 5. All of these analyses were repeated on a second measure of exploration behaviour (EB(2), measured during a 2-min assay) to facilitate comparison with other studies. EB and EB(2) were strongly correlated to one another at the genetic level, but were only moderately correlated at the phenotypic level and V(PE) was undetected in EB(2). Selection on EB(2) was similar to that on EB; we conclude that both traits are broadly equivalent from an evolutionary perspective. 6. Our analyses suggest that to the extent that the temperament trait 'exploration behaviour' is subject to natural selection in this population, this selection is highly context dependent and most evident along two environmental gradients. Furthermore, the strong V(PE) effect detected suggests that understanding the causes and consequences of variation in this trait will require studies firmly embedded in an environmental context.