evolutionary genomics of host microbe interactions
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evolutionary genomics of host microbe interactions
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Rescooped by Jessie Uehling from MycorWeb Plant-Microbe Interactions
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Genome Sequences Reveal Cryptic Speciation in the Human Pathogen Histoplasma capsulatum

Genome Sequences Reveal Cryptic Speciation in the Human Pathogen Histoplasma capsulatum | evolutionary genomics of host microbe interactions | Scoop.it
Histoplasma capsulatum is a pathogenic fungus that causes life-threatening lung infections. About 500,000 people are exposed to H. capsulatum each year in the United States, and over 60% of the U.S. population has been exposed to the fungus at some point in their life. We performed genome-wide population genetics and phylogenetic analyses with 30 Histoplasma isolates representing four recognized areas where histoplasmosis is endemic and show that the Histoplasma genus is composed of at least four species that are genetically isolated and rarely interbreed. Therefore, we propose a taxonomic rearrangement of the genus. 
 IMPORTANCE The evolutionary processes that give rise to new pathogen lineages are critical to our understanding of how they adapt to new environments and how frequently they exchange genes with each other. The fungal pathogen Histoplasma capsulatum provides opportunities to precisely test hypotheses about the origin of new genetic variation. We find that H. capsulatum is composed of at least four different cryptic species that differ genetically and also in virulence. These results have implications for the epidemiology of histoplasmosis because not all Histoplasma species are equivalent in their geographic range and ability to cause disease.

Via Steve Marek, Francis Martin
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Dimorphism in Fungal Pathogens of Mammals, Plants, and Insects

Dimorphism in Fungal Pathogens of Mammals, Plants, and Insects | evolutionary genomics of host microbe interactions | Scoop.it

The capacity for pathogenic fungi to change morphology during their lifecycle is widespread. However, relatively few fungi are considered dimorphic, which refers to the ability to switch between two morphologies, yeast and hyphae (Table 1). These pathogens can be roughly subdivided into thermal (morphologic switch induced by temperature) and non-thermal dimorphic fungi

Worldwide, the thermally dimorphic fungi cause several million human infections each year. In the United States, Histoplasma capsulatum and Coccidioides spp. are estimated to infect 500,000 and 150,000 persons annually, respectively [1,2]. The incidence of coccidioidomycosis has recently increased and its endemic range has extended beyond the Southwest to include eastern Washington state [3]. Although the thermally dimorphic fungi typically infect healthy hosts, these pathogens account for 5.3% of fungal infections in solid organ transplant recipients [4]. Immunosuppressed patients are at risk for respiratory failure and extrapulmonary dissemination [4].


Phytopathogenic dimorphic fungi have had a major impact on urban landscapes and agriculture. Ophiostoma ulmi, which caused the first Dutch elm disease epidemic, has been replaced by a more virulent species, Ophiostoma novo-ulmi, which has destroyed millions of elm trees in the US and Europe [5]. Taphrina deformans, the etiologic agent of peach leaf curl, results in economic losses of $2.5–3 million in the US [6]. Although Ustilago maydis, which causes corn smut, is not a major agricultural threat, the galls (i.e., huitlacoche) caused by infection are eaten as a delicacy [7]. Entomopathogenic fungi have been utilized to control insects harmful to agriculture and to study how pathogens control host behavior [8,9].

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The genome and microbiome of a dikaryotic fungus (Inocybe terrigena, Inocybaceae) revealed by metagenomics

The genome and microbiome of a dikaryotic fungus (Inocybe terrigena, Inocybaceae) revealed by metagenomics | evolutionary genomics of host microbe interactions | Scoop.it
Recent advances in molecular methods have increased our understanding of various fungal symbioses. However, little is known about genomic and microbiome features of most uncultured symbiotic fungal clades. Here, we analysed the genome and microbiome of Inocybaceae (Agaricales, Basidiomycota), a largely uncultured ectomycorrhizal clade known to form symbiotic associations with a wide variety of plant species. We used metagenomic sequencing and assembly of dikaryotic fruiting‐body tissues from Inocybe terrigena (Fr.) Kuyper, to classify fungal and bacterial genomic sequences, and obtained a nearly complete fungal genome containing 93% of core eukaryotic genes. Comparative genomics reveals that I. terrigena is more similar to ectomycorrhizal and brown rot fungi than to white rot fungi. The reduction in lignin degradation capacity has been independent from and significantly faster than in closely related ectomycorrhizal clades supporting that ectomycorrhizal symbiosis evolved independently in Inocybe. The microbiome of I. terrigena fruiting‐bodies includes bacteria with known symbiotic functions in other fungal and non‐fungal host environments, suggesting potential symbiotic functions of these bacteria in fungal tissues regardless of habitat conditions. Our study demonstrates the usefulness of direct metagenomics analysis of fruiting‐body tissues for characterizing fungal genomes and microbiome.

Via Francis Martin
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Not in your usual Top 10: protists that infect plants and algae - Schwelm - 2018 - Molecular Plant Pathology -

Not in your usual Top 10: protists that infect plants and algae - Schwelm - 2018 - Molecular Plant Pathology - | evolutionary genomics of host microbe interactions | Scoop.it
Fungi, nematodes and oomycetes belong to the most prominent eukaryotic plant pathogenic organisms. Unicellular organisms from other eukaryotic lineages, commonly addressed as protists, also infect plants. This review provides an introduction to plant pathogenic protists, including algae infecting oomycetes, and their current state of research.
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Host‐ and stage‐dependent secretome of the arbuscular mycorrhizal fungus Rhizophagus irregularis 

Host‐ and stage‐dependent secretome of the arbuscular mycorrhizal fungus Rhizophagus irregularis  | evolutionary genomics of host microbe interactions | Scoop.it
Figure 5. Laser microdissection combined with RNAseq to study stage-dependent expression. (a) Arbuscules (ARB) and intraradical mycelium (IRM) were collected by laser microdissection. Scales 100 µm. 14 µM-thick section of a mycorrhized Medicago root before and after laser dissection are shown. Regions selected for microdissection are indicated. (b) Stage-dependent secretome of Rhizophagus irregularis. 310 expressed SPs were grouped into arbuscule (ARB), intraradical mycelium (IRM) or extraradical mycelium (ERM) using the following criteria: FDR p<0.05 and fold change>4. (c) 12 out of 66 SPs showing ERMenriched expression shown in (a) are significantly higher expressed (FDR p value<0.05, fold change>4) in ERM compared to germinating spores (GS); 2 ERM-enriched SPs show higher expression in germinating spores.

Arbuscular mycorrhizal fungi form the most wide-spread endosymbiosis with plants. There is very little host-specificity in this interaction, however host preferences as well as varying symbiotic efficiencies have been observed. We hypothesize that secreted proteins (SPs) may act as fungal effectors to control symbiotic efficiency in a host-dependent manner. Therefore, we studied whether AM fungi adjust their secretome in a host- and stage-dependent manner to contribute to their extremely wide host-range. We investigated the expression of SP-encoding genes of Rhizophagus irregularis in three evolutionary distantly-related plant species, Medicago truncatula, Nicotiana benthamiana and Allium schoenoprasum. In addition we used laser microdissection in combination with RNAseq to study SP expression at different stages of the interaction in Medicago. Our data indicate that most expressed SPs show roughly equal expression levels in the interaction with all three host plants. In addition, a subset shows significant differential expression depending on the host plant. Furthermore, SP expression is controlled locally in the hyphal network in response to host dependent cues. Overall, this study presents a comprehensive analysis of the R. irregularis secretome, which now offers a solid basis to direct functional studies on the role of fungal SPs in AM symbiosis.

Via Steve Marek
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The origin and evolution of mycorrhizal symbioses: from palaeomycology to phylogenomics

The ability of fungi to form mycorrhizas with plants is one of the most remarkable and enduring adaptations to life on land. The occurrence of mycorrhizas is now well established in c. 85% of extant plants, yet the geological record of these associations is sparse. Fossils preserved under exceptional conditions provide tantalizing glimpses into the evolutionary history of mycorrhizas, showing the extent of their occurrence and aspects of their evolution in extinct plants. The fossil record has important roles to play in establishing a chronology of when key fungal associations evolved and in understanding their importance in ecosystems through time. Together with calibrated phylogenetic trees, these approaches extend our understanding of when and how groups evolved in the context of major environmental change on a global scale. Phylogenomics furthers this understanding into the evolution of different types of mycorrhizal associations, and genomic studies of both plants and fungi are shedding light on how the complex set of symbiotic traits evolved. Here we present a review of the main phases of the evolution of mycorrhizal interactions from palaeontological, phylogenetic and genomic perspectives, with the aim of highlighting the potential of fossil material and a geological perspective in a cross‐disciplinary approach.

Via Philip Carella
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N-hydroxy-pipecolic acid is a mobile signal that induces systemic disease resistance in Arabidopsis

Systemic acquired resistance (SAR) is a global response in plants induced at the site of infection that leads to long-lasting and broad-spectrum disease resistance at distal, uninfected tissues. Despite the importance of this priming mechanism, the identity of the mobile defense signal that moves systemically throughout plants to initiate SAR has remained elusive. In this paper, we describe a new metabolite, N-hydroxy-pipecolic acid (N-OH-Pip), and provide evidence that this molecule is a mobile signal that plays a central role in initiating SAR signal transduction in Arabidopsis thaliana. We demonstrate that FLAVIN-DEPENDENT MONOOXYGENASE 1 (FMO1), a key regulator of SAR-associated defense priming, can synthesize N-OH-Pip from pipecolic acid in planta, and exogenously applied N-OH-PIP moves systemically in Arabidopsis and can rescue the SAR-deficiency of fmo1 mutants. We also demonstrate that N-OH-Pip treatment causes systemic changes in the expression of pathogenesis-related genes and metabolic pathways throughout the plant, and enhances resistance to a bacterial pathogen. This work provides new insight into the chemical nature of a mobile signal for SAR and also suggests that the N-OH-Pip pathway is a promising target for metabolic engineering to enhance disease resistance.

Via Philip Carella
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Frontiers | Genetic and Molecular Mechanisms Underlying Symbiotic Specificity in Legume-Rhizobium Interactions | Plant Science

Frontiers | Genetic and Molecular Mechanisms Underlying Symbiotic Specificity in Legume-Rhizobium Interactions | Plant Science | evolutionary genomics of host microbe interactions | Scoop.it
“ Legumes are able to form a symbiotic relationship with nitrogen-fixing soil bacteria called rhizobia. The result of this symbiosis is to form nodules on the plant root, within which the bacteria can convert atmospheric nitrogen into ammonia that can be used by the plant. Establishment of a successful symbiosis requires the two symbiotic partners to be compatible with each other throughout the process of symbiotic development. However, incompatibility frequently occurs, such that a bacterial strain is unable to nodulate a particular host plant or forms nodules that are incapable of fixing nitrogen. Genetic and molecular mechanisms that regulate symbiotic specificity are diverse, involving a wide range of host and bacterial genes/signals with various modes of action. In this review, we will provide an update on our current knowledge of how the recognition specificity has evolved in the context of symbiosis signaling and plant immunity.”
Via Philip Carella, Steve Marek
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Scientists’ approach to saving the “Chocolate Trees” from extinction

Scientists’ approach to saving the “Chocolate Trees” from extinction | evolutionary genomics of host microbe interactions | Scoop.it
Scientists predicted that cacao trees may be extinct by 2050 due to factors including climate change, pests and fungal infections. To save chocolate, "the food of the gods", researchers within the chocolate industry is trying to use the innovative CRISPR genome editing technology to save these delicate plants. Genome editing for cacao is an effective way to build tougher cacao plants and help them survive the climate change. In fact, genetically modified chocolate is already on the market. Despite so, a chocolate deficit is still in our near future due to the increasing demand for it. Recently, the candy company, Mars, invested $1 billion into their "Sustainability Generation" R&D project and is teaming up with scientists to use the most effective genome editing tool, CRISPR/Cas9 technology, for editing and breeding stronger cacao plants. As part of their "Cocoa Sustainability Approach", Mars has already sequenced the cocoa genome and share their results to the public in 2013. With their new plan for making super chocolate, hopefully, we could avoid the predicted chocolate deficit from occurring.

Via Ed Rybicki, Chris Upton + helpers
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Evolutionary analysis of Porcine circovirus 3 (PCV3) indicates an ancient origin for its current strains and a worldwide dispersion

Virus Genes. 2018 Mar 3. doi: 10.1007/s11262-018-1545-4. [Epub ahead of print]

Via Ed Rybicki
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23andMe Will Now Test for BRCA Breast-Cancer Genes

23andMe Will Now Test for BRCA Breast-Cancer Genes | evolutionary genomics of host microbe interactions | Scoop.it
It’s the first FDA-authorized genetic-cancer-risk test available without a doctor’s note.

Via Krishan Maggon
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Gene Flow between Divergent Cereal- and Grass-Specific Lineages of the Rice Blast Fungus Magnaporthe oryzae

Gene Flow between Divergent Cereal- and Grass-Specific Lineages of the Rice Blast Fungus Magnaporthe oryzae | evolutionary genomics of host microbe interactions | Scoop.it
IMPORTANCE Infection of novel hosts is a major route for disease emergence by pathogenic microorganisms. Understanding the evolutionary history of multihost pathogens is therefore important to better predict the likely spread and emergence of new diseases. Magnaporthe oryzae is a multihost fungus that causes serious cereal diseases, including the devastating rice blast disease and wheat blast, a cause of growing concern due to its recent spread from South America to Asia. Using whole-genome analysis of 76 fungal strains from different hosts, we have documented the divergence of M. oryzae into numerous lineages, each infecting a limited number of host species. Our analyses provide evidence that interlineage gene flow has contributed to the genetic makeup of multiple M. oryzae lineages within the same species. Plant health surveillance is therefore warranted to safeguard against disease emergence in regions where multiple lineages of the fungus are in contact with one another.

Via Steve Marek
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Bacterial distribution in the environment: A communal catalogue reveals Earth’s multiscale microbial diversity

Bacterial distribution in the environment: A communal catalogue reveals Earth’s multiscale microbial diversity | evolutionary genomics of host microbe interactions | Scoop.it
Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity.

Via Francis Martin, Petr Baldrian
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Dimorphism in Fungal Pathogens of Mammals, Plants, and Insects

Dimorphism in Fungal Pathogens of Mammals, Plants, and Insects | evolutionary genomics of host microbe interactions | Scoop.it

The capacity for pathogenic fungi to change morphology during their lifecycle is widespread. However, relatively few fungi are considered dimorphic, which refers to the ability to switch between two morphologies, yeast and hyphae (Table 1). These pathogens can be roughly subdivided into thermal (morphologic switch induced by temperature) and non-thermal dimorphic fungi

Worldwide, the thermally dimorphic fungi cause several million human infections each year. In the United States, Histoplasma capsulatum and Coccidioides spp. are estimated to infect 500,000 and 150,000 persons annually, respectively [1,2]. The incidence of coccidioidomycosis has recently increased and its endemic range has extended beyond the Southwest to include eastern Washington state [3]. Although the thermally dimorphic fungi typically infect healthy hosts, these pathogens account for 5.3% of fungal infections in solid organ transplant recipients [4]. Immunosuppressed patients are at risk for respiratory failure and extrapulmonary dissemination [4].


Phytopathogenic dimorphic fungi have had a major impact on urban landscapes and agriculture. Ophiostoma ulmi, which caused the first Dutch elm disease epidemic, has been replaced by a more virulent species, Ophiostoma novo-ulmi, which has destroyed millions of elm trees in the US and Europe [5]. Taphrina deformans, the etiologic agent of peach leaf curl, results in economic losses of $2.5–3 million in the US [6]. Although Ustilago maydis, which causes corn smut, is not a major agricultural threat, the galls (i.e., huitlacoche) caused by infection are eaten as a delicacy [7]. Entomopathogenic fungi have been utilized to control insects harmful to agriculture and to study how pathogens control host behavior [8,9].

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Codon usage biases co-evolve with transcription termination machinery to suppress premature cleavage and polyadenylation

Codon usage biases co-evolve with transcription termination machinery to suppress premature cleavage and polyadenylation | evolutionary genomics of host microbe interactions | Scoop.it

Codon usage biases are found in all genomes and influence protein expression levels. The codon usage effect on protein expression was thought to be mainly due to its impact on translation. Here, we show that transcription termination is an important driving force for codon usage bias in eukaryotes. Using Neurospora crassa as a model organism, we demonstrated that introduction of rare codons results in premature transcription termination (PTT) within open reading frames and abolishment of full-length mRNA. PTT is a wide-spread phenomenon in Neurospora, and there is a strong negative correlation between codon usage bias and PTT events. Rare codons lead to the formation of putative poly(A) signals and PTT. A similar role for codon usage bias was also observed in mouse cells. Together, these results suggest that codon usage biases co-evolve with the transcription termination machinery to suppress premature termination of transcription and thus allow for optimal gene expression.


Via Pierre-Marc Delaux
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Subtilisin‐like proteases in plant defence: the past, the present and beyond - Figueiredo - 2018 - Molecular Plant Pathology -

Subtilisin‐like proteases in plant defence: the past, the present and beyond - Figueiredo - 2018 - Molecular Plant Pathology - | evolutionary genomics of host microbe interactions | Scoop.it
Subtilisin‐like proteases (or subtilases) are a very diverse family of serine peptidases present in many organisms, but mostly in plants. With a broad spectrum of biological functions, ranging from protein turnover and plant development to interactions with the environment, subtilases have been gaining increasing attention with regard to their involvement in plant defence responses against the most diverse pathogens. Over the last 5 years, the number of published studies associating plant subtilases with pathogen resistance and plant immunity has increased tremendously. In addition, the observation of subtilases and serine protease inhibitors secreted by pathogens has also gained prominence. In this review, we focus on the active participation of subtilases in the interactions established by plants with the environment, highlighting their role in plant–pathogen communication.
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Microbial interactions within the plant holobiont | Microbiome |

Microbial interactions within the plant holobiont | Microbiome | | evolutionary genomics of host microbe interactions | Scoop.it
Since the colonization of land by ancestral plant lineages 450 million years ago, plants and their associated microbes have been interacting with each other, forming an assemblage of species that is often referred to as a “holobiont.” Selective pressure acting on holobiont components has likely shaped plant-associated microbial communities and selected for host-adapted microorganisms that impact plant fitness. However, the high microbial densities detected on plant tissues, together with the fast generation time of microbes and their more ancient origin compared to their host, suggest that microbe-microbe interactions are also important selective forces sculpting complex microbial assemblages in the phyllosphere, rhizosphere, and plant endosphere compartments. Reductionist approaches conducted under laboratory conditions have been critical to decipher the strategies used by specific microbes to cooperate and compete within or outside plant tissues. Nonetheless, our understanding of these microbial interactions in shaping more complex plant-associated microbial communities, along with their relevance for host health in a more natural context, remains sparse. Using examples obtained from reductionist and community-level approaches, we discuss the fundamental role of microbe-microbe interactions (prokaryotes and micro-eukaryotes) for microbial community structure and plant health. We provide a conceptual framework illustrating that interactions among microbiota members are critical for the establishment and the maintenance of host-microbial homeostasis.

Via Stéphane Hacquard, Matt Agler, Steve Marek
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Sniffing bacterial volatile compounds for healthier plants

Sniffing bacterial volatile compounds for healthier plants | evolutionary genomics of host microbe interactions | Scoop.it
Bacterial volatile compounds (BVCs) are not waste or by-products of primary metabolism but rather have critical roles in the biology and ecological competence of bacteria. BVCs are exploited as a source of nutrients and information in plant–bacteria interactions. They target key points in plant physiology, activating downstream metabolic pathways by a domino effect. BVCs are an ancient signal and are involved in plant–bacteria communication, which was shaped during evolutionary history and established before the development of higher plants. This type of communication is not exclusive to mutualistic interactions, because pathogens also use volatiles to alter plant physiology. Here, fragmented information is drawn together to provide a clearer view of how BVCs affect such interactions.

Via Philip Carella
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Effects of timber harvesting on the genetic potential for carbon and nitrogen cycling in five North American forest ecozones

Effects of timber harvesting on the genetic potential for carbon and nitrogen cycling in five North American forest ecozones | evolutionary genomics of host microbe interactions | Scoop.it

Forest ecosystems are critical to global biogeochemical cycles but under pressure from harvesting and climate change. We investigated the effects of organic matter (OM) removal during forest harvesting on the genetic potential of soil communities for biomass decomposition and nitrogen cycling in five ecozones across North America. We analyzed 107 samples, representing four treatments with varied levels of OM removal, at Long-Term Soil Productivity Study sites. Samples were collected more than ten years after harvesting and replanting and were analyzed via shotgun metagenomics. High-quality short reads totaling 1.2 Tbp were compared to the Carbohydrate Active Enzyme (CAZy) database and a custom database of nitrogen cycle genes. Gene profile variation was mostly explained by ecozone and soil layer. Eleven CAZy and nine nitrogen cycle gene families were associated with particular soil layers across all ecozones. Treatment effects on gene profiles were mainly due to harvesting, and only rarely to the extent of OM removal. Harvesting generally decreased the relative abundance of CAZy genes while increasing that of nitrogen cycle genes, although these effects varied among ecozones. Our results suggest that ecozone-specific nutrient availability modulates the sensitivity of the carbon and nitrogen cycles to harvesting with possible consequences for long-term forest sustainability.


Via Petr Baldrian, Francis Martin
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Symbiont interactions with non-native hosts limit the formation of new symbioses | BMC Evolutionary Biology | Full Text

Symbiont interactions with non-native hosts limit the formation of new symbioses | BMC Evolutionary Biology | Full Text | evolutionary genomics of host microbe interactions | Scoop.it

Facultative symbionts are common in eukaryotes and can provide their hosts with significant fitness benefits. Despite the advantage of carrying these microbes, they are typically only found in a fraction of the individuals within a population and are often non-randomly distributed among host populations. It is currently unclear why facultative symbionts are only found in certain host individuals and populations. Here we provide evidence for a mechanism to help explain this phenomenon: that when symbionts interact with non-native host genotypes it can limit the horizontal transfer of symbionts to particular host lineages and populations of related hosts. Using reciprocal transfections of the facultative symbiont Hamiltonella defensa into different pea aphid clones, we demonstrate that particular symbiont strains can cause high host mortality and inhibit offspring production when injected into aphid clones other than their native host lineage. However, once established, the symbiont’s ability to protect against parasitoids was not influenced by its origin. We then demonstrate that H. defensa is also more likely to establish a symbiotic relationship with aphid clones from a plant-adapted population (biotype) that typically carry H. defensa in nature, compared to clones from a biotype that does not normally carry this symbiont. These results provide evidence that certain aphid lineages and populations of related hosts are predisposed to establishing a symbiotic relationship with H. defensa. Our results demonstrate that host-symbiont genotype interactions represent a potential barrier to horizontal transmission that can limit the spread of symbionts, and adaptive traits they carry, to certain host lineages. 

Photo Cred: Myrmecos Blog


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Convergent and Divergent Signaling in PAMP-Triggered Immunity and Effector-Triggered Immunity | Molecular Plant-Microbe Interactions

Convergent and Divergent Signaling in PAMP-Triggered Immunity and Effector-Triggered Immunity | Molecular Plant-Microbe Interactions | evolutionary genomics of host microbe interactions | Scoop.it
Plants use diverse immune receptors to sense pathogen attacks. Recognition of pathogen-associated molecular patterns (PAMPs) by pattern recognition receptors localized on the plasma membrane leads to PAMP-triggered immunity (PTI). Detection of pathogen effectors by intracellular or plasma membrane–localized immune receptors results in effector-triggered immunity (ETI). Despite the large variations in the magnitude and duration of immune responses triggered by different PAMPs or pathogen effectors during PTI and ETI, plasma membrane–localized immune receptors activate similar downstream molecular events such as mitogen-activated protein kinase activation, oxidative burst, ion influx, and increased biosynthesis of plant defense hormones, indicating that defense signals initiated at the plasma membrane converge at later points. On the other hand, activation of ETI by immune receptors localized to the nucleus appears to be more directly associated with transcriptional regulation of defense gene expression. Here, we review recent progress in signal transductions downstream of different groups of plant immune receptors, highlighting the converging and diverging molecular events.
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Together Forever: Bacterial–Viral Interactions in Infection and Immunity

Together Forever: Bacterial–Viral Interactions in Infection and Immunity | evolutionary genomics of host microbe interactions | Scoop.it
Most viruses first encounter host cells at mucosal surfaces, which are typically colonized by a complex ecosystem of microbes collectively referred to as the microbiota. Recent studies demonstrate the microbiota plays an important role in mediating host–viral interactions and determining the outcomes of these encounters. This review outlines recently described examples of how bacteria and viruses impact each other particularly during infectious processes. Mechanistically, these effects can be broadly categorized as reflecting direct bacterial–viral interactions and/or involving microbial impacts upon innate and/or adaptive immunity.

Via Cindy
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Functional and Expression Analyses of the Pneumocystis MAT Genes Suggest Obligate Sexuality through Primary Homothallism within Host Lungs

Functional and Expression Analyses of the Pneumocystis MAT Genes Suggest Obligate Sexuality through Primary Homothallism within Host Lungs | evolutionary genomics of host microbe interactions | Scoop.it
Fungi of the genus Pneumocystis colonize the lungs of mammals. In immunosuppressed human hosts, Pneumocystis jirovecii may cause severe pneumonia that can be fatal. This disease is one of the most frequent life-threatening invasive fungal infections in humans. The analysis of the genome sequences of these uncultivable pathogens suggested that their sexual reproduction involves a single partner (self-fertilization). Here, we report laboratory experiments that support this hypothesis. The function of the three genes responsible for sexual differentiation was ascertained by the restoration of sexual reproduction in the corresponding mutant of another fungus. As predicted by self-fertilization, all P. jirovecii isolates harbored the same three genes that were often concomitantly expressed within human lungs during infection. Our observations suggest that the sexuality of these pathogens relies on the self-fertility of each isolate and is obligate within host lungs to complete the cell cycle and allow dissemination of the fungus to new hosts.

Via Steve Marek
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Cell-Free Approaches in Synthetic Biology Utilizing Microfluidics

Synthetic biology is a rapidly growing multidisciplinary branch of science which aims to mimic complex biological systems by creating similar forms. Constructing an artificial system requires optimization at the gene and protein levels to allow the formation of entire biological pathways. Advances in cell-free synthetic biology have helped in discovering new genes, proteins, and pathways bypassing the complexity of the complex pathway interactions in living cells. Furthermore, this method is cost- and time-effective with access to the cellular protein factory without the membrane boundaries. The freedom of design, full automation, and mimicking of in vivo systems reveal advantages of synthetic biology that can improve the molecular understanding of processes, relevant for life science applications. In parallel, in vitro approaches have enhanced our understanding of the living system. This review highlights the recent evolution of cell-free gene design, proteins, and cells integrated with microfluidic platforms as a promising technology, which has allowed for the transformation of the concept of bioprocesses. Although several challenges remain, the manipulation of biological synthetic machinery in microfluidic devices as suitable 'homes' for in vitro protein synthesis has been proposed as a pioneering approach for the development of new platforms, relevant in biomedical and diagnostic contexts towards even the sensing and monitoring of environmental issues.

Via Gerd Moe-Behrens
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Spatial organization of bacterial populations in response to oxygen and carbon counter-gradients in pore networks

Spatial organization of bacterial populations in response to oxygen and carbon counter-gradients in pore networks | evolutionary genomics of host microbe interactions | Scoop.it

Microbial activity in soil is spatially heterogeneous often forming spatial hotspots that contribute disproportionally to biogeochemical processes. Evidence suggests that bacterial spatial organization contributes to the persistence of anoxic hotspots even in unsaturated soils. Such processes are difficult to observe in situ at the microscale, hence mechanisms and time scales relevant for bacterial spatial organization remain largely qualitative. Here we develop an experimental platform based on glass-etched micrometric pore networks that mimics resource gradients postulated in soil aggregates to observe spatial organization of fluorescently tagged aerobic and facultative anaerobic bacteria. Two initially intermixed bacterial species, Pseudomonas putida and Pseudomonas veronii, segregate into preferential regions promoted by opposing gradients of carbon and oxygen (such persistent coexistence is not possible in well-mixed cultures). The study provides quantitative visualization and modeling of bacterial spatial organization within aggregate-like hotspots, a key step towards developing a mechanistic representation of bacterial community organization in soil pores.


Via Giannis Stringlis, Tatsuya Nobori
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