Biology subjects

Currie, C. R.

Publications and source records attributed to Currie, C. R..

17 recordsLinked to original sources

bioRxiv2026

Bioactive Natural Products Produced by Streptomyces from the Microbiome of Cadaveric Fly Larvae

Streptomyces are prolific producers of bioactive compounds and increasingly recognized as members of insect microbiomes, yet the microbiome of cadaveric fly larvae remain an overlooked system for discovering metabolically versatile Streptomyces species. Here, we conduct targeted bacterial isolations from the microbiome of fly larvae collected from pig cadavers, generating 42 Streptomyces isolates of interest, and systematically evaluated their metabolic potential through genomic analysis, antimicrobial screening, biosynthetic gene cluster assessment, untargeted LC-MS/MS metabolomics, and compound purification. The Streptomyces isolates spanned nine species, including underrepresented lineages for which we added genomic representatives. Streptomyces from carrion fly larvae exhibited broad-spectrum antimicrobial activity and substantial BGC diversity, supported by metabolomic detection of antimycins, surugamides, and macrotetrolides. From a deep phylogenetic lineage, we purified JBIR-68 and Simamycin and demonstrated their potent anthelmintic activity against Brugia malayi microfilariae. GNPS molecular networking revealed three additional JBIR-68 analogs, establishing the first taxonomically resolved Streptomyces lineage capable of producing these rare metabolites. Our findings position cadaveric fly larvae as a rich ecological reservoir for discovering Streptomyces with the potential to produce chemically diverse natural products with biomedical applications.

biochemistry↗

bioRxiv2026

The Evolution of Biomineral Armor in Fungus-farming Ants

Biomineralization has enabled remarkable adaptations across the animal kingdom, including defensive structures and rock-grinding teeth. Although calcium carbonate is a common biogenically formed mineral found in all extant animal phyla, it is only recently known in insects and almost universally occurs with minimal magnesium content. A high-Mg calcite armor layer, covering most of the exoskeleton, was recently discovered in the fungus-farming ant Acromyrmex echinatior. Here, using a combination of scanning electron microscopy, energy-dispersive spectroscopy, and X-ray diffraction, paired with genome-scale phylogenetic analysis based on ultraconserved elements (UCEs), we characterize the evolution of biomineralization in fungus-farming ants. We show the presence of high-Mg calcite biomineral in 35 of 50 fungus-farming ant species studied, including taxa that span all major agricultural lineages. The biomineral is absent in all 16 myrmicine outgroup ant species, indicating an origin of the biomineral within ant agriculture, with ancestral state reconstruction analysis slightly supporting multiple origins within the fungus-farming ant clade. We then show that the occurrence of the biomineral is closely associated with the ancient mutualism with antimicrobial-producing Pseudonocardia, finding biomineral presence to be significantly correlated with the Pseudonocardia symbiont and the cuticular symbiotic structures that maintain these bacteria. Furthermore, we reveal significant inter-species variation in mineral composition and coverage, as well as intra-colony caste-specific differences, highlighting its adaptive complexity. Collectively, this work demonstrates that the innovation of a high-Mg calcite armor is strongly associated with the evolution of ant agriculture, revealing a rare biomineral to be widespread in the fungus-farming ants.

evolutionary biology↗

bioRxiv2026

Ecological Interactions Drive Metabolomic Diversification in Amazonian Pseudonocardia Symbionts

Fungus-growing ants engage in a multipartite symbiosis, including Pseudonocardia bacteria that produce antifungal metabolites to protect their fungal cultivar from the specialized pathogen Escovopsis. While different bioactive metabolites have been reported from ant-associated Pseudonocardia, most studies have focused on a limited number of strains, leaving the extent of chemical diversity across broader ecological contexts less resolved. Here, we investigated the antagonistic potential and metabolomic repertoires of 36 Pseudonocardia strains isolated from Amazonian Paratrachymyrmex ants. Pairwise bioactivity assays against two Escovopsis isolates revealed striking variability, with inhibition generally stronger and more diverse against the pathogenic fungus originating from the same ant genus. Untargeted LC-MS/MS metabolomics coupled with 16S rRNA-based phylogenetic analyses showed that closely related strains harbored highly divergent chemical profiles, underscoring a decoupling between taxonomy and metabolite output. Detailed analyses of selected isolates revealed the production of structurally diverse metabolites, including dentigerumycin analogs, provipeptide A, {beta}-carbolines, and tetracycline-related compounds. Co-culture analysis uncovered metabolites absent in monocultures, including lichenysins, pepstatins, and hallobacillins, as well as conserved attinimicin, whose production was enhanced under pathogen challenge. These results highlight that both strain-specific metabolic repertoires and interaction-induced chemistry contribute to the defensive arsenal of Pseudonocardia. Together, our findings likely demonstrate that ecological pressures and local adaptation, rather than phylogeny alone, drive metabolomic diversification in this defensive symbiosis. Beyond their potential for novel bioactive compound discovery, these results provide insights into the chemical basis of multipartite symbioses, the dynamics of defensive mutualisms, and the ecological forces shaping microbial diversity in underexplored environments such as the Amazon. IMPORTANCEMicrobial symbionts are central to host defense and natural product discovery, yet the factors driving their chemical diversification remain unclear. The fungus-growing ant-Pseudonocardia-Escovopsis system offers a powerful model to study how ecological context shapes microbial metabolism. By systematically characterizing multiple Amazonian Pseudonocardia strains, we show that antagonistic capacity and metabolomic repertoires vary widely, even among strains with highly similar 16S rRNA gene sequences, revealing a pronounced discordance between 16S-based phylogenetic relatedness and specialized metabolite production. These findings highlight the likely importance of ecological pressures and local adaptation in shaping metabolomic output, emphasizing symbiotic actinobacteria as both key ecological players and promising sources of antifungal natural products.

microbiology↗

bioRxiv2025

Complex multicellularity linked with expanded chemical arsenals in microbes

Single-celled microorganisms evolving to form cooperative multicellular units represents a key innovation in the history of life. Multicellularity is required for cell differentiation and, as such, is critical to the emergence of biological complexity. Here, we propose and find support for our hypothesis that multicellularity facilitated massive expansions in the biosynthetic potential to produce specialized metabolites across microbial life. Our systematic characterization of biosynthetic gene clusters (BGCs) across bacteria confirms that most taxa have limited predicted potential to produce natural products. In contrast with primarily unicellular lineages, we show that the origins of biosynthetic expansion in Actinomycetota, Cyanobacteriota, and Myxococcota coincide with independent origins of multicellular structures such as mycelia, filaments, and fruiting bodies. Further, we reveal that the two primary origins of expansions in specialized metabolism for fungi, corresponding to the Pezizomycotina and Agaricomycetes, similarly coincide with the emergence of complex multicellularity and fruiting body formation as well as mechanisms for self-identification during haplontic life cycles. Interestingly, all five of the biosynthetically talented multicellular microbial lineages are concomitantly enriched in carbohydrate utilization enzymes, suggesting that ancient chemical innovations have been further shaped by catabolic processes. Intraspecific cooperation shaping the evolution of specialized metabolism further informs our understanding of the major transitions in life and will help guide efforts to discover new antimicrobial compounds to counter the emergence of antibiotic resistance.

evolutionary biology↗

bioRxiv2024

Upper respiratory microbial communities of healthy populations are shaped by niche and age

BackgroundAlterations in upper respiratory microbiomes have been implicated in shaping host health trajectories, including by limiting mucosal pathogen colonization. However, limited comparative studies of respiratory microbiome development and functioning across age groups have been performed. Herein, we perform shotgun metagenomic sequencing paired with pathogen inhibition assays to elucidate differences in nasal and oral microbiome composition and functioning across healthy 24-month-old infant (n=229) and adult (n=100) populations. ResultsWe find that beta diversity of nasal and oral microbiomes varies with age, with nasal microbiomes showing greater population-level variation compared to oral microbiomes. Infant microbiome alpha diversity was significantly lower across nasal samples and higher in oral samples, relative to adults. Accordingly, we demonstrate significant differences in genus- and species-level composition of microbiomes between sites and age groups. Antimicrobial resistome patterns likewise varied across body sites, with oral microbiomes showing higher resistance gene abundance compared to nasal microbiomes. Biosynthetic gene clusters encoding specialized metabolite production were found in higher abundance across infant oral microbiomes, relative to adults. Investigation of pathogen inhibition revealed greater inhibition of gram-negative and gram-positive bacteria by oral commensals, while nasal isolates had higher antifungal activity. ConclusionsIn summary, we identify significant differences in the microbial communities inhabiting nasal and oral cavities of healthy infants relative to adults. These findings inform our understanding of the interactions impacting respiratory microbiome composition and functioning, with important implications for host health across the lifespan.

microbiology↗

bioRxiv2023

Disturbance-Diversity Relationships of Microbial Communities Change Based on Growth Substrate

Disturbance events can impact ecological community dynamics. Understanding how communities respond to disturbances, and how those responses can vary, is a challenge in microbial ecology. In this study, we grew a previously enriched specialized microbial community on either cellulose or glucose as a sole carbon source, and subjected them to one of five different disturbance regimes of varying frequencies ranging from low to high. Using 16S rRNA gene amplicon sequencing, we show that community structure is largely driven by substrate, but disturbance frequency affects community composition and successional dynamics. When grown on cellulose, bacteria in the genera Cellvibrio, Lacunisphaera, and Asticaccacaulis are the most abundant microbes. However, Lacunisphaera is only abundant in the lower disturbance frequency treatments, while Asticaccaulis is more abundant in the highest disturbance frequency treatment. When grown on glucose, the most abundant microbes are two Pseudomonas sequence variants, and a Cohnella sequence variant that is only abundant in the highest disturbance frequency treatment. Communities grown on cellulose exhibited a greater range of diversity (0.67-1.99 Shannon diversity and 1.38-5.25 Inverse Simpson diversity) that peak at the intermediate disturbance frequency treatment, or 1 disturbance every 3 days. Communities grown on glucose, however, ranged from 0.49-1.43 Shannon diversity and 1.37-3.52 Inverse Simpson with peak diversity at the greatest disturbance frequency treatment. These results demonstrate that the dynamics of a microbial community can vary depending on substrate and the disturbance frequency, and may potentially explain the variety of diversity-disturbance relationships observed in microbial ecosystems. Abstract ImportanceA generalizable diversity-disturbance relationship (DDR) of microbial communities remains a contentious topic. Various microbial systems have different DDRs. Rather than finding support or refuting specific DDRs, we investigated the underlying factors that lead to different DDRs. In this study, we measured a cellulose-enriched microbial communitys response to a range of disturbance frequencies from high to low, across two different substrates: cellulose and glucose. We demonstrate that the community displays a unimodal DDR when grown on cellulose, and a monotonically increasing DDR when grown on glucose. Our findings suggest that the same community can display different DDRs. These results suggest that the range of DDRs we observe across different microbial systems may be due to the nutritional resources microbial communities can access and the interactions between bacteria and their environment.

microbiology↗

bioRxiv2023

Bacillus subtilis derived lipopeptides disrupt quorum sensing and biofilm assembly in Staphylococcus aureus

Multidrug-resistant Staphylococcus aureus is one of the most clinically important pathogens in the world with infections leading to high rates of morbidity and mortality in both humans and animals. S. aureus ability to form biofilm protects individual cells from antibiotics and promotes the transfer of antibiotic resistance genes. Therefore, new strategies aimed to inhibit biofilm growth and disassemble mature biofilms are urgently needed. Probiotic species, namely Bacillus subtilis, are gaining interest as a potential therapeutic against S. aureus for their ability to reduce S. aureus colonization and virulence. Here, we collected and screened 1123 Bacillus strains obtained from a variety of agricultural environments in search of isolates with strong antibiofilm activity against clinical multi-drug resistant S. aureus. We selected a single strain, B. subtilis 6D1, based on its ability to inhibit biofilm growth, disassemble mature biofilm, and improve antibiotic sensitivity of S. aureus biofilms through an Agr quorum sensing interference mechanism. Biochemical and molecular networking analysis of an active organic fraction revealed multiple surfactin isoforms and an uncharacterized compound were both driving this antibiofilm activity. Furthermore, when compared against commercial HPLC grade surfactin obtained from B. subtilis, this active fraction inhibited biofilm formation against all four S. aureus Agr backgrounds and prevented S. aureus-induced cytotoxicity when applied to HT29 human intestinal cell lines better than the commercial standard. Our results demonstrate the mixture of compounds produced by B. subtilis 6D1 can mitigate S. aureus virulence through multiple mechanisms. Contribution to the FieldThe biofilm formation capability of bacterial pathogens, such as Staphylococcus aureus, increases these microorganisms virulence potential and decreases the efficacy of common antibiotic regiments. Probiotics possess a variety of strain-specific strategies to reduce biofilm formation in competing organisms, however, the mechanisms and compounds responsible for these phenomena often go uncharacterized. In this study, we identified a mixture of small probiotic-derived peptides capable of Agr quorum sensing interference as one of the mechanisms driving antibiofilm activity against S. aureus. This collection of peptides also improved antibiotic killing and protected human gut epithelial cells from S. aureus-induced toxicity by stimulating an adaptive immune response. We conclude that purposeful strain screening and selection efforts can be used to identify unique probiotic strains that possess specially desired mechanisms of action. This information can be used to further improve our understanding of the ways in which probiotic and probiotic-derived compounds can be applied to prevent bacterial infections in clinical and agricultural settings.

microbiology↗

bioRxiv2021

Burkholderia from fungus gardens of fungus-growing ants produce antifungals that inhibit the specialized parasite Escovopsis

Within animal associated microbiomes, the functional roles of specific microbial taxa are often uncharacterized. Here, we use the fungus-growing ant system, a model for microbial symbiosis, to determine the potential defensive roles of key bacterial taxa present in the ants fungus gardens. Fungus gardens serve as an external digestive system for the ants, with mutualistic fungi in the genus Leucoagaricus spp. converting plant substrate into energy for the ants. The fungus garden is host to specialized parasitic fungi in the genus Escovopsis. Here, we examine the potential role of Burkholderia spp. that occur within ant fungus gardens in inhibiting Escovopsis. We isolated members of the bacterial genera Burkholderia spp. and Paraburkholderia spp. from 50% of the 52 colonies sampled, indicating that the family Burkholderiaceae are common fungus garden inhabitants of a diverse range of fungus-growing ant genera. Using antimicrobial inhibition bioassays, we found that 28 out of 32 isolates inhibited at least one Escovopsis strain with a zone of inhibition greater than 1 cm. Genomic assessment of Burkholderiaceae isolates indicated that isolates with strong inhibition all belonged to the genus Burkholderia and contained biosynthetic gene clusters that encoded the production of two antifungals: burkholdine1213 and pyrrolnitrin. Organic extracts of cultured isolates confirmed these compounds as responsible for antifungal activity that inhibit Escovopsis but, at low concentrations, not Leucoagaricus spp. Overall, these new findings, combined with previous evidence, suggest that members of the fungus garden microbiome play an important role in maintaining the health and function of the fungus-farming ant colony. IMPORTANCEMany organisms partner with microbes to defend themselves against parasites and pathogens. Fungus-growing ants must protect Leucoagaricus spp., the fungal mutualist that provides sustenance for the ants, from a specialized fungal parasite, Escovopsis spp. The ants take multiple approaches, including weeding their fungus gardens to remove Escovopsis spores, as well as harboring Pseudonocardia that produce antifungals that inhibit Escovopsis. In addition, a genus of bacteria commonly found in fungus gardens, Burkholderia spp., is known to produce secondary metabolites that inhibit Escovopsis spp. In this study, we isolated Burkholderia spp. from fungus-growing ants, assessed the isolates ability to inhibit Escovopsis spp., and identified two compounds responsible for inhibition. Our findings suggest that Burkholderia spp. are often found in fungus gardens, adding another possible mechanism within the fungus-growing ant system to suppress the growth of the specialized parasite Escovopsis.

microbiology↗

bioRxiv2020

Long-term cellulose enrichment selects for highly cellulolytic consortia and competition for public goods

The complexity of microbial communities hinders our understanding of how microbial diversity and microbe-microbe interactions impact community functions. Here, using six independent communities originating from the refuse dumps of leaf-cutter ants and enriched using the plant polymer cellulose as the sole source of carbon, we examine how changes in bacterial diversity and interactions impact plant biomass decomposition. Over up to 60 serial transfers ([~]8 months), cellulolytic ability increased then stabilized in four enrichment lines and was variable in two lines. Bacterial community characterization using 16S rRNA gene amplicon sequencing showed community succession differed between the highly cellulolytic and variably cellulolytic enrichment lines. Metagenomic and metatranscriptomic analyses revealed that Cellvibrio and/or Cellulomonas dominated each enrichment line and produced the majority of cellulase enzymes, while diverse taxa were retained within these communities over the duration of transfers. Interestingly, the less cellulolytic communities had a higher diversity of organisms competing for the cellulose breakdown product cellobiose, suggesting that cheating slowed cellulose degradation. In addition, we found competitive exclusion as an important factor shaping all the communities, with the mutual exclusion of specific cellulolytic taxa within individual enrichment lines and the high expression of genes associated with the production of antagonistic compounds. Our results provide insights into how microbial diversity and competition affect the stability and function of cellulose-degrading communities. ImportanceMicrobial communities are a key driver of the carbon cycle through the breakdown of complex polysaccharides in diverse environments including soil, marine systems, and the mammalian gut.However, due to the complexity of these communities, the species-species interactions that impact community structure and ultimately shape the rate of decomposition are difficult to define. Here we performed serial enrichment on cellulose using communities inoculated from leaf-cutter ant refuse dumps, a cellulose-rich environment. By concurrently tracking cellulolytic ability and community composition and through metagenomic and metatranscriptomic sequencing, we analyzed the ecological dynamics of the enrichment lines. Our data suggest that antagonism is prevalent in these communities and that competition for soluble sugars may slow degradation and lead to community instability. Together, these results help reveal the relationships between competition and polysaccharide decomposition, with implications in diverse areas ranging from microbial community ecology to cellulosic biofuels production.

microbiology↗

bioRxiv2020

Experimental warming reduces gut prokaryotic diversity, survival and thermal tolerance of the eastern subterranean termite, Reticulitermes flavipes (Kollar)

Understanding the effects of environmental disturbances on the health and physiology of insects is crucial in predicting the impact of climate change on their distribution, abundance, and ecology. As microbial symbionts have been shown to play an integral role in a diversity of functions within the insect host, research examining how organisms adapt to environmental fluctuations should include their associated microbiota. Previous studies have shown that temperature affects the diversity of protists in termite gut, but less is known about the bacterial symbionts. In this study, subterranean termites (Reticulitermes flavipes (Kollar)) were exposed to three different temperature treatments characterized as low (15 {degrees}C), medium (27 {degrees}C), and high (35 {degrees}C). Results showed low temperature exposed termites had significantly lower CTmin and significantly higher SCP values compared to termites from medium or high temperature groups. This suggests that pre-exposure to cold allowed termites to stay active longer in decreasing temperatures but caused termites to freeze at higher temperatures. High temperature exposure had the most deleterious effects on termites with a significant reduction in termite survival as well as reduced ability to withstand cold stress. The microbial community of high temperature exposed termites showed a reduction in bacterial richness and decreased relative abundance of Spirochaetes, Elusimicrobia, and methanogenic Euryarchaeota. Our results indicate a potential link between gut bacterial symbionts and termites physiological response to environmental changes and highlight the need to consider microbial symbionts in studies relating to insect thermosensitivity.

microbiology↗

bioRxiv2020

From plants to ants: Fungal modification of leaf lipids for nutrition and communication in the leaf-cutter ant fungal garden ecosystem

Lipids are essential to all living organisms, as an energy source, as an important cellular structural component, and as a communication tool. In this study, we used global lipidomic methods to evaluate the lipids in leaf-cutter ant fungal gardens. Leaf-cutter ants and their coevolved fungal cultivar, Leucoagaricus gongylophorus, are a model mutualistic system. The fungus enzymatically digests fresh plant material that the ants cut and deliver, converting energy and nutrients from plants, and providing them to the ants through specialized hyphal swellings called gongylidia. Using combined liquid chromatography, ion mobility spectrometry, and tandem mass spectrometry we evaluated differences between the molecular speciation of lipids in the leaf-cutter ant fungal garden ecosystem. This lipidomic study characterized leaves that are fed to the gardens, gongylidia that are produced by the fungus to feed the ants, and spatially resolved regions of the fungal garden through stages of leaf degradation. Lipids containing alpha-linolenic acid (18:3) were enriched in leaves and the top of the gardens, but not dominant in the middle or bottom regions. Gongylidia were dominated by lipids containing linoleic acid (18:2). To evaluate the communicative potential of the lipids in fungal gardens we conducted a behavioral experiment that showed Atta leaf-cutter ants responded differently to 18:3 and 18:2 fatty acids, with aggression towards 18:3 and attraction for 18:2. This work demonstrates the role of lipids in both the transfer of energy and as an inter-kingdom communication tool in leaf-cutter ant fungal gardens. ImportanceIn this work we examined the role of lipids in the mutualism between leaf-cutter ants and fungus. These ants cut fresh leaf material, which they provide to their fungal cultivar, that converts energy and nutrients from the plants and provides it to the ants in specialized hyphal swellings called gongylidia. This work constitutes the first example of a global lipidomics study of a symbiotic system and provides insights as to how the fungus modifies plant lipids into a usable source for the ants. Through a behavioral experiment, this work also demonstrates how lipids can be used as an inter-kingdom communication tool, in this case an attractant, rather than as a repellant, which is more often seen.

systems biology↗

bioRxiv2020

Biomineral armor in leaf-cutter ants

Although calcareous anatomical structures have evolved in diverse animal groups, such structures have been unknown in insects. Here, we report the discovery of high-magnesium calcite [CaMg(CO3)2] armor overlaying the exoskeletons of major workers of the leaf-cutter ant Acromyrmex echinatior. Live-rearing and in vitro synthesis experiments indicate that the biomineral layer accumulates rapidly as ant workers mature, that the layer is continuously distributed, covering nearly the entire integument, and that the ant epicuticle catalyzes biomineral nucleation and growth. In situ nanoindentation demonstrates that the biomineral layer significantly hardens the exoskeleton. Increased survival of ant workers with biomineralized exoskeletons during aggressive encounters with other ants and reduced infection by entomopathogenic fungi demonstrate the protective role of the biomineral layer. The discovery of biosynthesized high-magnesium calcite in the relatively well-studied leaf-cutting ants suggests that calcareous biominerals enriched in magnesium may be more common in metazoans than previously recognized.

biophysics↗

bioRxiv2019

Bacteria contribute to plant secondary compound degradation in a generalist herbivore system

Herbivores must overcome a variety of plant defenses, including coping with plant secondary compounds (PSCs). To help detoxify these defensive chemicals, several insect herbivores are known to harbor gut microbiota with the metabolic capacity to degrade PSCs. Leaf-cutter ants are generalist herbivores, obtaining sustenance from specialized fungus gardens that act as external digestive systems, degrading the diverse collection of plants foraged by the ants. There is in vitro evidence that certain PSCs harm Leucoagaricus gongylophorus, the fungal cultivar of leaf-cutter ants, suggesting a role for the Proteobacteria-dominant bacterial community present within fungus gardens. Here, we investigate the ability of symbiotic bacteria present within fungus gardens of leaf-cutter ants to degrade PSCs. We cultured fungus garden bacteria, sequenced the genomes of 42 isolates, and identified genes involved in PSC degradation, including genes encoding cytochrome p450s and genes in geraniol, cumate, cinnamate, and -pinene/limonene degradation pathways. Using metatranscriptomic analysis, we show that some of these degradation genes are expressed in situ. Most of the bacterial isolates grew unhindered in the presence of PSCs and, using GC-MS, we determined that isolates from the genera Bacillus, Burkholderia, Enterobacter, Klebsiella, and Pseudomonas degrade -pinene, {beta}-caryophyllene, or linalool. Using a headspace sampler, we show that sub-colonies of fungus gardens reduced -pinene and linalool over a 36-hour period, while L. gongylophorus strains alone only reduced linalool. Overall, our results reveal that the bacterial community in fungus gardens play a pivotal role in alleviating the effect of PSCs on the leaf-cutter ant system. ImportanceLeaf-cutter ants are dominant neotropical herbivores capable of deriving energy from a wide range of plant substrates. The success of leaf-cutter ants is largely due to their external gut composed of key microbial symbionts, specifically, the fungal mutualist L. gongylophorus and a consistent bacterial community. Both symbionts are known to have critical roles in extracting energy from plant material, yet comparatively little is known about their role in the detoxification of plant secondary compounds. Here, we assess if the bacterial community associated with leaf-cutter ant fungus gardens can degrade harmful plant chemicals. We identify plant secondary compound detoxification in leaf-cutter ant gardens as a process that depends on the degradative potential of both the bacterial community and L. gongylophorus. Our findings suggest the fungus garden and its associated microbial community influences the generalist foraging abilities of the ants, underscoring the importance of microbial symbionts in plant substrate suitability for herbivores.

ecology↗

bioRxiv2019

Biogeography and Microscale Diversity Shape the Biosynthetic Potential of Fungus-growing Ant-associated Pseudonocardia

The geographic and phylogenetic scale of ecologically relevant microbial diversity is still poorly understood. Using a model mutualism, fungus-growing ants and their defensive bacterial associate Pseudonocardia, we analyzed genetic diversity and biosynthetic potential in 46 strains isolated from ant colonies in a 20km transect near Barro Colorado Island in Panama. Despite an average pairwise core genome similarity of greater than 99%, population genomic analysis revealed several distinct bacterial populations matching ant host geographic distribution. We identified both genetic diversity signatures and divergent genes distinct to each lineage. We also identify natural product biosynthesis clusters specific to isolation locations. These geographic patterns were observable despite the populations living in close proximity to each other and provides evidence of ongoing genetic exchange. Our results add to the growing body of literature suggesting that variation in traits of interest can be found at extremely fine phylogenetic scales.

microbiology↗

bioRxiv2019

Cycloheximide-Producing Streptomyces Associated with Xyleborinus saxesenii and Xyleborus affinis Fungus-Farming Ambrosia Beetles

Symbiotic microbes help a myriad of insects acquire nutrients. Recent work suggests that insects also frequently associate with actinobacterial symbionts that produce molecules to help defend against parasites and predators. Here we explore a potential association between Actinobacteria and two species of fungus-farming ambrosia beetles, Xyleborinus saxesenii and Xyleborus affinis. We isolated and identified actinobacterial and fungal symbionts from laboratory reared nests, and characterized small molecules produced by the putative actinobacterial symbionts. One 16S rRNA phylotype of Streptomyces (XylebKG-1) was abundantly and consistently isolated from the nests and adults of X. saxesenii and X. affinis nests. In addition to Raffaelea sulphurea, the symbiont that X. saxesenii cultivates, we also repeatedly isolated a strain of Nectria sp. that is an antagonist of this mutualism. Inhibition bioassays between S. griseus XylebKG-1 and the fungal symbionts from X. saxesenii revealed strong inhibitory activity of the actinobacterium towards the fungal antagonist Nectria sp. but not the fungal mutualist R. sulphurea. Bioassay guided HPLC fractionation of S. griseus XylebKG-1 culture extracts, followed by NMR and mass spectrometry identified cycloheximide as the compound responsible for the observed growth inhibition. A biosynthetic gene cluster putatively encoding cycloheximide was also identified in S. griseus XylebKG-1. The consistent isolation of a single 16S phylotype of Streptomyces from two species of ambrosia beetles, and our finding that a representative isolate of this phylotype produces cycloheximide, which inhibits a parasite of the system but not the cultivated fungus, suggests that these actinobacteria may play defensive roles within these systems.

microbiology↗

bioRxiv2018

Bacterial competition mediated by siderophore production among the human nasal microbiota

Resources available in the human nasal cavity are limited. Therefore, to successfully colonize the nasal cavity, bacteria must compete for scarce nutrients. Competition may occur directly through interference (e.g., antibiotics) or indirectly by nutrient sequestration. To investigate the nature of nasal bacterial competition, we performed co-culture inhibition assays between nasal Actinobacteria and Staphylococcus spp. We found that Staphylococcus epidermidis isolates were sensitive to growth inhibition by Actinobacteria but Staphylococcus aureus isolates were resistant to inhibition. Among Actinobacteria, we observed that Corynebacterium spp. were variable in their ability to inhibit S. epidermidis. We sequenced the genomes of ten Corynebacterium spp. isolates, including three Corynebacterium propinquum that strongly inhibited S. epidermidis and seven other Corynebacterium spp. isolates that only weakly inhibited S. epidermidis. Using a comparative genomics approach, we found that the C. propinquum genomes were enriched in genes for iron acquisition and encoded a biosynthetic gene cluster (BGC) for siderophore production, absent in the non-inhibitory Corynebacterium spp. genomes. Using a chromeazurol S assay, we confirmed that C. propinquum produced siderophores. We demonstrated that iron supplementation rescued S. epidermidis from inhibition by C. propinquum, suggesting that inhibition was due to iron restriction through siderophore production. Using comparative metabolomics, we identified the siderophore produced by C. propinquum as dehydroxynocardamine. Finally, we confirmed that the dehydroxynocardamine BGC is expressed in vivo by analyzing human nasal metatranscriptomes from the NIH Human Microbiome Project.\n\nTogether, our results suggest that bacteria produce siderophores to compete for limited available iron in the nasal cavity and improve their fitness.\n\nIMPORTANCEWithin the nasal cavity, interference competition through antimicrobial production is prevalent. For instance, nasal Staphylococcus spp. strains can inhibit the growth of other bacteria through the production of nonribosomal peptides and ribosomally synthesized and post-translationally modified peptides. In contrast, bacteria engaging in exploitation competition modify the external environment to prevent competitors from growing, usually by depleting access to essential nutrients. As the nasal cavity is a nutrient limited environment, we hypothesized that exploitation competition occurs in this system. We determined that Corynebacterium propinquum produces an iron-chelating siderophore and is able to use this molecule to sequester iron and inhibit the growth of Staphylococcus epidermidis. Further, we found that the genes required for siderophore production are expressed in vivo. Thus, though siderophore production by bacteria is often considered a virulence trait, our work indicates that bacteria may produce siderophores to compete for limited iron in the human nasal cavity.

microbiology↗

bioRxiv2018

Metagenomics reveals diet-specific specialization in fungus gardens of grass- and dicot-cutter ants

Leaf-cutter ants in the genus Atta are dominant herbivores in the Neotropics. While most species of Atta cut dicots to incorporate into their fungus gardens, some species specialize on grasses. Here we examine the bacterial community associated with the fungus gardens of grass- and dicot-cutter ants to examine how changes in substrate input affect the bacterial community. We sequenced the metagenomes of 12 Atta fungus gardens, across four species of ants, with a total of 5.316 Gbp of sequence data. We show significant differences in the fungus garden bacterial community composition between dicot- and grass-cutter ants, with grass-cutter ants having lower diversity. Reflecting this difference in community composition, the bacterial functional profiles between the fungus gardens are significantly different. Specifically, grass-cutter ant fungus garden metagenomes are particularly enriched for genes responsible for amino acid, siderophore, and terpenoid biosynthesis while dicot-cutter ant fungus gardens metagenomes are enriched in genes involved in membrane transport. These differences in bacterial community composition and functional capacity show that different substrate inputs matter for fungus garden bacteria, and sheds light on the potential role of bacteria in mediating the ants transition to the use of a novel substrate.

microbiology↗