Candicidin-producing Streptomyces support leaf-cutting ants to protect their fungus garden against the pathogenic fungus Escovopsis

Deletions of conserved extracytoplasmic function sigma factors-encoding genes in Streptomyces have a major impact on secondary metabolism

BACKGROUND

Ethanol shock significantly affects expression of over 1200 genes in Streptomyces venezuelae NRRL B-65,442, including those involved in secondary metabolite biosynthesis and a cryptic gene pepX, which encodes a 19-amino acid peptide with an unknown function.

RESULTS

To establish a possible correlation between the PepX peptide and secondary metabolism in S. venezuelae, its gene was deleted, followed by analyses of the transcriptome and secondary metabolome of the mutant. Although the secondary metabolome of the pepX mutant was not strongly affected, pepX deletion, similar to ethanol shock, mostly resulted in downregulated expression of secondary metabolite biosynthesis gene clusters (BGCs). At the same time, there was a reverse correlation between the expression of certain extracytoplasmic function sigma factors (ECFs) and several BGCs. Individual deletions of three selected ECF-coding genes conserved in Streptomyces that were upregulated upon both pepX deletion and ethanol shock, had a profound positive effect on the expression of BGCs, which also correlated with the overproduction of specific secondary metabolites. Deletion of one such ECF-coding gene in a marine sponge-derived Streptomyces sp. also significantly altered the secondary metabolite profile, suggesting an important role of this ECF in the regulation of secondary metabolism.

CONCLUSIONS

These findings pave the way for the activation or upregulation of BGCs in Streptomyces bacteria harboring genes for ECFs homologous to those identified in this study, hereby assisting in the discovery of novel bioactive secondary metabolites.

The insect microbiome is a vast source of bioactive small molecules

Covering: September 1964 to June 2023Bacteria and fungi living in symbiosis with insects have been studied over the last sixty years and found to be important sources of bioactive natural products. Not only classic producers of secondary metabolites such as Streptomyces and other members of the phylum Actinobacteria but also numerous bacteria from the phyla Proteobacteria and Firmicutes and an impressive array of fungi (usually pathogenic) serve as the source of a structurally diverse number of small molecules with important biological activities including antimicrobial, cytotoxic, antiparasitic and specific enzyme inhibitors. The insect niche is often the exclusive provider of microbes producing unique types of biologically active compounds such as gerumycins, pederin, dinactin, and formicamycins. However, numerous insects still have not been described taxonomically, and in most cases, the study of their microbiota is completely unexplored. In this review, we present a comprehensive survey of 553 natural products produced by microorganisms isolated from insects by collating and classifying all the data according to the type of compound (rather than the insect or microbial source). The analysis of the correlations among the metadata related to insects, microbial partners, and their produced compounds provides valuable insights into the intricate dynamics between insects and their symbionts as well as the impact of their metabolites on these relationships. Herein, we focus on the chemical structure, biosynthesis, and biological activities of the most relevant compounds.

Volatile communication in Actinobacteria: a language for secondary metabolism regulation

BACKGROUND

Volatile compounds are key elements in the interaction and communication between organisms at both interspecific and intraspecific levels. In complex bacterial communities, the emission of these fast-acting chemical messengers allows an exchange of information even at a certain distance that can cause different types of responses in the receiving organisms. The changes in secondary metabolism as a consequence of this interaction arouse great interest in the field of searching for bioactive compounds since they can be used as a tool to activate silenced metabolic pathways. Regarding the great metabolic potential that the Actinobacteria group presents in the production of compounds with attractive properties, we evaluated the reply the emitted volatile compounds can generate in other individuals of the same group.

RESULTS

We recently reported that volatile compounds released by different streptomycete species trigger the modulation of biosynthetic gene clusters in Streptomyces spp. which finally leads to the activation/repression of the production of secondary metabolites in the recipient strains. Here we present the application of this rationale in a broader bacterial community to evaluate volatiles as signaling effectors that drive the activation of biosynthesis of bioactive compounds in other members of the Actinobacteria group. Using cocultures of different actinobacteria (where only the volatile compounds reach the recipient strain) we were able to modify the bacterial secondary metabolism that drives overproduction (e.g., granaticins, actiphenol, chromomycins) and/or de novo production (e.g., collismycins, skyllamycins, cosmomycins) of compounds belonging to different chemical species that present important biological activities.

CONCLUSIONS

This work shows how the secondary metabolism of different Actinobacteria species can vary significantly when exposed in co-culture to the volatile compounds of other phylum-shared bacteria, these effects being variable depending on strains and culture media. This approach can be applied to the field of new drug discovery to increase the battery of bioactive compounds produced by bacteria that can potentially be used in treatments for humans and animals.

Enhanced surface colonisation and competition during bacterial adaptation to a fungus

Bacterial-fungal interactions influence microbial community performance of most ecosystems and elicit specific microbial behaviours, including stimulating specialised metabolite production. Here, we use a co-culture experimental evolution approach to investigate bacterial adaptation to the presence of a fungus, using a simple model of bacterial-fungal interactions encompassing the bacterium Bacillus subtilis and the fungus Aspergillus niger. We find in one evolving population that B. subtilis was selected for enhanced production of the lipopeptide surfactin and accelerated surface spreading ability, leading to inhibition of fungal expansion and acidification of the environment. These phenotypes were explained by specific mutations in the DegS-DegU two-component system. In the presence of surfactin, fungal hyphae exhibited bulging cells with delocalised secretory vesicles possibly provoking an RlmA-dependent cell wall stress. Thus, our results indicate that the presence of the fungus selects for increased surfactin production, which inhibits fungal growth and facilitates the competitive success of the bacterium.

Ecology shapes the genomic and biosynthetic diversification of Streptomyces bacteria from insectivorous bats

Streptomyces are prolific producers of secondary metabolites from which many clinically useful compounds have been derived. They inhabit diverse habitats but have rarely been reported in vertebrates. Here, we aim to determine to what extent the ecological source (bat host species and cave sites) influence the genomic and biosynthetic diversity of Streptomyces bacteria. We analysed draft genomes of 132 Streptomyces isolates sampled from 11 species of insectivorous bats from six cave sites in Arizona and New Mexico, USA. We delineated 55 species based on the genome-wide average nucleotide identity and core genome phylogenetic tree. Streptomyces isolates that colonize the same bat species or inhabit the same site exhibit greater overall genomic similarity than they do with Streptomyces from other bat species or sites. However, when considering biosynthetic gene clusters (BGCs) alone, BGC distribution is not structured by the ecological or geographical source of the Streptomyces that carry them. Each genome carried between 19-65 BGCs (median=42.5) and varied even among members of the same Streptomyces species. Nine major classes of BGCs were detected in ten of the 11 bat species and in all sites: terpene, non-ribosomal peptide synthetase, polyketide synthase, siderophore, RiPP-like, butyrolactone, lanthipeptide, ectoine, melanin. Finally, Streptomyces genomes carry multiple hybrid BGCs consisting of signature domains from two to seven distinct BGC classes. Taken together, our results bring critical insights to understanding Streptomyces-bat ecology and BGC diversity that may contribute to bat health and in augmenting current efforts in natural product discovery, especially from underexplored or overlooked environments.

Biosynthetic potential of the sediment microbial subcommunities of an unexplored karst ecosystem and its ecological implications

Microbial communities from various environments have been studied in the quest for new natural products with a broad range of applications in medicine and biotechnology. We employed an enrichment method and genome mining tools to examine the biosynthetic potential of microbial communities in the sediments of a coastal sinkhole within the karst ecosystem of the Yucatán Peninsula, Mexico. Our investigation led to the detection of 203 biosynthetic gene clusters (BGCs) and 55 secondary metabolites (SMs) within 35 high-quality metagenome-assembled genomes (MAGs) derived from these subcommunities. The most abundant types of BGCs were Terpene, Nonribosomal peptide-synthetase, and Type III polyketide synthase. Some of the in silico identified BGCs and SMs have been previously reported to exhibit biological activities against pathogenic bacteria and fungi. Others could play significant roles in the sinkhole ecosystem, such as iron solubilization and osmotic stress protection. Interestingly, 75% of the BGCs showed no sequence homology with bacterial BGCs previously reported in the MiBIG database. This suggests that the microbial communities in this environment could be an untapped source of genes encoding novel specialized compounds. The majority of the BGCs were identified in pathways found in the genus Virgibacillus, followed by Sporosarcina, Siminovitchia, Rhodococcus, and Halomonas. The latter, along with Paraclostridium and Lysinibacillus, had the highest number of identified BGC types. This study offers fresh insights into the potential ecological role of SMs from sediment microbial communities in an unexplored environment, underscoring their value as a source of novel natural products.

Streptomyces extracellular vesicles are a broad and permissive antimicrobial packaging and delivery system

Streptomyces are the primary source of bioactive specialized metabolites used in research and medicine, including many antimicrobials. These are presumed to be secreted and function as freely soluble compounds. However, increasing evidence suggests that extracellular vesicles are an alternative secretion system. We assessed environmental and lab-adapted Streptomyces (sporulating filamentous actinomycetes) and found frequent production of antimicrobial vesicles. The molecular cargo included actinomycins, anthracyclines, candicidin, and actinorhodin, reflecting both diverse chemical properties and diverse antibacterial and antifungal activity. The levels of packaged antimicrobials correlated with the level of inhibitory activity of the vesicles, and a strain knocked out for the production of anthracyclines produced vesicles that lacked antimicrobial activity. We demonstrated that antimicrobial containing vesicles achieve direct delivery of the cargo to other microbes. Notably, this delivery via membrane fusion occurred to a broad range of microbes, including pathogenic bacteria and yeast. Vesicle encapsulation offers a broad and permissive packaging and delivery system for antimicrobial specialized metabolites, with important implications for ecology and translation.IMPORTANCEExtracellular vesicle encapsulation changes our picture of how antimicrobial metabolites function in the environment and provides an alternative translational approach for the delivery of antimicrobials. We find many Streptomyces strains are capable of releasing antimicrobial vesicles, and at least four distinct classes of compounds can be packaged, suggesting this is widespread in nature. This is a striking departure from the primary paradigm of the secretion and action of specialized metabolites as soluble compounds. Importantly, the vesicles deliver antimicrobial metabolites directly to other microbes via membrane fusion, including pathogenic bacteria and yeast. This suggests future applications in which lipid-encapsulated natural product antibiotics and antifungals could be used to solve some of the most pressing problems in drug resistance.

Antimicrobials: An update on new strategies to diversify treatment for bacterial infections

Ninety-five years after Fleming's discovery of penicillin, a bounty of antibiotic compounds have been discovered, modified, or synthesised. Diversification of target sites, improved stability and altered activity spectra have enabled continued antibiotic efficacy, but overwhelming reliance and misuse has fuelled the global spread of antimicrobial resistance (AMR). An estimated 1.27 million deaths were attributable to antibiotic resistant bacteria in 2019, representing a major threat to modern medicine. Although antibiotics remain at the heart of strategies for treatment and control of bacterial diseases, the threat of AMR has reached catastrophic proportions urgently calling for fresh innovation. The last decade has been peppered with ground-breaking developments in genome sequencing, high throughput screening technologies and machine learning. These advances have opened new doors for bioprospecting for novel antimicrobials. They have also enabled more thorough exploration of complex and polymicrobial infections and interactions with the healthy microbiome. Using models of infection that more closely resemble the infection state in vivo, we are now beginning to measure the impacts of antimicrobial therapy on host/microbiota/pathogen interactions. However new approaches are needed for developing and standardising appropriate methods to measure efficacy of novel antimicrobial combinations in these contexts. A battery of promising new antimicrobials is now in various stages of development including co-administered inhibitors, phages, nanoparticles, immunotherapy, anti-biofilm and anti-virulence agents. These novel therapeutics need multidisciplinary collaboration and new ways of thinking to bring them into large scale clinical use.

How host species and body part determine the microbial communities of five ambrosia beetle species

The ambrosia beetles are farming insects that feed mainly on their cultivated fungi, which in some occasions are pathogens from forest and fruit trees. We used a culture-independent approach based on 16S and 18S rRNA gene metabarcoding analysis to investigate the diversity and composition of the bacterial and fungal communities associated with five ambrosia beetle species: four species native to America (Monarthrum dimidiatum, Dryocoetoides capucinus, Euwallacea discretus, Corthylus consimilis) and an introduced species (Xylosandrus morigerus). For the bacterial community, the beetle species hosted a broad diversity with 1,579 amplicon sequence variants (ASVs) and 66 genera, while for the fungal community they hosted 288 ASVs and 39 genera. Some microbial groups dominated the community within a host species or a body part (Wolbachia in the head-thorax of E. discretus; Ambrosiella in the head-thorax and abdomen of X. morigerus). The taxonomic composition and structure of the microbial communities appeared to differ between beetle species; this was supported by beta-diversity analysis, which indicated that bacterial and fungal communities were clustered mainly by host species. This study characterizes for the first time the microbial communities associated with unexplored ambrosia beetle species, as well as the factors that affect the composition and taxonomic diversity per se, contributing to the knowledge of the ambrosia beetle system.

Novel strains of Actinobacteria associated with neotropical social wasps (Vespidae; Polistinae, Epiponini) with antimicrobial potential for natural product discovery

Antimicrobial resistance has been considered a public health threat. The World Health Organization has warned about the urgency of detecting new antibiotics from novel sources. Social insects could be crucial in the search for new antibiotic metabolites, as some of them survive in places that favor parasite development. Recent studies have shown the potential of social insects to produce antimicrobial metabolites (e.g. ants, bees, and termites). However, most groups of social wasps remain unstudied. Here, we explored whether Actinobacteria are associated with workers in the Neotropical Social Wasps (Epiponini) of Costa Rica and evaluated their putative inhibitory activity against other bacteria. Most isolated strains (67%) have antagonistic effects, mainly against Bacillus thuringensis and Escherichia coli ATCC 25992. Based on genome analysis, some inhibitory Actinobacteria showed biosynthetic gene clusters (BGCs) related to the production of antimicrobial molecules such as Selvamycin, Piericidin A1, and Nystatin. The Actinobacteria could be associated with social wasps to produce antimicrobial compounds. For these reasons, we speculate that Actinobacteria associated with social wasps could be a novel source of antimicrobial compounds, mainly against Gram-negative bacteria.

Characterization of a selective, iron-chelating antifungal compound that disrupts fungal metabolism and synergizes with fluconazole

Fungal infections are a growing global health concern due to the limited number of available antifungal therapies as well as the emergence of fungi that are resistant to first-line antimicrobials, particularly azoles and echinocandins. Development of novel, selective antifungal therapies is challenging due to similarities between fungal and mammalian cells. An attractive source of potential antifungal treatments is provided by ecological niches co-inhabited by bacteria, fungi, and multicellular organisms, where complex relationships between multiple organisms have resulted in evolution of a wide variety of selective antimicrobials. Here, we characterized several analogs of one such natural compound, collismycin A. We show that NR-6226C has antifungal activity against several pathogenic Candida species, including C. albicans and C. glabrata, whereas it only has little toxicity against mammalian cells. Mechanistically, NR-6226C selectively chelates iron, which is a limiting factor for pathogenic fungi during infection. As a result, NR-6226C treatment causes severe mitochondrial dysfunction, leading to formation of reactive oxygen species, metabolic reprogramming, and a severe reduction in ATP levels. Using an in vivo model for fungal infections, we show that NR-6226C significantly increases survival of Candida-infected Galleria mellonella larvae. Finally, our data indicate that NR-6226C synergizes strongly with fluconazole in inhibition of C. albicans. Taken together, NR-6226C is a promising antifungal compound that acts by chelating iron and disrupting mitochondrial functions.IMPORTANCEDrug-resistant fungal infections are an emerging global threat, and pan-resistance to current antifungal therapies is an increasing problem. Clearly, there is a need for new antifungal drugs. In this study, we characterized a novel antifungal agent, the collismycin analog NR-6226C. NR-6226C has a favorable toxicity profile for human cells, which is essential for further clinical development. We unraveled the mechanism of action of NR-6226C and found that it disrupts iron homeostasis and thereby depletes fungal cells of energy. Importantly, NR-6226C strongly potentiates the antifungal activity of fluconazole, thereby providing inroads for combination therapy that may reduce or prevent azole resistance. Thus, NR-6226C is a promising compound for further development into antifungal treatment.

Diversity and antimicrobial activity of the tropical ant-derived actinomycetes isolated from Thailand

Antibiotic resistance is one of the most important global healthcare challenges and is responsible for the mortality of millions of people worldwide every year. It is a crisis attributed to misuse of antibiotics and a lack of new drug development. Actinomycetes constitute a group of Gram-positive bacteria known for their distinctive high guanine-cytosine (G+C) content in their genomic DNA. These microorganisms are widely recognized for their capability to generate a wide range of secondary metabolites with diverse biological activities. These versatile microorganisms are ubiquitous in diverse ecosystems, including soil, freshwater, marine sediments, and within the bodies of insects. A recent study has demonstrated that social insects, such as ants, host a diverse array of these bacteria. In this study, we involved the isolation and characterization of a total of 72 actinomycete strains obtained from 18 distinct ant species collected from various regions across Thailand. Utilizing 16S rRNA gene analysis, these isolated actinomycetes were classified into four distinct genera: Amycolatopsis (2 isolates), Micromonospora (1 isolate), Nocardia (8 isolates), and Streptomyces (61 isolates). Among the Streptomyces strains, 23 isolates exhibited antimicrobial activity against a panel of Gram-positive bacteria, including Bacillus subtilis ATCC 6633, Staphylococcus epidermidis ATCC 12228, Staphylococcus aureus ATCC 25923, Kocuria rhizophila ATCC 9341, and Methicillin-resistant Staphylococcus aureus (MRSA) DMST 20646. Additionally, two isolates displayed antifungal activity against Candida albicans TISTR 5554. Based on 16S rRNA gene sequence similarity studies, these two isolates, ODS25 and ODS28, were demonstrated to be closely related to Streptomyces lusitanus NBRC 13464T (98.07%) and Streptomyces haliclonae DSM 41970T (97.28%), respectively. The level of 16S rRNA gene sequence similarity below 98.65% cutoff indicates its potential as a novel actinomycete species. These findings underscore the potential of actinomycetes sourced from ants as a valuable reservoir of novel antimicrobials.

Genomic Insights into the Microbial Agent Streptomyces albidoflavus MGMM6 for Various Biotechnology Applications

Microbial biotechnology plays a crucial role in improving industrial processes, particularly in the production of compounds with diverse applications. In this study, we used bioinformatic approaches to analyze the genomic architecture of Streptomyces albidoflavus MGMM6 and identify genes involved in various metabolic pathways that have significant biotechnological potential. Genome mining revealed that MGMM6 consists of a linear chromosome of 6,932,303 bp, with a high G+C content of 73.5%, lacking any plasmid contigs. Among the annotated genes, several are predicted to encode enzymes such as dye peroxidase, aromatic ring-opening dioxygenase, multicopper oxidase, cytochrome P450 monooxygenase, and aromatic ring hydroxylating dioxygenases which are responsible for the biodegradation of numerous endogenous and xenobiotic pollutants. In addition, we identified genes associated with heavy metal resistance, such as arsenic, cadmium, mercury, chromium, tellurium, antimony, and bismuth, suggesting the potential of MGMM6 for environmental remediation purposes. The analysis of secondary metabolites revealed the presence of multiple biosynthesis gene clusters responsible for producing compounds with potent antimicrobial and metal-chelating activities. Furthermore, laboratory tests conducted under controlled conditions demonstrated the effectiveness of MGMM6 in inhibiting phytopathogenic microbes, decolorizing and degrading aromatic triphenylmethane dyes, particularly Blue Brilliant G250, from wastewater by up to 98 ± 0.15%. Overall, the results of our study highlight the promising biotechnological potential of S. albidoflavus MGMM6.

Innate functions of natural products: A promising path for the identification of novel therapeutics

In the course of evolution, living organisms have become well equipped with diverse natural products that serve important functions, including defence from biotic and abiotic stress, growth regulation, reproduction, metabolism, and epigenetic regulation. It seems to be the organism's ecological niche that influences the natural product's structural and functional diversity. Indeed, natural products constitute the nuts and bolts of molecular co-evolution and ecological relationships among different life forms. Since natural products in the form of specialized secondary metabolites exhibit biological functions via interactions with specific target proteins, they can provide a simultaneous glimpse of both new therapeutics and therapeutic targets in humans as well. In this review, we have discussed the innate role of natural products in the ecosystem and how this intrinsic role provides a futuristic opportunity to identify new drugs and therapeutic targets rapidly.

Insect Microbial Symbionts: Ecology, Interactions, and Biological Significance

The guts of insect pests are typical habitats for microbial colonization and the presence of bacterial species inside the gut confers several potential advantages to the insects. These gut bacteria are located symbiotically inside the digestive tracts of insects and help in food digestion, phytotoxin breakdown, and pesticide detoxification. Different shapes and chemical assets of insect gastrointestinal tracts have a significant impact on the structure and makeup of the microbial population. The number of microbial communities inside the gastrointestinal system differs owing to the varying shape and chemical composition of digestive tracts. Due to their short generation times and rapid evolutionary rates, insect gut bacteria can develop numerous metabolic pathways and can adapt to diverse ecological niches. In addition, despite hindering insecticide management programs, they still have several biotechnological uses, including industrial, clinical, and environmental uses. This review discusses the prevalent bacterial species associated with insect guts, their mode of symbiotic interaction, their role in insecticide resistance, and various other biological significance, along with knowledge gaps and future perspectives. The practical consequences of the gut microbiome and its interaction with the insect host may lead to encountering the mechanisms behind the evolution of pesticide resistance in insects.

Symbiotic Bacteria Regulating Insect-Insect/Fungus/Virus Mutualism

Bacteria associated with insects potentially provide many beneficial services and have been well documented. Mutualism that relates to insects is widespread in ecosystems. However, the interrelation between "symbiotic bacteria" and "mutualism" has rarely been studied. We introduce three systems of mutualism that relate to insects (ants and honeydew-producing Hemiptera, fungus-growing insects and fungi, and plant persistent viruses and vector insects) and review the species of symbiotic bacteria in host insects, as well as their functions in host insects and the mechanisms underlying mutualism regulation. A deeper understanding of the molecular mechanisms and role of symbiotic bacteria, based on metagenomics, transcriptomics, proteomics, metabolomics, and microbiology, will be required for describing the entire interaction network.

Antifungal Compounds from Microbial Symbionts Associated with Aquatic Animals and Cellular Targets: A Review

Fungal infections continue to be a serious public health problem, leading to an estimated 1.6 million deaths annually. It remains a major cause of mortality for people with a weak or affected immune system, such as those suffering from cancer under aggressive chemotherapies. On the other hand, pathogenic fungi are counted among the most destructive factors affecting crops, causing a third of all food crop losses annually and critically affecting the worldwide economy and food security. However, the limited number currently available and the cytotoxicity of the conventional antifungal drugs, which are not yet properly diversified in terms of mode of action, in addition to resistance phenomena, make the search for new antifungals imperative to improve both human health and food protection. Symbiosis has been a crucial alternative for drug discovery, through which many antimicrobials have been discovered. This review highlights some antifungal models of a defensive symbiosis of microbial symbiont natural products derived from interacting with aquatic animals as one of the best opportunities. Some recorded compounds with supposed novel cell targets such as apoptosis could lead to the development of a multitherapy involving the mutual treatment of fungal infections and other metabolic diseases involving apoptosis in their pathogenesis pathways.

Neglected skin-associated microbial communities: a unique immune defense strategy of Bufo raddei under environmental heavy metal pollution

Amphibians defend against pathogens using skin microbial communities, in addition to innate and adaptive immunity. Despite skin microbial communities play a key role in the immune function of amphibians, few studies have focused on the changes in its composition and function. In the present study, we identified the variation in adaptive immunity, as well as the corresponding changes in skin microbiome of Bufo raddei living in a heavy metal polluted area. The adaptive immunity of B. raddei in heavy metal polluted area was significantly lower than that in relatively unpolluted area. Further, different skin bacterial communities were found in the two areas. In the heavy metal polluted area, Actinobacteria and Microbacterium were the dominant bacteria in the skin microbiome of B. raddei, which showed broad-spectrum antibacterial activity. Besides, the antibiotic synthesis was also increased in metabolic pathways. The present study suggested that the adaptive immunity of B. raddei was weakened under long-term heavy metal stress. However, the toads increased the abundance of bacteriostatic bacteria by regulating the composition of skin microbiome, which released a large number of bacteriostatic metabolites and enhanced the host resistance to external pathogens in turn.

In Vitro Studies Reveal that Pseudomonas, from Odontotermes obesus Colonies, can Function as a Defensive Mutualist as it Prevents the Weedy Fungus While Keeping the Crop Fungus Unaffected

Insects that farm monocultures of fungi are canonical examples of nutritional symbiosis as well as independent evolution of agriculture in non-human animals. But just like in human agriculture, these fungal crops face constant threat of invasion by weeds which, if unchecked, take over the crop fungus. In fungus-growing termites, the crop fungus (Termitomyces) faces such challenges from the weedy fungus Pseudoxylaria. The mechanism by which Pseudoxylaria is suppressed is not known. However, evidence suggests that some bacterial secondary symbionts can serve as defensive mutualists by preventing the growth of Pseudoxylaria. However, such secondary symbionts must possess the dual, yet contrasting, capabilities of suppressing the weedy fungus while keeping the growth of the crop fungus unaffected. This study describes the isolation, identification, and culture-dependent estimation of the roles of several such putative defensive mutualists from the colonies of the wide-spread fungus-growing termite from India, Odontotermes obesus. From the 38 bacterial cultures tested, a strain of Pseudomonas showed significantly greater suppression of the weedy fungus than the crop fungus. Moreover, a 16S rRNA pan-microbiome survey, using the Nanopore platform, revealed Pseudomonas to be a part of the core microbiota of O. obesus. A meta-analysis of microbiota composition across different species of Odontotermes also confirms the widespread prevalence of Pseudomonas within this termite. These lines of evidence indicate that Pseudomonas could be playing the role of defensive mutualist within Odontotermes.

Observation of the Antimicrobial Activities of Two Actinomycetes in the Harvester Ant Messor orientalis

Simple Summary

Observations in the animal room have shown that the seeds stored by harvester ants, although in a damp environment, are less likely to mold. It was hypothesized that harvester ants may use actinomycetes to protect their seed stores, given that leafcutter ants use actinomycetes as producers of defensive substances. Two actinomycetes were isolated from the harvester ant Messor orientalis. The fermentation broth of the actinomycetes showed significant inhibitory effects on the three indicator fungi. Coculture experiments supported the observed inhibitory effects. The antifungal activities of actinomycetes in harvester ants were revealed. This research provides a significant theoretical reference for the abovementioned hypothesis and for the potential agricultural applications of these actinomycetes for multiple crops.

Abstract

Observations have shown that seeds collected by harvester ants are less likely to mold. Based on evolutionary analysis and other research, it was hypothesized that harvester ants could apply actinomycetes to protect seeds, similar to the protection of mutualistic fungi by leafcutter ants. Two actinomycetes were successfully isolated from the harvester ant Messor orientalis. The taxonomic status of the actinomycetes was determined by 16S rRNA sequence analysis and biochemical experimental observations. Their inhibitory effects on plant pathogens were measured. One of the bacteria was identified as Brachybacterium phenoliresistens and denoted as B. phenoliresistens MO. The other belonged to the genus Microbacterium. It was named Microbacterium sp. Growth rate determination and coculture experiments were performed to explore the inhibitory effect of actinomycetes on indicator plant pathogens. The inhibition rates of the actinomycetes toward Peronophythora litchii and Rhizoctonia solani were 100% in media containing 30% or more fermentation broth, and they also showed an inhibitory effect on Colletotrichum siamense. The coculture experiment supported this result by showing that the growth of P. litchii and R. solani was inhibited in the presence of actinomycetes. Therefore, the results of this study show the agricultural application potential of these bacteria and may provide a reference for research on the symbiosis of harvester ants with actinomycetes.

Microbiome assembly on Drosophila body surfaces benefits the flies to combat fungal infections

In contrast to the well-characterized gut microbiomes, the composition and function of the insect body-surface microbiotas are still elusive and highly underexplored. Here we report the dynamic features of the Drosophila melanogaster surface microbiomes. It was found that the microbiomes assembled on fly surfaces could defend insects against fungal parasitic infections. The substantial increase of bacterial loads occurred within 10 days of fly eclosion, especially the expansion of Gilliamella species. The culturable bacteria such as Lactiplantibacillus plantarum could effectively inhibit fungal spore germinations, and the gnotobiotic addition of the isolated bacteria could substantially delay fungal infection of axenic flies. We found that the fly tarsal segments were largely accumulated with bacterial cells, which could accelerate cell dispersal onto different body parts to deter fungal spore germinations. Our findings will facilitate future investigations of the surface microbiotas affecting insect physiologies.

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Bacterial loads quickly increase on the body surface of fruit fly after eclosion

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Surface bacteria can defend flies against fungal parasitic infections

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Surface bacteria can inhibit fungal spore germinations

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Expansion of the γ-Proteobacteria Gilliamella on fly surfaces

The polyene antifungal candicidin is selectively packaged into membrane vesicles in Streptomyces S4

In recent years, much attention has been focused on the biogenesis, engineering and utilisation of outer membrane vesicles (OMVs) in Gram-negative bacteria in a range of environments and niches. While the precise mechanism of biogenesis is unknown, it is focused on the modification of the Gram-negative cell wall to facilitate blebbing at sites of weakness in and around the characteristically thin peptidoglycan layer within the periplasm. Here, we investigate the biogenesis of membrane vesicles (MVs) in the Gram-positive organism Streptomyces albus S4 (Seipke et al. J Bacteriol 193:4270–4271, 2011 and Fazal et al. Antonie Van Leeuwenhoek 113:511–520, 2020). The S. albus S4 strain is an antifungal (candicidin and antimycin) producing organism that was isolated from attine ants (Barke et al. BMC Biol 8:109, 2010). The biogenesis and characterisation of S. albus S4 MVs is demonstrated using the wild-type (WT) and mutant strains ΔantC (no antimycin production) ΔfscC (no candicidin production) and ΔantC ΔfscC (produces neither antimycin nor candicidin). Here, we have shown that the S. albus S4 strain produces MVs and that these are comprised of both specific protein profiles and secondary metabolites, with a clear demonstration of the ability to selectively package one antifungal (candicidin) but not the other (antimycin).

Uncovering the biodiversity and biosynthetic potentials of rare actinomycetes

Background

Antibiotic resistance is on the rise, and new antibiotic research has slowed in recent years, necessitating the discovery of possibly novel microbial resources capable of producing bioactive compounds. Microbial infections are gaining resistance to existing antibiotics, emphasizing the need for novel medicinal molecules to be discovered as soon as possible. Because the possibilities of isolating undiscovered actinomycetes strains have decreased, the quest for novel products has shifted to rare actinomycetes genera from regular environments or the identification of new species identified in unusual habitats.

Main body of the abstract

The non-streptomyces actinobacteria are known as rare actinomycetes that are extremely difficult to cultivate. Rare actinomycetes are known to produce a variety of secondary metabolites with varying medicinal value. In this review, we reported the diversity of rare actinomycetes in several habitat including soil, plants, aquatic environment, caves, insects and extreme environments. We also reported some isolation methods to easily recover rare Actinobacteria from various sources guided with some procedures to identify the rare Actinobacteria isolates. Finally, we reported the biosynthetic potential of rare actinomycetes and its role in the production of unique secondary metabolites that could be used in medicine, agriculture, and industry. These microbial resources will be of interest to humanity, as antibiotics, insecticides, anticancer, antioxidants, to mention but a few.

Short conclusion

Rare actinomycetes are increasingly being investigated for new medicinal compounds that could help to address existing human health challenges such as newly emerging infectious illnesses, antibiotic resistance, and metabolic disorders. The bioactive secondary metabolites from uncommon actinomycetes are the subject of this review, which focuses on their diversity in different habitats, isolation, identification and biosynthetic potentials.

Habitat Adaptation Drives Speciation of a Streptomyces Species with Distinct Habitats and Disparate Geographic Origins

Microbial diversification is driven by geographic and ecological factors, but how the relative importance of these factors varies among species, geographic scales, and habitats remains unclear. Streptomyces, a genus of antibiotic-producing, spore-forming, and widespread bacteria, offers a robust model for identifying the processes underlying population differentiation. We examined the population structure of 37 Streptomyces olivaceus strains isolated from various sources, showing that they diverged into two habitat-associated (free-living and insect-associated) and geographically disparate lineages. More frequent gene flow within than between the lineages confirmed genetic isolation in S. olivaceus. Geographic isolation could not explain the genetic isolation; instead, habitat type was a strong predictor of genetic distance when controlling for geographic distance. The identification of habitat-specific genetic variations, including genes involved in regulation, resource use, and secondary metabolism, suggested a significant role of habitat adaptation in the diversification process. Physiological assays revealed fitness trade-offs under different environmental conditions in the two lineages. Notably, insect-associated isolates could outcompete free-living isolates in a free-iron-deficient environment. Furthermore, substrate (e.g., sialic acid and glycogen) utilization but not thermal traits differentiated the two lineages. Overall, our results argue that adaptive processes drove ecological divergence among closely related streptomycetes, eventually leading to dispersal limitation and gene flow barriers between the lineages. S. olivaceus may best be considered a species complex consisting of two cryptic species. IMPORTANCE Both isolation by distance and isolation by environment occur in bacteria, and different diversification patterns may apply to different species. Streptomyces species, typified by producing useful natural products, are widespread in nature and possess high genetic diversity. However, the ecological processes and evolutionary mechanisms that shape their distribution are not well understood. Here, we show that the population structure of a ubiquitous Streptomyces species complex matches its habitat distribution and can be defined by gene flow discontinuities. Using comparative genomics and physiological assays, we reveal that gains and losses of specific genomic traits play a significant role in the transition between free-living and host-associated lifestyles, driving speciation of the species. These results provide new insights into the evolutionary trajectory of Streptomyces and the notion of species.

Beyond Soil-Dwelling Actinobacteria: Fantastic Antibiotics and Where to Find Them

Bacterial secondary metabolites represent an invaluable source of bioactive molecules for the pharmaceutical and agrochemical industries. Although screening campaigns for the discovery of new compounds have traditionally been strongly biased towards the study of soil-dwelling Actinobacteria, the current antibiotic resistance and discovery crisis has brought a considerable amount of attention to the study of previously neglected bacterial sources of secondary metabolites. The development and application of new screening, sequencing, genetic manipulation, cultivation and bioinformatic techniques have revealed several other groups of bacteria as producers of striking chemical novelty. Biosynthetic machineries evolved from independent taxonomic origins and under completely different ecological requirements and selective pressures are responsible for these structural innovations. In this review, we summarize the most important discoveries related to secondary metabolites from alternative bacterial sources, trying to provide the reader with a broad perspective on how technical novelties have facilitated the access to the bacterial metabolic dark matter.

Symbiont-Mediated Protection of Acromyrmex Leaf-Cutter Ants from the Entomopathogenic Fungus Metarhizium anisopliae

Many fungus-growing ants engage in a defensive symbiosis with antibiotic-producing ectosymbiotic bacteria in the genus Pseudonocardia, which help protect the ants' fungal mutualist from a specialized mycoparasite, Escovopsis. Here, using germfree ant rearing and experimental pathogen infection treatments, we evaluate if Acromyrmex ants derive higher immunity to the entomopathogenic fungus Metarhizium anisopliae from their Pseudonocardia symbionts. We further examine the ecological dynamics and defensive capacities of Pseudonocardia against M. anisopliae across seven different Acromyrmex species by controlling Pseudonocardia acquisition using ant-nonnative Pseudonocardia switches, in vitro challenges, and in situ mass spectrometry imaging (MSI). We show that Pseudonocardia protects the ants against M. anisopliae across different Acromyrmex species and appears to afford higher protection than metapleural gland (MG) secretions. Although Acromyrmex echinatior ants with nonnative Pseudonocardia symbionts receive protection from M. anisopliae regardless of the strain acquired compared with Pseudonocardia-free conditions, we find significant variation in the degree of protection conferred by different Pseudonocardia strains. Additionally, when ants were reared in Pseudonocardia-free conditions, some species exhibit more susceptibility to M. anisopliae than others, indicating that some ant species depend more on defensive symbionts than others. In vitro challenge experiments indicate that Pseudonocardia reduces Metarhizium conidiospore germination area. Our chemometric analysis using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) reveals that Pseudonocardia-carrying ants produce more chemical signals than Pseudonocardia-free treatments, indicating that Pseudonocardia produces bioactive metabolites on the Acromyrmex cuticle. Our results indicate that Pseudonocardia can serve as a dual-purpose defensive symbiont, conferring increased immunity for both the obligate fungal mutualist and the ants themselves. IMPORTANCE In some plants and animals, beneficial microbes mediate host immune response against pathogens, including by serving as defensive symbionts that produce antimicrobial compounds. Defensive symbionts are known in several insects, including some leaf-cutter ants where antifungal-producing Actinobacteria help protect the fungal mutualist of the ants from specialized mycoparasites. In many defensive symbioses, the extent and specificity of defensive benefits received by the host are poorly understood. Here, using "aposymbiotic" rearing, symbiont switching experiments, and imaging mass spectrometry, we explore the ecological and chemical dynamics of the model defensive symbiosis between Acromyrmex ants and their defensive symbiotic bacterium Pseudonocardia. We show that the defensive symbiont not only protects the fungal crop of Acromyrmex but also provides protection from fungal pathogens that infect the ant workers themselves. Furthermore, we reveal that the increased immunity to pathogen infection differs among strains of defensive symbionts and that the degree of reliance on a defensive symbiont for protection varies across congeneric ant species. Taken together, our results suggest that Acromyrmex-associated Pseudonocardia have evolved broad antimicrobial defenses that promote strong immunity to diverse fungal pathogens within the ancient fungus-growing ant-microbe symbiosis.

Interactions among Escovopsis, Antagonistic Microfungi Associated with the Fungus-Growing Ant Symbiosis

Fungi in the genus Escovopsis (Ascomycota: Hypocreales) are prevalent associates of the complex symbiosis between fungus-growing ants (Tribe Attini), the ants' cultivated basidiomycete fungi and a consortium of both beneficial and harmful microbes found within the ants' garden communities. Some Escovopsis spp. have been shown to attack the ants' cultivated fungi, and co-infections by multiple Escovopsis spp. are common in gardens in nature. Yet, little is known about how Escovopsis strains impact each other. Since microbe-microbe interactions play a central role in microbial ecology and evolution, we conducted experiments to assay the types of interactions that govern Escovopsis-Escovopsis relationships. We isolated Escovopsis strains from the gardens of 10 attine ant genera representing basal (lower) and derived groups in the attine ant phylogeny. We conducted in vitro experiments to determine the outcome of both intraclonal and interclonal Escovopsis confrontations. When paired with self (intraclonal interactions), Escovopsis isolated from lower attine colonies exhibited antagonistic (inhibitory) responses, while strains isolated from derived attine colonies exhibited neutral or mutualistic interactions, leading to a clear phylogenetic pattern of interaction outcome. Interclonal interactions were more varied, exhibiting less phylogenetic signal. These results can serve as the basis for future studies on the costs and benefits of Escovopsis coinfection, and on the genetic and chemical mechanisms that regulate the compatibility and incompatibility observed here.

Enzyme producing insect gut microbes: an unexplored biotechnological aspect

To explore the unmapped biotechnologically important microbial platforms for human welfare, the insect gut system is such a promising arena. Insects, the inhabitant of all ecological niches, harbor a healthy diversified microbial population in their versatile gut environment. This deep-rooted symbiotic relationship between insects and gut microbes is the result of several indispensable microbial performances that include: enzyme production, detoxification of plant defense compounds and insecticides, maintenance of life cycle, host fertility, bioremediation, pest biocontrol, production of antimicrobial compounds, and in addition provide vitamins, amino acids, and lactic acids to their hosts. Insects have developed such symbiotic interactions with different microorganisms for nutritional benefits like the digestion of dietary compounds by the production of several key hydrolytic enzymes viz: amylase, cellulase, lignocellulase, protease, lipase, xylanase, pectinase, chitinase, laccase, etc. The nutritional enrichment offered by these microbes to insects may be the key factor in the evolutionary attainment of this group. Around one million insect species are grouped under 31 orders, however, only ten of such groups' have been studied in relation to enzyme-producing gut microbes. Moreover, insect gut symbionts are a potential source of biotechnologically active biomolecules as these microbes go through a course of selection pressures in their host gut environment. As symbiosis has pronounced potential regarding the production of novel compounds, especially enzymes with multidimensional industrial capabilities, so there are ample scopes to explore this treasure box for human welfare. Biological significance as well as industrially compatible capabilities can categorize these insect gut symbionts as an unexplored biotechnological aspect.

Competition-based screening helps to secure the evolutionary stability of a defensive microbiome

BACKGROUND

The cuticular microbiomes of Acromyrmex leaf-cutting ants pose a conundrum in microbiome biology because they are freely colonisable, and yet the prevalence of the vertically transmitted bacteria Pseudonocardia, which contributes to the control of Escovopsis fungus garden disease, is never compromised by the secondary acquisition of other bacterial strains. Game theory suggests that competition-based screening can allow the selective recruitment of antibiotic-producing bacteria from the environment, by providing abundant resources to foment interference competition between bacterial species and by using Pseudonocardia to bias the outcome of competition in favour of antibiotic producers.

RESULTS

Here, we use RNA-stable isotope probing (RNA-SIP) to confirm that Acromyrmex ants can maintain a range of microbial symbionts on their cuticle by supplying public resources. We then used RNA sequencing, bioassays, and competition experiments to show that vertically transmitted Pseudonocardia strains produce antibacterials that differentially reduce the growth rates of other microbes, ultimately biassing the bacterial competition to allow the selective establishment of secondary antibiotic-producing strains while excluding non-antibiotic-producing strains that would parasitise the symbiosis.

CONCLUSIONS

Our findings are consistent with the hypothesis that competition-based screening is a plausible mechanism for maintaining the integrity of the co-adapted mutualism between the leaf-cutting ant farming symbiosis and its defensive microbiome. Our results have broader implications for explaining the stability of other complex symbioses involving horizontal acquisition.

Screening and Purification of Natural Products from Actinomycetes that Induce a "Rounded" Morphological Phenotype in Fission Yeast

This study was designed to identify and investigate bioactive natural product compounds that alter the cellular shape of the fission yeast Schizosaccharomyces pombe and induce a "rounded" or "small" cellular morphological phenotype. Bioassays using a range of antifungal agents against a multidrug-sensitive fission yeast strain, SAK950 showed that many induced a "rounded" phenotype. We then investigated whether 46 of the actinomycete strains identified in our previous study as inducing a similar phenotype produced antifungal agents of similar classes. We show that five of the strains produced streptothricin and that 26 strains produced polyenes, including fungichromin, filipin and candicidin, the last of which was produced by 24 strains. A taxonomic study of the strains indicated that the majority of the candicidin only producers were Streptomyces hydrogenans and S. albidoflavus whilst those that additionally produced streptothricin were related to S. enissocaesilis. A follow-up study to investigate the natural products made by related strains indicated that they followed a similar pattern. The identification of several compounds from the actinomycete strains similar to the antifungal agents initially tested confirm the validity of an approach using the S. pombe morphological phenotype and actinomycete taxonomy as a predictive tool for natural product identification.

Ammonia Production by Streptomyces Symbionts of Acromyrmex Leaf-Cutting Ants Strongly Inhibits the Fungal Pathogen Escovopsis

Leaf-cutting ants live in mutualistic symbiosis with their garden fungus Leucoagaricus gongylophorus that can be attacked by the specialized pathogenic fungus Escovopsis. Actinomyces symbionts from Acromyrmex leaf-cutting ants contribute to protect L. gongylophorus against pathogens. The symbiont Streptomyces sp. Av25_4 exhibited strong activity against Escovopsis weberi in co-cultivation assays. Experiments physically separating E. weberi and Streptomyces sp. Av25_4 allowing only exchange of volatiles revealed that Streptomyces sp. Av25_4 produces a volatile antifungal. Volatile compounds from Streptomyces sp. Av25_4 were collected by closed loop stripping. Analysis by NMR revealed that Streptomyces sp. Av25_4 overproduces ammonia (up to 8 mM) which completely inhibited the growth of E. weberi due to its strong basic pH. Additionally, other symbionts from different Acromyrmex ants inhibited E. weberi by production of ammonia. The waste of ca. one third of Acomyrmex and Atta leaf-cutting ant colonies was strongly basic due to ammonia (up to ca. 8 mM) suggesting its role in nest hygiene. Not only complex and metabolically costly secondary metabolites, such as polyketides, but simple ammonia released by symbionts of leaf-cutting ants can contribute to control the growth of Escovopsis that is sensitive to ammonia in contrast to the garden fungus L. gongylophorus.

The Genome Analysis of the Human Lung-Associated Streptomyces sp. TR1341 Revealed the Presence of Beneficial Genes for Opportunistic Colonization of Human Tissues

Streptomyces sp. TR1341 was isolated from the sputum of a man with a history of lung and kidney tuberculosis, recurrent respiratory infections, and COPD. It produces secondary metabolites associated with cytotoxicity and immune response modulation. In this study, we complement our previous results by identifying the genetic features associated with the production of these secondary metabolites and other characteristics that could benefit the strain during its colonization of human tissues (virulence factors, modification of the host immune response, or the production of siderophores). We performed a comparative phylogenetic analysis to identify the genetic features that are shared by environmental isolates and human respiratory pathogens. The results showed a high genomic similarity of Streptomyces sp. TR1341 to the plant-associated Streptomyces sp. endophyte_N2, inferring a soil origin of the strain. Putative virulence genes, such as mammalian cell entry (mce) genes were not detected in the TR1341’s genome. The presence of a type VII secretion system, distinct from the ones found in Mycobacterium species, suggests a different colonization strategy than the one used by other actinomycete lung pathogens. We identified a higher diversity of genes related to iron acquisition and demonstrated that the strain produces ferrioxamine B in vitro. These results indicate that TR1341 may have an advantage in colonizing environments that are low in iron, such as human tissue.

Incipient genome erosion and metabolic streamlining for antibiotic production in a defensive symbiont

Genome reduction is commonly observed in bacteria of several phyla engaging in obligate nutritional symbioses with insects. In Actinobacteria, however, little is known about the process of genome evolution, despite their importance as prolific producers of antibiotics and their increasingly recognized role as defensive partners of insects and other organisms. Here, we show that “Streptomyces philanthi,” a defensive symbiont of digger wasps, has a G+C-enriched genome in the early stages of erosion, with inactivating mutations in a large proportion of genes, causing dependency on its hosts for certain nutrients, which was validated in axenic symbiont cultures. Additionally, overexpressed catabolic and biosynthetic pathways of the bacteria inside the host indicate host–symbiont metabolic integration for streamlining and control of antibiotic production.

Genome erosion is a frequently observed result of relaxed selection in insect nutritional symbionts, but it has rarely been studied in defensive mutualisms. Solitary beewolf wasps harbor an actinobacterial symbiont of the genus Streptomyces that provides protection to the developing offspring against pathogenic microorganisms. Here, we characterized the genomic architecture and functional gene content of this culturable symbiont using genomics, transcriptomics, and proteomics in combination with in vitro assays. Despite retaining a large linear chromosome (7.3 Mb), the wasp symbiont accumulated frameshift mutations in more than a third of its protein-coding genes, indicative of incipient genome erosion. Although many of the frameshifted genes were still expressed, the encoded proteins were not detected, indicating post-transcriptional regulation. Most pseudogenization events affected accessory genes, regulators, and transporters, but “Streptomyces philanthi” also experienced mutations in central metabolic pathways, resulting in auxotrophies for biotin, proline, and arginine that were confirmed experimentally in axenic culture. In contrast to the strong A+T bias in the genomes of most obligate symbionts, we observed a significant G+C enrichment in regions likely experiencing reduced selection. Differential expression analyses revealed that—compared to in vitro symbiont cultures—“S. philanthi” in beewolf antennae showed overexpression of genes for antibiotic biosynthesis, the uptake of host-provided nutrients and the metabolism of building blocks required for antibiotic production. Our results show unusual traits in the early stage of genome erosion in a defensive symbiont and suggest tight integration of host–symbiont metabolic pathways that effectively grants the host control over the antimicrobial activity of its bacterial partner.

Polyene-Producing Streptomyces spp. From the Fungus-Growing Termite Macrotermes barneyi Exhibit High Inhibitory Activity Against the Antagonistic Fungus Xylaria

Fungus-growing termites are engaged in a tripartite mutualism with intestinal microbes and a monocultivar (Termitomyces sp.) in the fungus garden. The termites are often plagued by entomopathogen (Metarhizium anisopliae) and fungus garden is always threatened by competitors (Xylaria spp.). Here, we aim to understand the defensive role of intestinal microbes, the actinomycetes which were isolated from the gut of Macrotermes barneyi. We obtained 44 antifungal isolates, which showed moderate to strong inhibition to Xylaria sp. HPLC analysis indicated that different types of polyenes (tetraene, pentene, and heptaene) existed in the metabolites of 10 strong antifungal Streptomyces strains. Two pentene macrolides (pentamycin and 1′14-dihydroxyisochainin) were firstly purified from Streptomyces strain HF10, both exhibiting higher activity against Xylaria sp. and M. anisopliae than cultivar Termitomyces. Subsequently, tetraene and heptaene related gene disruption assay showed that the mutant strains lost the ability to produce corresponding polyenes, and they also had significantly decreased activities against Xylaria sp. and M. anisopliae compared to that of wild type strains. These results indicate that polyene-producing Streptomyces from the guts of M. barneyi have strong inhibition to competitor fungus and polyenes contribute to inhibitory effects on Xylaria sp.

Antagonistic Effects of Delia antiqua (Diptera: Anthomyiidae)-Associated Bacteria Against Four Phytopathogens

Recent studies have revealed multiple roles of insect-associated microbes such as lignin degradation, entomopathogen inhibition, and antibiotic production. These functions improve insect host fitness, and provide a novel source of discovering beneficial microbes for industrial and agricultural production. Previously published research found that in the symbiosis formed by the dipteran pest Delia antiqua (Meigen) (Diptera: Anthomyiidae) and its associated bacteria, the bacteria showed effective inhibition of one fungal entomopathogen, Beauveria bassiana. The antifungal activity of those associated bacteria indicates their potential to be used as biocontrol agents for fungal phytopathogens. In this study, we first isolated and identified bacteria associated with D. antiqua using a culture-dependent method. Second, we tested the antifungal activity of these bacteria against four phytopathogens including Fusarium moniliforme, Botryosphaeria dothidea, and two Fusarium oxysporum strains using the dual-culture method. In total, 74 species belonging to 30 genera, 23 families, eight classes, and four phyla were isolated and identified. Among those bacteria, Ochrobactrum anthropi, Morganella morganii, Arthrobacter sp. 3, and Acinetobacter guillouiae showed significant volatile inhibition activity against F. moniliforme, B. dothidea, and both F. oxysporum, respectively. Moreover, bacteria including Rhodococcus equi, Leucobacter aridicollis, Paenibacillus sp. 3, and Lampropedia sp. showed significant contact inhibition activity against F. moniliforme, B. dothidea, and both F. oxysporum. Our work provides a new source for discovering biocontrol agents against phytopathogens.

Ancient Antibiotics, Ancient Resistance

As the spread of antibiotic resistance threatens our ability to treat infections, avoiding the return of a preantibiotic era requires the discovery of new drugs. While therapeutic use of antibiotics followed by the inevitable selection of resistance is a modern phenomenon, these molecules and the genetic determinants of resistance were in use by environmental microbes long before humans discovered them. In this review, we discuss evidence that antibiotics and resistance were present in the environment before anthropogenic use, describing techniques including direct sampling of ancient DNA and phylogenetic analyses that are used to reconstruct the past. We also pay special attention to the ecological and evolutionary forces that have shaped the natural history of antibiotic biosynthesis, including a discussion of competitive versus signaling roles for antibiotics, proto-resistance, and substrate promiscuity of biosynthetic and resistance enzymes. Finally, by applying an evolutionary lens, we describe concepts governing the origins and evolution of biosynthetic gene clusters and cluster-associated resistance determinants. These insights into microbes' use of antibiotics in nature, a game they have been playing for millennia, can provide inspiration for discovery technologies and management strategies to combat the growing resistance crisis.

Chance or Necessity-The Fungi Co-Occurring with Formica polyctena Ants

Simple Summary

There are about 13,800 species of ants living around the world, but only some of them have been extensively studied in the context of their non−antagonistic relationships with fungi. The best−known example is the symbiosis between leaf−cutting ants and fungi serving them as food. Others include the relationship between ants living in carton nests in the trees’ canopy with fungi increasing the durability of the nest. Do ants utilize fungi in the northern hemisphere and cooler climatic zone? This question is still open. Our goal was to study the less−obvious interactions between ants and common fungi in temperate climates. In our study, we characterized the mycobiota of the surroundings of Formica polyctena ants. We identified nearly 600 strains and investigated their taxonomic affinity. The most abundant fungi in F. polyctena nests are strains belonging to Penicillium—a genus well−known as an antibiotic producer. Other common and widespread fungi related to Penicillium, such as the toxin−producing Aspergillus species, were isolated very rarely. Additionally, the high diversity and high frequency of Penicillium colonies isolated from ants in this study suggest that certain representatives of this genus may be adapted to survive in ant nests, or that they are preferentially sustained by the insects.

Abstract

Studies on carton nesting ants and domatia−dwelling ants have shown that ant–fungi interactions may be much more common and widespread than previously thought. Until now, studies focused predominantly on parasitic and mutualistic fungi–ant interactions occurring mostly in the tropics, neglecting less−obvious interactions involving the fungi common in ants’ surroundings in temperate climates. In our study, we characterized the mycobiota of the surroundings of Formica polyctena ants by identifying nearly 600 fungal colonies that were isolated externally from the bodies of F. polyctena workers. The ants were collected from mounds found in northern and central Poland. Isolated fungi were assigned to 20 genera via molecular identification (ITS rDNA barcoding). Among these, Penicillium strains were the most frequent, belonging to eight different taxonomic sections. Other common and widespread members of Eurotiales, such as Aspergillus spp., were isolated very rarely. In our study, we managed to characterize the genera of fungi commonly present on F. polyctena workers. Our results suggest that Penicillium, Trichoderma, Mucor, Schwanniomyces and Entomortierella are commonly present in F. polyctena surroundings. Additionally, the high diversity and high frequency of Penicillium colonies isolated from ants in this study suggest that representatives of this genus may be adapted to survive in ant nests environment better than the other fungal groups, or that they are preferentially sustained by the insects in nests.

Specialized Metabolites Reveal Evolutionary History and Geographic Dispersion of a Multilateral Symbiosis

Fungus-growing ants engage in a multilateral symbiosis: they cultivate a fungal garden as their primary food source and host symbiotic actinobacteria (Pseudonocardia spp.) that provide chemical defenses. The bacterial symbionts produce small specialized metabolites that protect the fungal garden from specific fungal pathogens (Escovopsis spp.), and in return, they are fed by the ant hosts. Multiple studies on the molecules underlying this symbiotic system have led to the discovery of a large number of structurally diverse antifungal molecules, but somewhat surprisingly no shared structural theme emerged from these studies. A large systematic study of Brazilian nests led to the discovery of the widespread production of a potent but overlooked antifungal agent, which we named attinimicin, by nearly two-thirds of all Pseudonocardia strains from multiple sites in Brazil. Here we report the structure of attinimicin, its putative biosynthetic gene cluster, and the evolutionary relationship between attinimicin and two related peptides, oxachelin A and cahuitamycin A. All three nonribosomal peptides are structural isomers with different primary peptide sequences. Attinimicin shows iron-dependent antifungal activity against specific environmental fungal parasites but no activity against the fungal cultivar. Attinimicin showed potent in vivo activity in a mouse Candida albicans infection model comparable to clinically used azole-containing antifungals. In situ detection of attinimicin in both ant nests and on worker ants supports an ecological role for attinimicin in protecting the fungal cultivar from pathogens. The geographic spread of the attinimicin biosynthetic gene cluster in Brazilian Pseudonocardia spp. marks attinimicin as the first specialized metabolite from ant-associated bacteria with broad geographic distribution.

Streptomyces sp. M54: an actinobacteria associated with a neotropical social wasp with high potential for antibiotic production

Streptomyces symbionts in insects have shown to be a valuable source of new antibiotics. Here, we report the genome sequence and the potential for antibiotic production of "Streptomyces sp. M54", an Actinobacteria associated with the eusocial wasp, Polybia plebeja. The Streptomyces sp. M54 genome is composed of a chromosome (7.96 Mb), and a plasmid (1.91 Kb) and harbors 30 biosynthetic gene clusters for secondary metabolites, of which only one third has been previously characterized. Growth inhibition bioassays show that this bacterium produces antimicrobial compounds that are active against Hirsutella citriformis, a natural fungal enemy of its host, and the human pathogens Staphylococcus aureus and Candida albicans. Analyses through TLC-bioautography, LC-MS/MS and NMR allowed the identification of five macrocyclic ionophore antibiotics, with previously reported antibacterial, antitumor and antiviral properties. Phylogenetic analyses placed Streptomyces sp. M54 in a clade of other host-associated strains taxonomically related to Streptomyces griseus. Pangenomic and ANI analyses confirm the identity of one of its closest relatives as Streptomyces sp. LaPpAH-199, a strain isolated from an ant-plant symbiosis in Africa. In summary, our results suggest an insect-microbe association in distant geographic areas and showcase the potential of Streptomyces sp. M54 and related strains for the discovery of novel antibiotics.

Uncharted territories in the discovery of antifungal and antivirulence natural products from bacteria

Many fungi can cause deadly diseases in humans, and nearly every human will suffer from some kind of fungal infection in their lives. Only few antifungals are available, and some of these fail to treat intrinsically resistant species and the ever-increasing number of fungal strains that have acquired resistance. In nature, bacteria and fungi display versatile interactions that range from friendly co-existence to predation. The first antifungal drugs, nystatin and amphotericin B, were discovered in bacteria as mediators of such interactions, and bacteria continue to be an important source of antifungals. To learn more about the ecological bacterial-fungal interactions that drive the evolution of natural products and exploit them, we need to identify environments where such interactions are pronounced, and diverse. Here, we systematically analyze historic and recent developments in this field to identify potentially under-investigated niches and resources. We also discuss alternative strategies to treat fungal infections by utilizing the antagonistic potential of bacteria to target fungal stress pathways and virulence factors, and thereby suppress the evolution of antifungal resistance.

Antileishmanial macrolides from ant-associated Streptomyces sp. ISID311

Three antifungal macrolides cyphomycin (1), caniferolide C (2) and GT-35 (3) were isolated from Streptomyces sp. ISID311, a bacterial symbiont associated with Cyphomyrmex fungus-growing ants. The planar structures of these compounds were established by 1 and 2D NMR data and MS analysis. The relative configurations of 1-3 were established using Kishi's universal NMR database method, NOE/ROE analysis and coupling constants analysis assisted by comparisons with NMR data of related compounds. Detailed bioinformatic analysis of cyphomycin biosynthetic gene cluster confirmed the stereochemical assignments. Compounds 1-3 displayed high antagonism against different strains of Escovopsis sp., pathogen fungi specialized to the fungus-growing ant system. Compounds 1-3 also exhibited potent antiprotozoal activity against intracellular amastigotes of the human parasite Leishmania donovani with IC₅₀ values of 2.32, 0.091 and 0.073 µM, respectively, with high selectivity indexes.

Pseudonocardia Symbionts of Fungus-Growing Ants and the Evolution of Defensive Secondary Metabolism

Actinobacteria belonging to the genus Pseudonocardia have evolved a close relationship with multiple species of fungus-growing ants, where these bacteria produce diverse secondary metabolites that protect the ants and their fungal mutualists from disease. Recent research has charted the phylogenetic diversity of this symbiosis, revealing multiple instances where the ants and Pseudonocardia have formed stable relationships in which these bacteria are housed on specific regions of the ant's cuticle. Parallel chemical and genomic analyses have also revealed that symbiotic Pseudonocardia produce diverse secondary metabolites with antifungal and antibacterial bioactivities, and highlighted the importance of plasmid recombination and horizontal gene transfer for maintaining these symbiotic traits. Here, we propose a multi-level model for the evolution of Pseudonocardia and their secondary metabolites that includes symbiont transmission within and between ant colonies, and the potentially independent movement and diversification of their secondary metabolite biosynthetic genes. Because of their well-studied ecology and experimental tractability, Pseudonocardia symbionts of fungus-growing ants are an especially useful model system to understand the evolution of secondary metabolites, and also comprise a significant source of novel antibiotic and antifungal agents.

Chemical Ecology of Streptomyces albidoflavus Strain A10 Associated with Carpenter Ant Camponotus vagus

Antibiotics produced by symbiotic microorganisms were previously shown to be of crucial importance for ecological communities, including ants. Previous works on ant–actinobacteria symbiosis are mainly focused on farming ants, which use antifungal microbial secondary metabolites to control pathogens in their fungal gardens. In this work, we studied microorganisms associated with carpenter ant Camponotus vagus. Pronounced antifungal activity of isolated actinobacteria strain A10 was found to be facilitated by biosynthesis of the antimycin A complex, consisting of small hydrophobic depsipeptides with high antimicrobial and cytotoxic activity. The actinomycete strain A10 was identified as Streptomyces albidoflavus. We studied the antagonistic activity of strain A10 against several entomopathogenic microorganisms. The antifungal activity of this strain potentially indicates a defensive symbiosis with the host ant, producing antimycins to protect carpenter ants against infections. The nature of this ant-microbe association however remains to be established.

Integrative analysis of transcriptomes highlights potential functions of transfer-RNA-derived small RNAs in experimental intracerebral hemorrhage

Transfer-RNA-derived small RNAs (tsRNAs) are a novel class of short non-coding RNAs, that possess regulatory functions. However, their biological roles in hemorrhagic stroke are not understood. In this study, by RNA sequencing, we investigated the tsRNA expression profiles of intracerebral hemorrhagic rat brains in the chronic phase. A total of 331 tsRNAs were identified (308 in sham and 309 in intracerebral hemorrhage). Among them, the validation revealed that 7 tsRNAs (1 up-regulated and 6 down-regulated) were significantly changed. Subsequently, we predicted the target mRNAs of the 7 tsRNAs. Through integrative analysis, the predicted targets were validated by mRNA microarray data. Moreover, we confirmed the functions of tsRNAs targeting mRNAs in vitro. Furthermore, using bioinformatics tools and databases, we developed a tsRNA-mRNA-pathway interaction network to visualize their potential functions. Bioinformatics analyses and confirmatory experiments indicated that the altered genes were mainly enriched in several signaling pathways. These pathways were interrelated with intracerebral hemorrhage, such as response to oxidative stress, endocytosis, and regulation of G protein-coupled receptor signaling pathway. In summary, this study systematically revealed the profiles of tsRNAs after an experimental intracerebral hemorrhage. These results may provide novel therapeutic targets following a hemorrhagic stroke in the chronic phase.

High-Throughput Cultivation for the Selective Isolation of Acidobacteria From Termite Nests

Microbial communities in the immediate environment of socialized invertebrates can help to suppress pathogens, in part by synthesizing bioactive natural products. Here we characterized the core microbiomes of three termite species (genus Coptotermes) and their nest material to gain more insight into the diversity of termite-associated bacteria. Sampling a healthy termite colony over time implicated a consolidated and highly stable microbiome, pointing toward the fact that beneficial bacterial phyla play a major role in termite fitness. In contrast, there was a significant shift in the composition of the core microbiome in one nest during a fungal infection, affecting the abundance of well-characterized Streptomyces species (phylum Actinobacteria) as well as less-studied bacterial phyla such as Acidobacteria. High-throughput cultivation in microplates was implemented to isolate and identify these less-studied bacterial phylogenetic group. Amplicon sequencing confirmed that our method maintained the bacterial diversity of the environmental samples, enabling the isolation of novel Acidobacteriaceae and expanding the list of cultivated species to include two strains that may define new species within the genera Terracidiphilus and Acidobacterium.

Chemical warfare between fungus-growing ants and their pathogens

Fungus-growing attine ants are under constant threat from fungal pathogens such as the specialized mycoparasite Escovopsis, which uses combined physical and chemical attack strategies to prey on the fungal gardens of the ants. In defence, some species assemble protective microbiomes on their exoskeletons that contain antimicrobial-producing Actinobacteria. Underlying this network of mutualistic and antagonistic interactions are an array of chemical signals. Escovopsis weberi produces the shearinine terpene-indole alkaloids, which affect ant behaviour, diketopiperazines to combat defensive bacteria, and other small molecules that inhibit the fungal cultivar. Pseudonocardia and Streptomyces mutualist bacteria produce depsipeptide and polyene macrolide antifungals active against Escovopsis spp. The ant nest metabolome is further complicated by competition between defensive bacteria, which produce antibacterials active against even closely related species.

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Specialist fungal pathogens attack the nests of fungus-growing ants.

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Ants form mutualistic relationships with defensive actinomycete bacteria.

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Specialised metabolites underpin these mutualistic and antagonistic interactions.

Chemical Mediators at the Bacterial-Fungal Interface

Interactions among microbes are key drivers of evolutionary progress and constantly shape ecological niches. Microorganisms rely on chemical communication to interact with each other and surrounding organisms. They synthesize natural products as signaling molecules, antibiotics, or modulators of cellular processes that may be applied in agriculture and medicine. Whereas major insight has been gained into the principles of intraspecies interaction, much less is known about the molecular basis of interspecies interplay. In this review, we summarize recent progress in the understanding of chemically mediated bacterial-fungal interrelations. We discuss pairwise interactions among defined species and systems involving additional organisms as well as complex interactions among microbial communities encountered in the soil or defined as microbiota of higher organisms. Finally, we give examples of how the growing understanding of microbial interactions has contributed to drug discovery and hypothesize what may be future directions in studying and engineering microbiota for agricultural or medicinal purposes.

Antimicrobial Activity of Microorganisms Isolated from Ant Nests of Lasius niger

In this study, the microbial communities of two nests of black garden ants (Lasius niger) in the hollows of stem branches of old apple trees were found to have similar species compositions: each community contained representatives of three species from the Bacillaceae family and one species of actinomycetes from the genus Streptomyces. In total, four types of bacilli and two actinomycetes were isolated. Actinomycetes were identified as Streptomyces antibioticus-like and Streptomyces sp. None of the bacilli had antibiotic activity, whereas both streptomycetes produced antibiotics that inhibited the growth of Gram-positive bacteria in vitro, including isolates from their community. Antibiotic compounds of S. antibioticus-like strain INA 01148 (Institute of New Antibiotics) were identified as actinomycin D and its closest homologue, actinomycin A. Actinomycins presumably change the microbial community of the ant nest substrate as they act against Gram-positive bacteria and against fungi and Gram-negative bacteria. The antibiotic activity of the isolated Streptomyces sp. INA 01156 is of interest, since the substances produced by this strain inhibit the growth of drug-resistant bacteria, including methicillin-resistant Staphylococcus aureus INA 00761 (MRSA) and vancomycin-resistant strain Leuconostoc mesenteroides VKPM B-4177 (VR) (VKPM-National Collection of Industrial Microorganisms (Russian acronym)).

Advances in actinomycete research: an ActinoBase review of 2019

The actinomycetes are Gram-positive bacteria belonging to the order Actinomycetales within the phylum Actinobacteria. They include members with significant economic and medical importance, for example filamentous actinomycetes such as Streptomyces species, which have a propensity to produce a plethora of bioactive secondary metabolites and form symbioses with higher organisms, such as plants and insects. Studying these bacteria is challenging, but also fascinating and very rewarding. As a Microbiology Society initiative, members of the actinomycete research community have been developing a Wikipedia-style resource, called ActinoBase, the purpose of which is to aid in the study of these filamentous bacteria. This review will highlight 10 publications from 2019 that have been of special interest to the ActinoBase community, covering 4 major components of actinomycete research: (i) development and regulation; (ii) specialized metabolites; (iii) ecology and host interactions; and (iv) technology and methodology.

Hexokinase II Inhibitory Effect of Secondary Metabolites Derived from a Streptomyces sp. Associated with Mud Dauber Wasp

Insect-microbial symbioses have vast biochemical diversity, which is beneficial to produce bioactive secondary metabolites. In this study, chemical examination of a Streptomyces sp. associated with a mud dauber wasp led to the isolation of fourteen compounds. Their structures were determined by spectroscopic methods and comparison with literature data. Among the isolates, compounds 1,2,3-benzotriazin-4(1H)-one and 4-(2-aminoethyl)phenyl acetate were first reported from this species. Bioactivities of the isolated compounds were assayed for the first time against hexokinase II. 4-(2-Aminoethyl)phenyl acetate, germicidin B, phenylacetic acid, isogermicidin A and germicidin C displayed significant inhibitory activity against hexokinase II, with the IC₅₀ values of 5.11, 7.11, 7.15, 8.45 and 8.78 μM, respectively.