Host-Pathogen Coevolution: The Selective Advantage of Bacillus thuringiensis Virulence and Its Cry Toxin Genes

The intricate triangular interaction between protective microbe, pathogen and host determines fitness of the metaorganism

The microbiota shapes host biology in numerous ways. One example is protection against pathogens, which is likely critical for host fitness in consideration of the ubiquity of pathogens. The host itself can affect abundance of microbiota or pathogens, which has usually been characterized in separate studies. To date, however, it is unclear how the host influences the interaction with both simultaneously and how this triangular interaction determines fitness of the host-microbe assemblage, the so-called metaorganism. To address this current knowledge gap, we focused on a triangular model interaction, consisting of the nematode Caenorhabditis elegans, its protective symbiont Pseudomonas lurida MYb11 and its pathogen Bacillus thuringiensis Bt679. We combined the two microbes with C. elegans mutants with altered immunity and/or microbial colonization, and found that (i) under pathogen stress, immunocompetence has a larger influence on metaorganism fitness than colonization with the protective microbe; (ii) in almost all cases, MYb11 still improves fitness; and (iii) disruption of p38 MAPK signalling, which contributes centrally to immunity against Bt679, completely reverses the protective effect of MYb11, which further reduces nematode survival and fitness upon infection with Bt679. Our study highlights the complex interplay between host, protective microbe and pathogen in shaping metaorganism biology.

Fungi's Swiss Army Knife: Pleiotropic Effect of Melanin in Fungal Pathogenesis during Cattle Mycosis

Fungal threats to public health, food security, and biodiversity have escalated, with a significant rise in mycosis cases globally. Around 300 million people suffer from severe fungal diseases annually, while one-third of food crops are decimated by fungi. Vertebrate, including livestock, are also affected. Our limited understanding of fungal virulence mechanisms hampers our ability to prevent and treat cattle mycoses. Here we aim to bridge knowledge gaps in fungal virulence factors and the role of melanin in evading bovine immune responses. We investigate mycosis in bovines employing a PRISMA-based methodology, bioinformatics, and data mining techniques. Our analysis identified 107 fungal species causing mycoses, primarily within the Ascomycota division. Candida, Aspergillus, Malassezia, and Trichophyton were the most prevalent genera. Of these pathogens, 25% produce melanin. Further research is required to explore the involvement of melanin and develop intervention strategies. While the literature on melanin-mediated fungal evasion mechanisms in cattle is lacking, we successfully evaluated the transferability of immunological mechanisms from other model mammals through homology. Bioinformatics enables knowledge transfer and enhances our understanding of mycosis in cattle. This synthesis fills critical information gaps and paves the way for proposing biotechnological strategies to mitigate the impact of mycoses in cattle.

Evolutionary repeatability of emergent properties of ecological communities

Most species belong to ecological communities where their interactions give rise to emergent community-level properties, such as diversity and productivity. Understanding and predicting how these properties change over time has been a major goal in ecology, with important practical implications for sustainability and human health. Less attention has been paid to the fact that community-level properties can also change because member species evolve. Yet, our ability to predict long-term eco-evolutionary dynamics hinges on how repeatably community-level properties change as a result of species evolution. Here, we review studies of evolution of both natural and experimental communities and make the case that community-level properties at least sometimes evolve repeatably. We discuss challenges faced in investigations of evolutionary repeatability. In particular, only a handful of studies enable us to quantify repeatability. We argue that quantifying repeatability at the community level is critical for approaching what we see as three major open questions in the field: (i) Is the observed degree of repeatability surprising? (ii) How is evolutionary repeatability at the community level related to repeatability at the level of traits of member species? (iii) What factors affect repeatability? We outline some theoretical and empirical approaches to addressing these questions. Advances in these directions will not only enrich our basic understanding of evolution and ecology but will also help us predict eco-evolutionary dynamics. This article is part of the theme issue 'Interdisciplinary approaches to predicting evolutionary biology'.

Investigating quorum-quenching marine bacilli as potential biocontrol agents for protection of shrimps against Early Mortality Syndrome (EMS)

Early Mortality Syndrome (EMS) has been a major problem for shrimp aquaculture in Southeast Asia due to its epizootic prevalence within the region since the first reported case in 2009. This study explores the application of halophilic marine bacilli isolated from coral mucus and their quorum-quenching abilities as potential biocontrol agents in aquaculture systems to combat the causative agent of EMS, Vibrio parahaemolyticus. N-acylhomoserine lactone (AHL)-degrading (AiiA) activity was first screened by PCR then confirmed by bio-reporter assay, and a combination of 16S rDNA sequence analysis and quantitative phenotype assays including biofilm-formation and temperature-growth responses were used to demonstrate diversity amongst these quorum-quenching isolates. Three phenotypically distinct strains showing notable potential were chosen to undergo co-cultivation as a method for strain improvement via long term exposure to the pathogenic V. parahaemolyticus. The novel approach taken led to significant improvements in antagonism and quorum quenching activities as compared to the ancestral wild-type strains and offers a potential solution as well as pathway to improve existing beneficial microbes for one of the most pressing issues in shrimp aquacultures worldwide.

Altered infective competence of the human gut microbiome in COVID-19

BACKGROUND

Infections with SARS-CoV-2 have a pronounced impact on the gastrointestinal tract and its resident microbiome. Clear differences between severe cases of infection and healthy individuals have been reported, including the loss of commensal taxa. We aimed to understand if microbiome alterations including functional shifts are unique to severe cases or a common effect of COVID-19. We used high-resolution systematic multi-omic analyses to profile the gut microbiome in asymptomatic-to-moderate COVID-19 individuals compared to a control group.

RESULTS

We found a striking increase in the overall abundance and expression of both virulence factors and antimicrobial resistance genes in COVID-19. Importantly, these genes are encoded and expressed by commensal taxa from families such as Acidaminococcaceae and Erysipelatoclostridiaceae, which we found to be enriched in COVID-19-positive individuals. We also found an enrichment in the expression of a betaherpesvirus and rotavirus C genes in COVID-19-positive individuals compared to healthy controls.

CONCLUSIONS

Our analyses identified an altered and increased infective competence of the gut microbiome in COVID-19 patients. Video Abstract.

High-throughput phenotyping of infection by diverse microsporidia species reveals a wild C. elegans strain with opposing resistance and susceptibility traits

Animals are under constant selective pressure from a myriad of diverse pathogens. Microsporidia are ubiquitous animal parasites, but the influence they exert on shaping animal genomes is mostly unknown. Using multiplexed competition assays, we measured the impact of four different species of microsporidia on 22 wild isolates of Caenorhabditis elegans. This resulted in the identification and confirmation of 13 strains with significantly altered population fitness profiles under infection conditions. One of these identified strains, JU1400, is sensitive to an epidermal-infecting species by lacking tolerance to infection. JU1400 is also resistant to an intestinal-infecting species and can specifically recognize and destroy this pathogen. Genetic mapping of JU1400 demonstrates that these two opposing phenotypes are caused by separate loci. Transcriptional analysis reveals the JU1400 sensitivity to epidermal microsporidia infection results in a response pattern that shares similarity to toxin-induced responses. In contrast, we do not observe JU1400 intestinal resistance being regulated at the transcriptional level. The transcriptional response to these four microsporidia species is conserved, with C. elegans strain-specific differences in potential immune genes. Together, our results show that phenotypic differences to microsporidia infection amongst C. elegans are common and that animals can evolve species-specific genetic interactions.

What Can Genetics Do for the Control of Infectious Diseases in Aquaculture?

Simple Summary

Infectious diseases place an economic burden on aquaculture and a limitation to its growth. This state-of-the-art review describes the application of genetics and genomics as novel tools to control infectious disease in aquaculture.

Abstract

Infectious diseases place an economic burden on aquaculture and a limitation to its growth. An innovative approach to mitigate their impact on production is breeding for disease resistance: selection for domestication, family-based selection, marker-assisted selection, and more recently, genomic selection. Advances in genetics and genomics approaches to the control of infectious diseases are key to increasing aquaculture efficiency, profitability, and sustainability and to reducing its environmental footprint. Interaction and co-evolution between a host and pathogen can, however, turn breeding to boost infectious disease resistance into a potential driver of pathogenic change. Parallel molecular characterization of the pathogen and its virulence and antimicrobial resistance genes is therefore essential to understand pathogen evolution over time in response to host immunity, and to apply appropriate mitigation strategies.

No major cost of evolved survivorship in Drosophila melanogaster populations coevolving with Pseudomonas entomophila

Rapid exaggeration of host and pathogen traits via arms race dynamics is one possible outcome of host-pathogen coevolution. However, the exaggerated traits are expected to incur costs in terms of resource investment in other life-history traits. The current study investigated the costs associated with evolved traits in a host-pathogen coevolution system. We used the Drosophila melanogaster (host)-Pseudomonas entomophila (pathogen) system to experimentally derive two selection regimes, one where the host and pathogen both coevolved, and the other, where only the host evolved against a non-evolving pathogen. After 17 generations of selection, we found that hosts from both selected populations had better post-infection survivorship than controls. Even though the coevolving populations tended to have better survivorship post-infection, we found no clear evidence that the two selection regimes were significantly different from each other. There was weak evidence for the coevolving pathogens being more virulent than the ancestral pathogen. We found no major cost of increased post-infection survivorship. The costs were not different between the coevolving hosts and the hosts evolving against a non-evolving pathogen. We found no evolved costs in the coevolving pathogens. Thus, our results suggest that increased host immunity and pathogen virulence may not be costly.

Innate immune pathways act synergistically to constrain RNA virus evolution in Drosophila melanogaster

Host-pathogen interactions impose recurrent selective pressures that lead to constant adaptation and counter-adaptation in both competing species. Here, we sought to study this evolutionary arms-race and assessed the impact of the innate immune system on viral population diversity and evolution, using Drosophila melanogaster as model host and its natural pathogen Drosophila C virus (DCV). We isogenized eight fly genotypes generating animals defective for RNAi, Imd and Toll innate immune pathways as well as pathogen sensing and gut renewal pathways. Wild-type or mutant flies were then orally infected with DCV, and the virus was serially passaged ten times via reinfection in naïve flies. Viral population diversity was studied after each viral passage by high-throughput sequencing, and infection phenotypes were assessed at the beginning and at the end of the evolution experiment. We found that the absence of any of the various immune pathways studied increased viral genetic diversity while attenuating virulence. Strikingly, these effects were observed in a range of host factors described as having mainly antiviral or antibacterial functions. Together, our results indicate that the innate immune system as a whole, and not specific antiviral defense pathways in isolation, generally constrains viral diversity and evolution.

Exploring Effects of C. elegans Protective Natural Microbiota on Host Physiology

The Caenorhabditis elegans natural microbiota was described only recently. Thus, our understanding of its effects on nematode physiology is still in its infancy. We previously showed that the C. elegans natural microbiota isolates Pseudomonas lurida MYb11 and P. fluorescens MYb115 protect the worm against pathogens such as Bacillus thuringiensis (Bt). However, the overall effects of the protective microbiota on worm physiology are incompletely understood. Here, we investigated how MYb11 and MYb115 affect C. elegans lifespan, fertility, and intestinal colonization. We further studied the capacity of MYb11 and MYb115 to protect the worm against purified Bt toxins. We show that while MYb115 and MYb11 affect reproductive timing and increase early reproduction only MYb11 reduces worm lifespan. Moreover, MYb11 aggravates killing upon toxin exposure. We conclude that MYb11 has a pathogenic potential in some contexts. This work thus highlights that certain C. elegans microbiota members can be beneficial and costly to the host in a context-dependent manner, blurring the line between good and bad.

Microbial protection favors parasite tolerance and alters host-parasite coevolutionary dynamics

Coevolution between hosts and parasites is a major driver of rapid evolutionary change¹ and diversification.^2,3 However, direct antagonistic interactions between hosts and parasites could be disrupted⁴ when host microbiota form a line of defense, a phenomenon widespread across animal and plant species.^5,6 By suppressing parasite infection, protective microbiota could reduce the need for host-based defenses and favor host support for microbiota colonization,⁶ raising the possibility that the microbiota can alter host-parasite coevolutionary patterns and processes.⁷ Here, using an experimental evolution approach, we co-passaged populations of nematode host (Caenorhabditis elegans) and parasites (Staphylococcus aureus) when hosts were colonized (or not) by protective bacteria (Enterococcus faecalis). We found that microbial protection during coevolution resulted in the evolution of host mortality tolerance—higher survival following parasite infection—and in parasites adapting to microbial defenses. Compared to unprotected host-parasite coevolution, the protected treatment was associated with reduced dominance of fluctuating selection dynamics in host populations. No differences in host recombination rate or genetic diversity were detected. Genomic divergence was observed between parasite populations coevolved in protected and unprotected hosts. These findings indicate that protective host microbiota can determine the evolution of host defense strategies and shape host-parasite coevolutionary dynamics.

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Microbial protection resulted in the evolution of host mortality tolerance

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Parasites adapted to counter microbial defenses within hosts

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Protective microbes reduced fluctuating selection dynamics

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Microbial protection did not impact host genetic diversity or recombination rates

Population size impacts host-pathogen coevolution

Ongoing host-pathogen interactions are characterized by rapid coevolutionary changes forcing species to continuously adapt to each other. The interacting species are often defined by finite population sizes. In theory, finite population size limits genetic diversity and compromises the efficiency of selection owing to genetic drift, in turn constraining any rapid coevolutionary responses. To date, however, experimental evidence for such constraints is scarce. The aim of our study was to assess to what extent population size influences the dynamics of host-pathogen coevolution. We used Caenorhabditus elegans and its pathogen Bacillus thuringiensis as a model for experimental coevolution in small and large host populations, as well as in host populations which were periodically forced through a bottleneck. By carefully controlling host population size for 23 host generations, we found that host adaptation was constrained in small populations and to a lesser extent in the bottlenecked populations. As a result, coevolution in large and small populations gave rise to different selection dynamics and produced different patterns of host-pathogen genotype-by-genotype interactions. Our results demonstrate a major influence of host population size on the ability of the antagonists to co-adapt to each other, thereby shaping the dynamics of antagonistic coevolution.

Increased Pathogenicity of the Nematophagous Fungus Drechmeria coniospora Following Long-Term Laboratory Culture

Domestication provides a window into adaptive change. Over the course of 2 decades of laboratory culture, a strain of the nematode-specific fungus Drechmeria coniospora became more virulent during its infection of Caenorhabditis elegans. Through a close comparative examination of the genome sequences of the original strain and its more pathogenic derivative, we identified a small number of non-synonymous mutations in protein-coding genes. In one case, the mutation was predicted to affect a gene involved in hypoxia resistance and we provide direct corroborative evidence for such an effect. The mutated genes with functional annotation were all predicted to impact the general physiology of the fungus and this was reflected in an increased in vitro growth, even in the absence of C. elegans. While most cases involved single nucleotide substitutions predicted to lead to a loss of function, we also observed a predicted restoration of gene function through deletion of an extraneous tandem repeat. This latter change affected the regulatory subunit of a cAMP-dependent protein kinase. Remarkably, we also found a mutation in a gene for a second protein of the same, protein kinase A, pathway. Together, we predict that they result in a stronger repression of the pathway for given levels of ATP and adenylate cyclase activity. Finally, we also identified mutations in a few lineage-specific genes of unknown function that are candidates for factors that influence virulence in a more direct manner.

Symbiosis in Digital Evolution: Past, Present, and Future

Symbiosis, the living together of unlike organisms as symbionts, is ubiquitous in the natural world. Symbioses occur within and across all scales of life, from microbial to macro-faunal systems. Further, the interactions between symbionts are multimodal in both strength and type, can span from parasitic to mutualistic within one partnership, and persist over generations. Studying the ecological and evolutionary dynamics of symbiosis in natural or laboratory systems poses a wide range of challenges, including the long time scales at which symbioses evolve de novo, the limited capacity to experimentally control symbiotic interactions, the weak resolution at which we can quantify interactions, and the idiosyncrasies of current model systems. These issues are especially challenging when seeking to understand the ecological effects and evolutionary pressures on and of a symbiosis, such as how a symbiosis may shift between parasitic and mutualistic modes and how that shift impacts the dynamics of the partner population. In digital evolution, populations of computational organisms compete, mutate, and evolve in a virtual environment. Digital evolution features perfect data tracking and allows for experimental manipulations that are impractical or impossible in natural systems. Furthermore, modern computational power allows experimenters to observe thousands of generations of evolution in minutes (as opposed to several months or years), which greatly expands the range of possible studies. As such, digital evolution is poised to become a keystone technique in our methodological repertoire for studying the ecological and evolutionary dynamics of symbioses. Here, we review how digital evolution has been used to study symbiosis, and we propose a series of open questions that digital evolution is well-positioned to answer.

Adaptation of Bacillus thuringiensis to Plant Colonization Affects Differentiation and Toxicity

The Bacillus cereus group (Bacillus cereus sensu lato) has a diverse ecology, including various species that are vertebrate or invertebrate pathogens. Few isolates from the B. cereus group have however been demonstrated to benefit plant growth. Therefore, it is crucial to explore how bacterial development and pathogenesis evolve during plant colonization. Herein, we investigated Bacillus thuringiensis (Cry-) adaptation to the colonization of Arabidopsis thaliana roots and monitored changes in cellular differentiation in experimentally evolved isolates. Isolates from two populations displayed improved iterative ecesis on roots and increased virulence against insect larvae. Molecular dissection and recreation of a causative mutation revealed the importance of a nonsense mutation in the rho transcription terminator gene. Transcriptome analysis revealed how Rho impacts various B. thuringiensis genes involved in carbohydrate metabolism and virulence. Our work suggests that evolved multicellular aggregates have a fitness advantage over single cells when colonizing plants, creating a trade-off between swimming and multicellularity in evolved lineages, in addition to unrelated alterations in pathogenicity. IMPORTANCE Biologicals-based plant protection relies on the use of safe microbial strains. During application of biologicals to the rhizosphere, microbes adapt to the niche, including genetic mutations shaping the physiology of the cells. Here, the experimental evolution of Bacillus thuringiensis lacking the insecticide crystal toxins was examined on the plant root to reveal how adaptation shapes the differentiation of this bacterium. Interestingly, evolution of certain lineages led to increased hemolysis and insect larva pathogenesis in B. thuringiensis driven by transcriptional rewiring. Further, our detailed study reveals how inactivation of the transcription termination protein Rho promotes aggregation on the plant root in addition to altered differentiation and pathogenesis in B. thuringiensis.

The effects of nested miRNAs and their host genes on immune defense against Bacillus thuringiensis infection in Caenorhabditis elegans

microRNAs (miRNAs) are small non-coding RNA-molecules that influence translation by binding to the target gene mRNA. Many miRNAs are found in nested arrangements within larger protein-coding host genes. miRNAs and host genes in a nested arrangement are often transcribed simultaneously, which may indicate that both have similar functions. miRNAs have been implicated in regulating defense responses against pathogen infection in C. elegans and in mammals. Here, we asked if miRNAs in nested arrangements and their host genes are involved in the C. elegans response against infection with Bacillus thuringiensis (Bt). We performed miRNA sequencing and subsequently focused on four nested miRNA-host gene arrangements for a functional genetic analysis. We identified mir-58.1 and mir-2 as negative regulators of C. elegans resistance to Bt infection. However, we did not find any miRNA/host gene pair in which both contribute to defense against Bt.

Plant-Microbe Interaction: Aboveground to Belowground, from the Good to the Bad

Soil health and fertility issues are constantly addressed in the agricultural industry. Through the continuous and prolonged use of chemical heavy agricultural systems, most agricultural lands have been impacted, resulting in plateaued or reduced productivity. As such, to invigorate the agricultural industry, we would have to resort to alternative practices that will restore soil health and fertility. Therefore, in recent decades, studies have been directed towards taking a Magellan voyage of the soil rhizosphere region, to identify the diversity, density, and microbial population structure of the soil, and predict possible ways to restore soil health. Microbes that inhabit this region possess niche functions, such as the stimulation or promotion of plant growth, disease suppression, management of toxicity, and the cycling and utilization of nutrients. Therefore, studies should be conducted to identify microbes or groups of organisms that have assigned niche functions. Based on the above, this article reviews the aboveground and below-ground microbiomes, their roles in plant immunity, physiological functions, and challenges and tools available in studying these organisms. The information collected over the years may contribute toward future applications, and in designing sustainable agriculture.

Enemies make you stronger: Coevolution between fruit fly host and bacterial pathogen increases postinfection survivorship in the host

Multiple laboratory studies have evolved hosts against a nonevolving pathogen to address questions about evolution of immune responses. However, an ecologically more relevant scenario is one where hosts and pathogens can coevolve. Such coevolution between the antagonists, depending on the mutual selection pressure and additive variance in the respective populations, can potentially lead to a different pattern of evolution in the hosts compared to a situation where the host evolves against a nonevolving pathogen. In the present study, we used Drosophila melanogaster as the host and Pseudomonas entomophila as the pathogen. We let the host populations either evolve against a nonevolving pathogen or coevolve with the same pathogen. We found that the coevolving hosts on average evolved higher survivorship against the coevolving pathogen and ancestral (nonevolving) pathogen relative to the hosts evolving against a nonevolving pathogen. The coevolving pathogens evolved greater ability to induce host mortality even in nonlocal (novel) hosts compared to infection by an ancestral (nonevolving) pathogen. Thus, our results clearly show that the evolved traits in the host and the pathogen under coevolution can be different from one-sided adaptation. In addition, our results also show that the coevolving host-pathogen interactions can involve certain general mechanisms in the pathogen, leading to increased mortality induction in nonlocal or novel hosts.

ORFograph: search for novel insecticidal protein genes in genomic and metagenomic assembly graphs

BACKGROUND

Since the prolonged use of insecticidal proteins has led to toxin resistance, it is important to search for novel insecticidal protein genes (IPGs) that are effective in controlling resistant insect populations. IPGs are usually encoded in the genomes of entomopathogenic bacteria, especially in large plasmids in strains of the ubiquitous soil bacteria, Bacillus thuringiensis (Bt). Since there are often multiple similar IPGs encoded by such plasmids, their assemblies are typically fragmented and many IPGs are scattered through multiple contigs. As a result, existing gene prediction tools (that analyze individual contigs) typically predict partial rather than complete IPGs, making it difficult to conduct downstream IPG engineering efforts in agricultural genomics.

METHODS

Although it is difficult to assemble IPGs in a single contig, the structure of the genome assembly graph often provides clues on how to combine multiple contigs into segments encoding a single IPG.

RESULTS

We describe ORFograph, a pipeline for predicting IPGs in assembly graphs, benchmark it on (meta)genomic datasets, and discover nearly a hundred novel IPGs. This work shows that graph-aware gene prediction tools enable the discovery of greater diversity of IPGs from (meta)genomes.

CONCLUSIONS

We demonstrated that analysis of the assembly graphs reveals novel candidate IPGs. ORFograph identified both already known genes "hidden" in assembly graphs and potential novel IPGs that evaded existing tools for IPG identification. As ORFograph is fast, one could imagine a pipeline that processes many (meta)genomic assembly graphs to identify even more novel IPGs for phenotypic testing than would previously be inaccessible by traditional gene-finding methods. While here we demonstrated the results of ORFograph only for IPGs, the proposed approach can be generalized to any class of genes. Video abstract.

New Insights Into Biomphalysin Gene Family Diversification in the Vector Snail Biomphalaria glabrata

Aerolysins initially characterized as virulence factors in bacteria are increasingly found in massive genome and transcriptome sequencing data from metazoans. Horizontal gene transfer has been demonstrated as the main way of aerolysin-related toxins acquisition in metazoans. However, only few studies have focused on their potential biological functions in such organisms. Herein, we present an extensive characterization of a multigene family encoding aerolysins - named biomphalysin - in Biomphalaria glabrata snail, the intermediate host of the trematode Schistosoma mansoni. Our results highlight that duplication and domestication of an acquired bacterial toxin gene in the snail genome result in the acquisition of a novel and diversified toxin family. Twenty-three biomphalysin genes were identified. All are expressed and exhibited a tissue-specific expression pattern. An in silico structural analysis was performed to highlight the central role played by two distinct domains i) a large lobe involved in the lytic function of these snail toxins which constrained their evolution and ii) a small lobe which is structurally variable between biomphalysin toxins and that matched to various functional domains involved in moiety recognition of targets cells. A functional approach suggests that the repertoire of biomphalysins that bind to pathogens, depends on the type of pathogen encountered. These results underline a neo-and sub-functionalization of the biomphalysin toxins, which have the potential to increase the range of effectors in the snail’s immune arsenal.

Beyond Standardization: Improving External Validity and Reproducibility in Experimental Evolution

Discussions of reproducibility are casting doubts on the credibility of experimental outcomes in the life sciences. Although experimental evolution is not typically included in these discussions, this field is also subject to low reproducibility, partly because of the inherent contingencies affecting the evolutionary process. A received view in experimental studies more generally is that standardization (i.e., rigorous homogenization of experimental conditions) is a solution to some issues of significance and internal validity. However, this solution hides several difficulties, including a reduction of external validity and reproducibility. After explaining the meaning of these two notions in the context of experimental evolution, we import from the fields of animal research and ecology and suggests that systematic heterogenization of experimental factors could prove a promising alternative. We also incorporate into our analysis some philosophical reflections on the nature and diversity of research objectives in experimental evolution.

The C. elegans GATA transcription factor elt-2 mediates distinct transcriptional responses and opposite infection outcomes towards different Bacillus thuringiensis strains

The nematode Caenorhabditis elegans has been extensively used as a model for the study of innate immune responses against bacterial pathogens. While it is well established that the worm mounts distinct transcriptional responses to different bacterial species, it is still unclear in how far it can fine-tune its response to different strains of a single pathogen species, especially if the strains vary in virulence and infection dynamics. To rectify this knowledge gap, we systematically analyzed the C. elegans response to two strains of Bacillus thuringiensis (Bt), MYBt18247 (Bt247) and MYBt18679 (Bt679), which produce different pore forming toxins (PFTs) and vary in infection dynamics. We combined host transcriptomics with cytopathological characterizations and identified both a common and also a differentiated response to the two strains, the latter comprising almost 10% of the infection responsive genes. Functional genetic analyses revealed that the AP-1 component gene jun-1 mediates the common response to both Bt strains. In contrast, the strain-specific response is mediated by the C. elegans GATA transcription factor ELT-2, a homolog of Drosophila SERPENT and vertebrate GATA4-6, and a known master regulator of intestinal responses in the nematode. elt-2 RNAi knockdown decreased resistance to Bt679, but remarkably, increased survival on Bt247. The elt-2 silencing-mediated increase in survival was characterized by reduced intestinal tissue damage despite a high pathogen burden and might thus involve increased tolerance. Additional functional genetic analyses confirmed the involvement of distinct signaling pathways in the C. elegans defense response: the p38-MAPK pathway acts either directly with or in parallel to elt-2 in mediating resistance to Bt679 infection but is not required for protection against Bt247. Our results further suggest that the elt-2 silencing-mediated increase in survival on Bt247 is multifactorial, influenced by the nuclear hormone receptors NHR-99 and NHR-193, and may further involve lipid metabolism and detoxification. Our study highlights that the nematode C. elegans with its comparatively simple immune defense system is capable of generating a differentiated response to distinct strains of the same pathogen species. Importantly, our study provides a molecular insight into the diversity of biological processes that are influenced by a single master regulator and jointly determine host survival after pathogen infection.

Salmon immunological defence and interplay with the modulatory capabilities of its ectoparasite Lepeophtheirus salmonis

The salmon louse Lepeophtheirus salmonis (Lsal) is an ectoparasitic copepod that exerts immunomodulatory and physiological effects on its host Atlantic salmon. Over 30 years of research on louse biology, control, host responses and the host-parasite relationship has provided a plethora of information on the intricacies of host resistance and parasite adaptation. Atlantic salmon exhibit temporal and spatial impairment of the immune system and wound healing ability during infection. This immunosuppression may render Atlantic salmon less tolerant to stress and other confounders associated with current management strategies. Contrasting susceptibility of salmonid hosts exists, and early pro-inflammatory Th1 type responses are associated with resistance. Rapid cellular responses to larvae appear to tip the balance of the host-parasite relationship in favour of the host, preventing severe immune-physiological impacts of the more invasive adults. Immunological, transcriptomic, genomic and proteomic evidence suggests pathological impacts occur in susceptible hosts through modulation of host immunity and physiology via pharmacologically active molecules. Co-evolutionary and farming selection pressures may have incurred preference of Atlantic salmon as a host for Lsal reflected in their interactome. Here, we review host-parasite interactions at the primary attachment/feeding site, and the complex life stage-dependent molecular mechanisms employed to subvert host physiology and immune responses.

Mammalian membrane trafficking as seen through the lens of bacterial toxins

A fundamental question of eukaryotic cell biology is how membrane organelles are organised and interact with each other. Cell biologists address these questions by characterising the structural features of membrane compartments and the mechanisms that coordinate their exchange. To do so, they must rely on variety of cargo molecules and treatments that enable targeted perturbation, localisation, and labelling of specific compartments. In this context, bacterial toxins emerged in cell biology as paradigm shifting molecules that enabled scientists to not only study them from the side of bacterial infection but also from the side of the mammalian host. Their selectivity, potency, and versatility made them exquisite tools for uncovering much of our current understanding of membrane trafficking mechanisms. Here, we will follow the steps that lead toxins until their intracellular targets, highlighting how specific events helped us comprehend membrane trafficking and establish the fundamentals of various cellular organelles and processes. Bacterial toxins will continue to guide us in answering crucial questions in cellular biology while also acting as probes for new technologies and applications.

Benefits and Costs of Animal Virulence for Microbes

This essay is written from the vantage point of the microbial world. While the focus of much thought in the microbial pathogenesis and infectious diseases fields has been on the impact of host-microbe interaction on the host, here we ask questions about what happens to the microbe.

This essay is written from the vantage point of the microbial world. While the focus of much thought in the microbial pathogenesis and infectious diseases fields has been on the impact of host-microbe interaction on the host, here we ask questions about what happens to the microbe. What are the costs and benefits for microbes of having the capacity for virulence? Our exploration of this topic leads us to conclude that virulence confers very few benefits for microbes, unless disease is necessary for microbial survival through host-to-host spread. In fact, the capacity for virulence is often fraught with risk for microbes, including host dependence and the threat of extinction. The costs of virulence may explain why, relative to their enormous numbers in nature, very few microbes are actually associated with human and animal disease.

Evolved Biofilm: Review on the Experimental Evolution Studies of Bacillus subtilis Pellicles

For several decades, laboratory evolution has served as a powerful method to manipulate microorganisms and to explore long-term dynamics in microbial populations. Next to canonical Escherichia coli planktonic cultures, experimental evolution has expanded into alternative cultivation methods and species, opening the doors to new research questions. Bacillus subtilis, the spore-forming and root-colonizing bacterium, can easily develop in the laboratory as a liquid-air interface colonizing pellicle biofilm. Here, we summarize recent findings derived from this tractable experimental model. Clonal pellicle biofilms of B. subtilis can rapidly undergo morphological and genetic diversification creating new ecological interactions, for example, exploitation by biofilm non-producers. Moreover, long-term exposure to such matrix non-producers can modulate cooperation in biofilms, leading to different phenotypic heterogeneity pattern of matrix production with larger subpopulation of "ON" cells. Alternatively, complementary variants of biofilm non-producers, each lacking a distinct matrix component, can engage in a genetic division of labor, resulting in superior biofilm productivity compared to the "generalist" wild type. Nevertheless, inter-genetic cooperation appears to be evanescent and rapidly vanquished by individual biofilm formation strategies altering the amount or the properties of the remaining matrix component. Finally, fast-evolving mobile genetic elements can unpredictably shift intra-species interactions in B. subtilis biofilms. Understanding evolution in clonal biofilm populations will facilitate future studies in complex multispecies biofilms that are more representative of nature.

The genomic basis of Red Queen dynamics during rapid reciprocal host-pathogen coevolution

Pathogens are omnipresent and by definition detrimental to their hosts. Pathogens thus exert high selection on their hosts, which, if adapting, can exert similar levels of selection on the pathogen, resulting in ongoing cycles of reciprocal adaptation between the antagonists. Such coevolutionary interactions have a central influence on the evolution of organisms. Surprisingly, we still know little about the exact selection dynamics and the genome regions involved. Our study uses a controlled experimental approach with an animal host to dissect coevolutionary selection. We find that distinct selective processes underlie rapid coadaptation in the two antagonists, including antagonistic frequency-dependent selection on toxin gene copy number in the pathogen, while the host response is likely influenced by changes in multiple genome regions.

Red Queen dynamics, involving coevolutionary interactions between species, are ubiquitous, shaping the evolution of diverse biological systems. To date, information on the underlying selection dynamics and the involved genome regions is mainly available for bacteria–phage systems or only one of the antagonists of a eukaryotic host–pathogen interaction. We add to our understanding of these important coevolutionary interactions using an experimental host–pathogen model, which includes the nematode Caenorhabditis elegans and its pathogen Bacillus thuringiensis. We combined experimental evolution with time-shift experiments, in which a focal host or pathogen is tested against a coevolved antagonist from the past, present, or future, followed by genomic analysis. We show that (i) coevolution occurs rapidly within few generations, (ii) temporal coadaptation at the phenotypic level is found in parallel across replicate populations, consistent with antagonistic frequency-dependent selection, (iii) genomic changes in the pathogen match the phenotypic pattern and include copy number variations of a toxin-encoding plasmid, and (iv) host genomic changes do not match the phenotypic pattern and likely involve selective responses at more than one locus. By exploring the dynamics of coevolution at the phenotypic and genomic level for both host and pathogen simultaneously, our findings demonstrate a more complex model of the Red Queen, consisting of distinct selective processes acting on the two antagonists during rapid and reciprocal coadaptation.

Enhanced Nicotiana benthamiana immune responses caused by heterologous plant genes from Pinellia ternata

BACKGROUND

Pinellia ternata is a Chinese traditional medicinal herb, used to cure diseases including insomnia, eclampsia and cervical carcinoma, for hundreds of years. Non-self-recognition in multicellular organisms can initiate the innate immunity to avoid the invasion of pathogens. A design for pathogen independent, heterosis based, fresh resistance can be generated in F1 hybrid was proposed.

RESULTS

By library functional screening, we found that P. ternata genes, named as ptHR375 and ptHR941, were identified with the potential to trigger a hypersensitive response in Nicotiana benthamiana. Significant induction of ROS and Callose deposition in N. benthamiana leaves along with activation of pathogenesis-related genes viz.; PR-1a, PR-5, PDF1.2, NPR1, PAL, RBOHB and ERF1 and antioxidant enzymes was observed. After transformation into N. benthamiana, expression of pathogenesis related genes was significantly up-regulated to generate high level of resistance against Phytophthora capsici without affecting the normal seed germination and morphological characters of the transformed N. benthamiana. UPLC-QTOF-MS analysis of ptHR375 transformed N. benthamiana revealed the induction of Oxytetracycline, Cuelure, Allantoin, Diethylstilbestrol and 1,2-Benzisothiazol-3(2H)-one as bioactive compounds. Here we also proved that F1 hybrids, produced by crossing of the ptHR375 and ptHR941 transformed and non-transformed N. benthamiana, show significant high levels of PR-gene expressions and pathogen resistance.

CONCLUSIONS

Heterologous plant genes can activate disease resistance in another plant species and furthermore, by generating F1 hybrids, fresh pathogen independent plant immunity can be obtained. It is also concluded that ptHR375 and ptHR941 play their role in SA and JA/ET defense pathways to activate the resistance against invading pathogens.

The rise of the rosette agent in Europe: An epidemiological enigma

International biodiversity assessments often overlook the role of emerging infectious pathogens in the decline of freshwater fish populations despite the many examples of emerging diseases in other more visible taxa on a global scale. Whilst the introduction of the rosette agent Sphaerothecum destruens in Europe remained an epidemiological enigma, recent findings have shown that this parasite arrived in Europe with the introduction of the healthy carrier Pseudorasbora parva from China nearly 60 years ago and its emergence went unnoticed for over 45 years despite its severe impact on European fish biodiversity. Recent reports on the host and pathogen phylogeny point towards an ancient host-pathogen co-evolution with direct implications on disease risk. Here, we postulate that the observed rapid population decline of native fish species following their infection with virulent strains of S. destruens has underpinned the rapid establishment of P. parva populations during the invasion process. We reviewed the existing evidence supporting the claim of an S. destruens' emergence worldwide and also suggest that the origin of the US strains is to be found among contaminated Asian Oncorhynchus tshawytscha living in sympatry with native Asian P. parva population. Finally, several important preventative steps are suggested as a way to manage the impact of S. destruens on local fish communities.

Interaction between Insects, Toxins, and Bacteria: Have We Been Wrong So Far?

Toxins are a major virulence factor produced by many pathogenic bacteria. In vertebrates, the response of hosts to the bacteria is inseparable from the response to the toxins, allowing a comprehensive understanding of this tripartite host-pathogen-toxin interaction. However, in invertebrates, this interaction has been investigated by two complementary but historically distinct fields of research: toxinology and immunology. In this article, I highlight how such dichotomy between these two fields led to a biased, or even erroneous view of the ecology and evolution of the interaction between insects, toxins, and bacteria. I focus on the reason behind such a dichotomy, on how to bridge the fields together, and on confounding effects that could bias the outcome of the experiments. Finally, I raise four questions at the border of the two fields on the cross-effects between toxins, bacteria, and spores that have been largely underexplored to promote a more comprehensive view of this interaction.

Comparative genome and phenotypic analysis of three Clostridioides difficile strains isolated from a single patient provide insight into multiple infection of C. difficile

BACKGROUND

Clostridioides difficile infections (CDI) have emerged over the past decade causing symptoms that range from mild, antibiotic-associated diarrhea (AAD) to life-threatening toxic megacolon. In this study, we describe a multiple and isochronal (mixed) CDI caused by the isolates DSM 27638, DSM 27639 and DSM 27640 that already initially showed different morphotypes on solid media.

RESULTS

The three isolates belonging to the ribotypes (RT) 012 (DSM 27639) and 027 (DSM 27638 and DSM 27640) were phenotypically characterized and high quality closed genome sequences were generated. The genomes were compared with seven reference strains including three strains of the RT 027, two of the RT 017, and one of the RT 078 as well as a multi-resistant RT 012 strain. The analysis of horizontal gene transfer events revealed gene acquisition incidents that sort the strains within the time line of the spread of their RTs within Germany. We could show as well that horizontal gene transfer between the members of different RTs occurred within this multiple infection. In addition, acquisition and exchange of virulence-related features including antibiotic resistance genes were observed. Analysis of the two genomes assigned to RT 027 revealed three single nucleotide polymorphisms (SNPs) and apparently a regional genome modification within the flagellar switch that regulates the fli operon.

CONCLUSION

Our findings show that (i) evolutionary events based on horizontal gene transfer occur within an ongoing CDI and contribute to the adaptation of the species by the introduction of new genes into the genomes, (ii) within a multiple infection of a single patient the exchange of genetic material was responsible for a much higher genome variation than the observed SNPs.

Back to the future in a petri dish: Origin and impact of resurrected microbes in natural populations

Current natural populations face new interactions because of the re-emergence of ancient microbes and viruses. These risks come from the re-emergence of pathogens kept in laboratories or from pathogens that are retained in the permafrost, which become available upon thawing due to climate change. We here focus on the effects of such re-emergence in natural host populations based on evolutionary theory of virulence and long-term studies, which investigate host-pathogen adaptations. Pathogens tend to be locally and temporally adapted to their co-occurring hosts, but when pathogens from a different environment or different time enter the host community, the degree to which a new host-pathogen interaction is a threat will depend on the specific genotypic associations, the time lag between the host and the pathogen, and the interactions with native or recent host and pathogen species. Some insights can be obtained from long-term studies using a resurrection ecology approach. These long-term studies based on time-shift experiments are essential to obtain insight into the mechanisms underlying host-pathogen coevolution at several ecological and temporal scales. As past pathogens and their corresponding host(s) can differ in infectivity and susceptibility, strong reciprocal selective pressures can be induced by the pathogen. These strong selective pressures often result in an escalating arms race, but do not necessarily result in increased infectivity over time. Human health can also be impacted by these resurrected pathogens as the majority of emerging infectious diseases are zoonoses, which are infectious diseases originating from animal populations naturally transmitted to humans. The sanitary risk associated with pathogen emergence from different environments (spatial or temporal) depends on a combination of socioeconomic, environmental, and ecological factors that affect the virulence or the pathogenic potential of microbes and their ability to infect susceptible host populations.

A Model for Evolutionary Ecology of Disease: The Case for Caenorhabditis Nematodes and Their Natural Parasites

Many of the outstanding questions in disease ecology and evolution call for combining observation of natural host-parasite populations with experimental dissection of interactions in the field and the laboratory. The "rewilding" of model systems holds great promise for this endeavor. Here, we highlight the potential for development of the nematode Caenorhabditis elegans and its close relatives as a model for the study of disease ecology and evolution. This powerful laboratory model was disassociated from its natural habitat in the 1960s. Today, studies are uncovering that lost natural history, with several natural parasites described since 2008. Studies of these natural Caenorhabditis-parasite interactions can reap the benefits of the vast array of experimental and genetic tools developed for this laboratory model. In this review, we introduce the natural parasites of C. elegans characterized thus far and discuss resources available to study them, including experimental (co)evolution, cryopreservation, behavioral assays, and genomic tools. Throughout, we present avenues of research that are interesting and feasible to address with caenorhabditid nematodes and their natural parasites, ranging from the maintenance of outcrossing to the community dynamics of host-associated microbes. In combining natural relevance with the experimental power of a laboratory supermodel, these fledgling host-parasite systems can take on fundamental questions in evolutionary ecology of disease.

Perspectives on the evolutionary ecology of arthropod antimicrobial peptides

Antimicrobial peptides (AMPs) are important elements of the innate immune defence in multicellular organisms that target and kill microbes. Here, we reflect on the various points that are raised by the authors of the 11 contributions to a special issue of Philosophical Transactions on the 'evolutionary ecology of arthropod antimicrobial peptides'. We see five interesting topics emerging. (i) AMP genes in insects, and perhaps in arthropods more generally, evolve much slower than most other immune genes. One explanation refers to the constraints set by AMPs being part of a finely tuned defence system. A new view argues that AMPs are under strong stabilizing selection. Regardless, this striking observation still invites many more questions than have been answered so far. (ii) AMPs almost always are expressed in combinations and sometimes show expression patterns that are dependent on the infectious agent. While it is often assumed that this can be explained by synergistic interactions, such interactions have rarely been demonstrated and need to be studied further. Moreover, how to define synergy in the first place remains difficult and needs to be addressed. (iii) AMPs play a very important role in mediating the interaction between a host and its mutualistic or commensal microbes. This has only been studied in a very small number of (insect) species. It has become clear that the very same AMPs play different roles in different situations and hence are under concurrent selection. (iv) Different environments shape the physiology of organisms; especially the host-associated microbial communities should impact on the evolution host AMPs. Studies in social insects and some organisms from extreme environments seem to support this notion, but, overall, the evidence for adaptation of AMPs to a given environment is scant. (v) AMPs are considered or already developed as new drugs in medicine. However, bacteria can evolve resistance to AMPs. Therefore, in the light of our limited understanding of AMP evolution in the natural context, and also the very limited understanding of the evolution of resistance against AMPs in bacteria in particular, caution is recommended. What is clear though is that study of the ecology and evolution of AMPs in natural systems could inform many of these outstanding questions, including those related to medical applications and pathogen control.This article is part of the themed issue 'Evolutionary ecology of arthropod antimicrobial peptides'.

Complete genome sequence of the nematicidal Bacillus thuringiensis MYBT18247

The Gram-positive spore forming bacterium Bacillus thuringiensis MYBT18247 encodes three cry toxin genes, (cry6Ba2, cry6Ba3 and cry21-like) which are active against nematodes. For a better understanding of the evolution of virulence and cry toxins, we present here the complete genome sequence of Bacillus thuringiensis MYBT18247. Various additional virulence factors such as bacteriocins, proteases and hemolysins were identified. In addition, the methylome and the metabolic potential of the strain were analyzed and the strain phylogenetically classified.

Complete Genome sequence of the nematicidal Bacillus thuringiensis MYBT18246

10.1601/nm.5000 is a rod-shaped facultative anaerobic spore forming bacterium of the genus 10.1601/nm.4857. The defining feature of the species is the ability to produce parasporal crystal inclusion bodies, consisting of δ-endotoxins, encoded by cry-genes. Here we present the complete annotated genome sequence of the nematicidal 10.1601/nm.5000 strain MYBT18246. The genome comprises one 5,867,749 bp chromosome and 11 plasmids which vary in size from 6330 bp to 150,790 bp. The chromosome contains 6092 protein-coding and 150 RNA genes, including 36 rRNA genes. The plasmids encode 997 proteins and 4 t-RNA's. Analysis of the genome revealed a large number of mobile elements involved in genome plasticity including 11 plasmids and 16 chromosomal prophages. Three different nematicidal toxin genes were identified and classified according to the Cry toxin naming committee as cry13Aa2, cry13Ba1, and cry13Ab1. Strikingly, these genes are located on the chromosome in close proximity to three separate prophages. Moreover, four putative toxin genes of different toxin classes were identified on the plasmids p120510 (Vip-like toxin), p120416 (Cry-like toxin) and p109822 (two Bin-like toxins). A comparative genome analysis of 10.1601/nm.5000 MYBT18246 with three closely related 10.1601/nm.5000 strains enabled determination of the pan-genome of 10.1601/nm.5000 MYBT18246, revealing a large number of singletons, mostly represented by phage genes, morons and cryptic genes.

Experimental evolution with a multicellular host causes diversification within and between microbial parasite populations-Differences in emerging phenotypes of two different parasite strains

Host-parasite coevolution is predicted to have complex evolutionary consequences, potentially leading to the emergence of genetic and phenotypic diversity for both antagonists. However, little is known about variation in phenotypic responses to coevolution between different parasite strains exposed to the same experimental conditions. We infected Caenorhabditis elegans with one of two strains of Bacillus thuringiensis and either allowed the host and the parasite to experimentally coevolve (coevolution treatment) or allowed only the parasite to adapt to the host (one-sided parasite adaptation). By isolating single parasite clones from evolved populations, we found phenotypic diversification of the ancestral strain into distinct clones, which varied in virulence toward ancestral hosts and competitive ability against other parasite genotypes. Parasite phenotypes differed remarkably not only between the two strains, but also between and within different replicate populations, indicating diversification of the clonal population caused by selection. This study highlights that the evolutionary selection pressure mediated by a multicellular host causes phenotypic diversification, but not necessarily with the same phenotypic outcome for different parasite strains.

Experimental Evolution with Caenorhabditis Nematodes

The hermaphroditic nematode Caenorhabditis elegans has been one of the primary model systems in biology since the 1970s, but only within the last two decades has this nematode also become a useful model for experimental evolution. Here, we outline the goals and major foci of experimental evolution with C. elegans and related species, such as C. briggsae and C. remanei, by discussing the principles of experimental design, and highlighting the strengths and limitations of Caenorhabditis as model systems. We then review three exemplars of Caenorhabditis experimental evolution studies, underlining representative evolution experiments that have addressed the: (1) maintenance of genetic variation; (2) role of natural selection during transitions from outcrossing to selfing, as well as the maintenance of mixed breeding modes during evolution; and (3) evolution of phenotypic plasticity and its role in adaptation to variable environments, including host-pathogen coevolution. We conclude by suggesting some future directions for which experimental evolution with Caenorhabditis would be particularly informative.

Experimental evolution of resistance against Bacillus thuringiensis in the insect model host Galleria mellonella results in epigenetic modifications

Epigenetic mechanisms have been proposed to translate environmental stimuli into heritable transgenerational phenotypic variations that can significantly influence natural selection. An intriguing example is exposure to pathogens, which imposes selection for host resistance. To test this hypothesis, we used larvae of the greater wax moth Galleria mellonella as model host to experimentally select for resistance to Bacillus thuringiensis (Bt), the most widely used bacterial agent for the biological control of pest insects. To determine whether epigenetic mechanisms contribute to the evolution of resistance against pathogens, we exposed G. mellonella larvae over 30 generations to spores and crystals mix of Bt and compared epigenetic markers in this selected line, exhibiting almost 11-fold enhanced resistance against Bt, to those in a non-selected control population. We found that experimental selection influenced acetylation of specific histones and DNA methylation as well as transcription of genes encoding the enzymatic writers and erasers of these epigenetic mechanisms. Using microarray analysis, we also observed differences in the expression of conserved miRNAs in the resistant and susceptible larvae, resulting in the repression of candidate genes that confer susceptibility to Bt. By combining in silico minimum free energy hybridization with RT-PCR experiments, we identified the functions and biological processes associated with the mRNAs targeted by these miRNAs. Our results suggest that epigenetic mechanisms operating at the pre-transcriptional and post-transcriptional levels contribute to the transgenerational inherited transcriptional reprogramming of stress and immunity-related genes, ultimately providing a mechanism for the evolution of insect resistance to pathogen.

Genomic evidence for population-specific responses to co-evolving parasites in a New Zealand freshwater snail

Reciprocal co-evolving interactions between hosts and parasites are a primary source of strong selection that can promote rapid and often population- or genotype-specific evolutionary change. These host-parasite interactions are also a major source of disease. Despite their importance, very little is known about the genomic basis of co-evolving host-parasite interactions in natural populations, especially in animals. Here, we use gene expression and sequence evolution approaches to take critical steps towards characterizing the genomic basis of interactions between the freshwater snail Potamopyrgus antipodarum and its co-evolving sterilizing trematode parasite, Microphallus sp., a textbook example of natural coevolution. We found that Microphallus-infected P. antipodarum exhibit systematic downregulation of genes relative to uninfected P. antipodarum. The specific genes involved in parasite response differ markedly across lakes, consistent with a scenario where population-level co-evolution is leading to population-specific host-parasite interactions and evolutionary trajectories. We also used an F_ST -based approach to identify a set of loci that represent promising candidates for targets of parasite-mediated selection across lakes as well as within each lake population. These results constitute the first genomic evidence for population-specific responses to co-evolving infection in the P. antipodarum-Microphallus interaction and provide new insights into the genomic basis of co-evolutionary interactions in nature.

The Natural Biotic Environment of Caenorhabditis elegans

Organisms evolve in response to their natural environment. Consideration of natural ecological parameters are thus of key importance for our understanding of an organism's biology. Curiously, the natural ecology of the model species Caenorhabditis elegans has long been neglected, even though this nematode has become one of the most intensively studied models in biological research. This lack of interest changed ∼10 yr ago. Since then, an increasing number of studies have focused on the nematode's natural ecology. Yet many unknowns still remain. Here, we provide an overview of the currently available information on the natural environment of C. elegans We focus on the biotic environment, which is usually less predictable and thus can create high selective constraints that are likely to have had a strong impact on C. elegans evolution. This nematode is particularly abundant in microbe-rich environments, especially rotting plant matter such as decomposing fruits and stems. In this environment, it is part of a complex interaction network, which is particularly shaped by a species-rich microbial community. These microbes can be food, part of a beneficial gut microbiome, parasites and pathogens, and possibly competitors. C. elegans is additionally confronted with predators; it interacts with vector organisms that facilitate dispersal to new habitats, and also with competitors for similar food environments, including competitors from congeneric and also the same species. Full appreciation of this nematode's biology warrants further exploration of its natural environment and subsequent integration of this information into the well-established laboratory-based research approaches.

Caenorhabditis elegans as a Model for Microbiome Research

The nematode Caenorhabditis elegans is used as a central model system across biological disciplines. Surprisingly, almost all research with this worm is performed in the absence of its native microbiome, possibly affecting generality of the obtained results. In fact, the C. elegans microbiome had been unknown until recently. This review brings together results from the first three studies on C. elegans microbiomes, all published in 2016. Meta-analysis of the data demonstrates a considerable conservation in the composition of the microbial communities, despite the distinct geographical sample origins, study approaches, labs involved and perturbations during worm processing. The C. elegans microbiome is enriched and in some cases selective for distinct phylotypes compared to corresponding substrate samples (e.g., rotting fruits, decomposing plant matter, and compost soil). The dominant bacterial groups include several Gammaproteobacteria (Enterobacteriaceae, Pseudomonaceae, and Xanthomonodaceae) and Bacteroidetes (Sphingobacteriaceae, Weeksellaceae, Flavobacteriaceae). They are consistently joined by several rare putative keystone taxa like Acetobacteriaceae. The bacteria are able to enhance growth of nematode populations, as well as resistance to biotic and abiotic stressors, including high/low temperatures, osmotic stress, and pathogenic bacteria and fungi. The associated microbes thus appear to display a variety of effects beneficial for the worm. The characteristics of these effects, their relevance for C. elegans fitness, the presence of specific co-adaptations between microbiome members and the worm, and the molecular underpinnings of microbiome-host interactions represent promising areas of future research, for which the advantages of C. elegans as an experimental system should prove of particular value.

Bacillus thuringiensis and Bacillus weihenstephanensis Inhibit the Growth of Phytopathogenic Verticillium Species

Verticillium wilt causes severe yield losses in a broad range of economically important crops worldwide. As many soil fumigants have a severe environmental impact, new biocontrol strategies are needed. Members of the genus Bacillus are known as plant growth-promoting bacteria (PGPB) as well as biocontrol agents of pests and diseases. In this study, we isolated 267 Bacillus strains from root-associated soil of field-grown tomato plants. We evaluated the antifungal potential of 20 phenotypically diverse strains according to their antagonistic activity against the two phytopathogenic fungi Verticillium dahliae and Verticillium longisporum. In addition, the 20 strains were sequenced and phylogenetically characterized by multi-locus sequence typing (MLST) resulting in 7 different Bacillus thuringiensis and 13 Bacillus weihenstephanensis strains. All B. thuringiensis isolates inhibited in vitro the tomato pathogen V. dahliae JR2, but had only low efficacy against the tomato-foreign pathogen V. longisporum 43. All B. weihenstephanensis isolates exhibited no fungicidal activity whereas three B. weihenstephanensis isolates showed antagonistic effects on both phytopathogens. These strains had a rhizoid colony morphology, which has not been described for B. weihenstephanensis strains previously. Genome analysis of all isolates revealed putative genes encoding fungicidal substances and resulted in identification of 304 secondary metabolite gene clusters including 101 non-ribosomal polypeptide synthetases and 203 ribosomal-synthesized and post-translationally modified peptides. All genomes encoded genes for the synthesis of the antifungal siderophore bacillibactin. In the genome of one B. thuringiensis strain, a gene cluster for zwittermicin A was detected. Isolates which either exhibited an inhibitory or an interfering effect on the growth of the phytopathogens carried one or two genes encoding putative mycolitic chitinases, which might contribute to antifungal activities. This indicates that chitinases contribute to antifungal activities. The present study identified B. thuringiensis isolates from tomato roots which exhibited in vitro antifungal activity against Verticillium species.

Reconstruction of Haplotype-Blocks Selected during Experimental Evolution

The genetic analysis of experimentally evolving populations typically relies on short reads from pooled individuals (Pool-Seq). While this method provides reliable allele frequency estimates, the underlying haplotype structure remains poorly characterized. With small population sizes and adaptive variants that start from low frequencies, the interpretation of selection signatures in most Evolve and Resequencing studies remains challenging. To facilitate the characterization of selection targets, we propose a new approach that reconstructs selected haplotypes from replicated time series, using Pool-Seq data. We identify selected haplotypes through the correlated frequencies of alleles carried by them. Computer simulations indicate that selected haplotype-blocks of several Mb can be reconstructed with high confidence and low error rates, even when allele frequencies change only by 20% across three replicates. Applying this method to real data from D. melanogaster populations adapting to a hot environment, we identify a selected haplotype-block of 6.93 Mb. We confirm the presence of this haplotype-block in evolved populations by experimental haplotyping, demonstrating the power and accuracy of our haplotype reconstruction from Pool-Seq data. We propose that the combination of allele frequency estimates with haplotype information will provide the key to understanding the dynamics of adaptive alleles.

CryGetter: a tool to automate retrieval and analysis of Cry protein data

Background

For many years, the use of chemical agents to control crop pests has been degrading the environment, bringing problems to humans and all living things. An alternative to deal with the pests is the use of biopesticides, biological agents capable of controlling these harmful organisms. One kind of biopesticide is Bacillus thuringiensis, a Gram-positive bacterium that synthesizes a protein that, when ingested by the pests, kills them and does not harm other species.

Results

Since the economical importance of Bacillus thuringiensis and its proteins significance, this work presents a software tool, called CryGetter, that is capable of retrieving data related to these proteins, store it and present it in a user friendly manner. The tool also aims to align the protein sequences and generate reports containing some statistical data concerning the alignments that were made.

Conclusions

CryGetter was created to help researchers of Bacillus thuringiensis and its proteins to speed up their data retrieval and analysis, allowing them to generate more accurate results. In this sense, the tool circumvents the error prone task of manually getting all the necessary data and processing them in various software systems to get the same result as CryGetter gets in a unique semiautomatic environment.