The coevolution of fungus-ant agriculture.

Fungus-farming ants cultivate multiple lineages of fungi for food, but, because fungal cultivar relationships are largely unresolved, the history of fungus-ant coevolution remains poorly known. We designed probes targeting >2000 gene regions to generate a dated evolutionary tree for 475 fungi and combined it with a similarly generated tree for 276 ants. We found that fungus-ant agriculture originated ~66 million years ago when the end-of-Cretaceous asteroid impact temporarily interrupted photosynthesis, causing global mass extinctions but favoring the proliferation of fungi. Subsequently, ~27 million years ago, one ancestral fungal cultivar population became domesticated, i.e., obligately mutualistic, when seasonally dry habitats expanded in South America, likely isolating the cultivar population from its free-living, wet forest-dwelling conspecifics. By revealing these and other major transitions in fungus-ant coevolution, our results clarify the historical processes that shaped a model system for nonhuman agriculture.

Insights into the Naso-Oropharyngeal Bacterial Composition in Suspected SARS-CoV-2 Cases.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was the causative agent of the coronavirus disease 2019 (COVID-19) pandemic. While research on COVID-19 has mainly focused on its epidemiology, pathogenesis, and treatment, studies on the naso-oropharyngeal microbiota have emerged in the last few years as an overlooked area of research. Here, we analyzed the bacterial community composition of the naso-oropharynx in 50 suspected SARS-CoV-2 cases (43 detected, 7 not detected) from Veraguas province (Panama) distributed across five age categories. Statistical analysis revealed no significant differences (p < 0.05) in bacterial alpha and beta diversities between the groups categorized by SARS-CoV-2 test results, age, or patient status. The genera Corynebacterium, Staphylococcus, Prevotella, Streptococcus, and Tepidiphilus were the most abundant in both detected and not-detected SARS-CoV-2 group. The linear discriminant analysis effect size (LEfSe) for biomarker exploration indicated that Veillonella and Prevotella were enriched in detected and hospitalized patients with SARS-CoV-2 relative to non-detected patients, while Thermoanaerobacterium and Haemophilus were enriched in non-detected patients with SARS-CoV-2. The results also indicated that the genus Corynebacterium was found to decrease in patients with detected SARS-CoV-2 relative to those with non-detected SARS-CoV-2. Understanding the naso-oropharyngeal microbiota provides insights into the diversity, composition, and resilience of the microbial community in patients with SARS-CoV-2.

HBeeID: a molecular tool that identifies honey bee subspecies from different geographic populations.

BACKGROUND: Honey bees are the principal commercial pollinators. Along with other arthropods, they are increasingly under threat from anthropogenic factors such as the incursion of invasive honey bee subspecies, pathogens and parasites. Better tools are needed to identify bee subspecies. Genomic data for economic and ecologically important organisms is increasing, but in its basic form its practical application to address ecological problems is limited. RESULTS: We introduce HBeeID a means to identify honey bees. The tool utilizes a knowledge-based network and diagnostic SNPs identified by discriminant analysis of principle components and hierarchical agglomerative clustering. Tests of HBeeID showed that it identifies African, Americas-Africanized, Asian, and European honey bees with a high degree of certainty even when samples lack the full 272 SNPs of HBeeID. Its prediction capacity decreases with highly admixed samples. CONCLUSION: HBeeID is a high-resolution genomic, SNP based tool, that can be used to identify honey bees and screen species that are invasive. Its flexible design allows for future improvements via sample data additions from other localities.

First large-scale study reveals important losses of managed honey bee and stingless bee colonies in Latin America.

Over the last quarter century, increasing honey bee colony losses motivated standardized large-scale surveys of managed honey bees (Apis mellifera), particularly in Europe and the United States. Here we present the first large-scale standardized survey of colony losses of managed honey bees and stingless bees across Latin America. Overall, 1736 beekeepers and 165 meliponiculturists participated in the 2-year survey (2016-2017 and 2017-2018). On average, 30.4% of honey bee colonies and 39.6% of stingless bee colonies were lost per year across the region. Summer losses were higher than winter losses in stingless bees (30.9% and 22.2%, respectively) but not in honey bees (18.8% and 20.6%, respectively). Colony loss increased with operation size during the summer in both honey bees and stingless bees and decreased with operation size during the winter in stingless bees. Furthermore, losses differed significantly between countries and across years for both beekeepers and meliponiculturists. Overall, winter losses of honey bee colonies in Latin America (20.6%) position this region between Europe (12.5%) and the United States (40.4%). These results highlight the magnitude of bee colony losses occurring in the region and suggest difficulties in maintaining overall colony health and economic survival for beekeepers and meliponiculturists.

Assessment of the Quality, Chemometric and Pollen Diversity of Apis mellifera Honey from Different Seasonal Harvests.

The parameters for assessing the quality of honey produced by Apis mellifera are standardized worldwide. The physicochemical properties of honey might vary extensively due to factors such as the geographical area where it was produced and the season in which it was harvested. Little information is available on variations in honey quality among different harvest periods in tropical areas, and particularly in neotropical dry forests. This study describes variations in seventeen physicochemical parameters and the pollen diversity of honey harvested from beehives during the dry season in February, March, and April 2021, in the dry arc of Panama. Potassium is the most abundant mineral in honey samples, and its concentration increases during the harvest period from February to April. A PCA analysis showed significant differences among the samples collected during different harvest periods. The pollen diversity also differs among honey samples from February compared with March and April. The results indicate that climatic conditions may play an important role in the quality of honey produced in the dry arc of Panama. Furthermore, these results might be useful for establishing quality-control parameters of bee honey produced in Panama in support of beekeeping activities in seasonal wet-dry areas of the tropics.

Dynamics of Mask Use as a Prevention Strategy against SARS-CoV-2 in Panama.

Early in the SARS-CoV-2 pandemic, many national public health authorities implemented non-pharmaceutical interventions to mitigate disease outbreaks. Panamá established mandatory mask use two months after its first documented case. Initial compliance was high, but diverse masks were used in public areas. We studied behavioral dynamics of mask use through the first two COVID-19 waves in Panama, to improve the implementation of effective, low-cost public health containment measures when populations are exposed to novel air-borne pathogens. Mask use behavior was recorded from pedestrians in four Panamanian populations (August to December 2020). We recorded facial coverings and if used, the type of mask, and gender and estimated age of the wearer. Our results showed that people were highly compliant (>95%) with mask mandates and demonstrated important population-level behaviors: (1) decreasing use of cloth masks over time, and increasing use of surgical masks; (2) mask use was 3-fold lower in suburban neighborhoods than other public areas and (3) young people were least likely to wear masks. Results help focus on highly effective, low-cost, public health interventions for managing and controlling a pandemic. Considerations of behavioral preferences for different masks, relative to pricing and availability, are essential for optimizing public health policies. Policies to increase the availability of effective masks, and behavioral nudges to increase acceptance, and to facilitate mask usage, during the ongoing SARS-CoV-2 pandemic, and for future pandemics of respiratory pathogens, are key tools, especially for nations lagging in access to expensive vaccines and pharmacological approaches.

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.

Disease management in two sympatric Apterostigma fungus-growing ants for controlling the parasitic fungus Escovopsis.

Antagonistic interactions between host and parasites are often embedded in networks of interacting species, in which hosts may be attacked by competing parasites species, and parasites may infect more than one host species. To better understand the evolution of host defenses and parasite counterdefenses in the context of a multihost, multiparasite system, we studied two sympatric species, of congeneric fungus-growing ants (Attini) species and their symbiotic fungal cultivars, which are attacked by multiple morphotypes of parasitic fungi in the genus, Escovopsis. To assess whether closely related ant species and their cultured fungi are evolving defenses against the same or different parasitic strains, we characterized Escovopsis that were isolated from colonies of sympatric Apterostigma dentigerum and A. pilosum. We assessed in vitro and in vivo interactions of these parasites with their hosts. While the ant cultivars are parasitized by similar Escovopsis spp., the frequency of infection by these pathogens differs between the two ant species. The ability of the host fungi to suppress Escovopsis growth, as well as ant defensive responses toward the parasites, differs depending on the parasite strain and on the host ant species.

Garden microbiomes of Apterostigma dentigerum and Apterostigma pilosum fungus-growing ants (Hymenoptera: Formicidae).

Fungus-growing ants share a complex symbiosis with microbes, including fungal mutualists, antibiotic-producing bacteria, and fungal pathogens. The bacterial communities associated with this symbiosis are poorly understood but likely play important roles in maintaining the health and function of fungal gardens. We studied bacterial communities in gardens of two Apterostigma species, A. dentigerum, and A. pilosum, using next-generation sequencing to evaluate differences between the two ant species, their veiled and no-veiled fungal garden types, and across three collection locations. We also compared different parts of nests to test for homogeneity within nests. Enterobacteriaceae dominated gardens of both species and common OTUs were shared across both species and nest types. However, differences in community diversity were detected between ant species, and in the communities of A. dentigerum veiled and no-veiled nests within sites. Apterostigma pilosum had a higher proportion of Phyllobacteriaceae and differed from A. dentigerum in the proportions of members of the order Clostridiales. Within A. dentigerum, nests with veiled and no-veiled fungus gardens had similar taxonomic profiles but differed in the relative abundance of some groups, with veiled gardens having more Rhodospirillaceae and Hyphomicrobiaceae, and no-veiled having more Xanthomonadaceae and certain genera in the Enterobacteriaceae C. However, bacterial communities in Apterostigma fungal gardens are highly conserved and resemble those of the nests of other attine ants with dominant taxa likely playing a role in biomass degradation and defense. Further work is required to understand and explain how bacterial community composition of fungus-growing nests is maintained.

Hygiene Defense Behaviors Used by a Fungus-Growing Ant Depend on the Fungal Pathogen Stages.

Parasites and their hosts use different strategies to overcome the defenses of the other, often resulting in an evolutionary arms race. Limited animal studies have explored the differential responses of hosts when challenged by differential parasite loads and different developmental stages of a parasite. The fungus-growing ant Trachymyrmex sp. 10 employs three different hygienic strategies to control fungal pathogens: Grooming the antibiotic-producing metapleural glands (MGs) and planting or weeding their mutualistic fungal crop. By inoculating Trachymyrmex colonies with different parasite concentrations (Metarhizium) or stages (germinated conidia or ungermianted conidia of Metarhizium and Escovopsis), we tested whether ants modulate and change hygienic strategies depending on the nature of the parasite challenge. There was no effect of the concentration of parasite on the frequencies of the defensive behaviors, indicating that the ants did not change defensive strategy according to the level of threat. However, when challenged with conidia of Escovopsis sp. and Metarhizium brunneum that were germinated or not-germinated, the ants adjusted their thygienic behavior to fungal planting and MG grooming behaviors using strategies depending on the conidia germination status. Our study suggests that fungus-growing ants can adjust the use of hygienic strategies based on the nature of the parasites.

Imaging mass spectrometry and MS/MS molecular networking reveals chemical interactions among cuticular bacteria and pathogenic fungi associated with fungus-growing ants.

The fungus-growing ant-microbe symbiosis is an ideal system to study chemistry-based microbial interactions due to the wealth of microbial interactions described, and the lack of information on the molecules involved therein. In this study, we employed a combination of MALDI imaging mass spectrometry (MALDI-IMS) and MS/MS molecular networking to study chemistry-based microbial interactions in this system. MALDI IMS was used to visualize the distribution of antimicrobials at the inhibition zone between bacteria associated to the ant Acromyrmex echinatior and the fungal pathogen Escovopsis sp. MS/MS molecular networking was used for the dereplication of compounds found at the inhibition zones. We identified the antibiotics actinomycins D, X2 and X0ß, produced by the bacterium Streptomyces CBR38; and the macrolides elaiophylin, efomycin A and efomycin G, produced by the bacterium Streptomyces CBR53.These metabolites were found at the inhibition zones using MALDI IMS and were identified using MS/MS molecular networking. Additionally, three shearinines D, F, and J produced by the fungal pathogen Escovopsis TZ49 were detected. This is the first report of elaiophylins, actinomycin X0ß and shearinines in the fungus-growing ant symbiotic system. These results suggest a secondary prophylactic use of these antibiotics by A. echinatior because of their permanent production by the bacteria.

Social life and sanitary risks: evolutionary and current ecological conditions determine waste management in leaf-cutting ants.

Adequate waste management is vital for the success of social life, because waste accumulation increases sanitary risks in dense societies. We explored why different leaf-cutting ants (LCA) species locate their waste in internal nest chambers or external piles, including ecological context and accounting for phylogenetic relations. We propose that waste location depends on whether the environmental conditions enhance or reduce the risk of infection. We obtained the geographical range, habitat and refuse location of LCA from published literature, and experimentally determined whether pathogens on ant waste survived to the high soil temperatures typical of xeric habitats. The habitat of the LCA determined waste location after phylogenetic correction: species with external waste piles mainly occur in xeric environments, whereas those with internal waste chambers mainly inhabit more humid habitats. The ancestral reconstruction suggests that dumping waste externally is less derived than digging waste nest chambers. Empirical results showed that high soil surface temperatures reduce pathogen prevalence from LCA waste. We proposed that LCA living in environments unfavourable for pathogens (i.e. xeric habitats) avoid digging costs by dumping the refuse above ground. Conversely, in environments suitable for pathogens, LCA species prevent the spread of diseases by storing waste underground, presumably, a behaviour that contributed to the colonization of humid habitats. These results highlight the adaptation of organisms to the hygienic challenges of social living, and illustrate how sanitary behaviours can result from a combination of evolutionary history and current environmental conditions.

Slowing them down will make them lose: a role for attine ant crop fungus in defending pupae against infections?

Fungus-growing ants (Attini) have evolved an obligate dependency upon a basidiomycete fungus that they cultivate as their food. Less well known is that the crop fungus is also used by many attine species to cover their eggs, larvae and pupae. The adaptive functional significance of this brood covering is poorly understood. One hypothesis to account for this behaviour is that it is part of the pathogen protection portfolio when many thousands of sister workers live in close proximity and larvae and pupae are not protected by cells, as in bees and wasps, and are immobile. We performed behavioural observations on brood covering in the leaf-cutting ant Acromyrmex echinatior, and we experimentally manipulated mycelial cover on pupae and exposed them to the entomopathogenic fungus Metarhizium brunneum to test for a role in pathogen resistance. Our results show that active mycelial brood covering by workers is a behaviourally plastic trait that varies temporally, and across life stages and castes. The presence of a fungal cover on the pupae reduced the rate at which conidia appeared and the percentage of pupal surface that produced pathogen spores, compared to pupae that had fungal cover experimentally removed or naturally had no mycelial cover. Infected pupae with mycelium had higher survival rates than infected pupae without the cover, although this depended upon the time at which adult sister workers were allowed to interact with pupae. Finally, workers employed higher rates of metapleural gland grooming to infected pupae without mycelium than to infected pupae with mycelium. Our results imply that mycelial brood covering may play a significant role in suppressing the growth and subsequent spread of disease, thus adding a novel layer of protection to their defence portfolio.

Functional role of phenylacetic acid from metapleural gland secretions in controlling fungal pathogens in evolutionarily derived leaf-cutting ants.

Fungus-farming ant colonies vary four to five orders of magnitude in size. They employ compounds from actinomycete bacteria and exocrine glands as antimicrobial agents. Atta colonies have millions of ants and are particularly relevant for understanding hygienic strategies as they have abandoned their ancestors' prime dependence on antibiotic-based biological control in favour of using metapleural gland (MG) chemical secretions. Atta MGs are unique in synthesizing large quantities of phenylacetic acid (PAA), a known but little investigated antimicrobial agent. We show that particularly the smallest workers greatly reduce germination rates of Escovopsis and Metarhizium spores after actively applying PAA to experimental infection targets in garden fragments and transferring the spores to the ants' infrabuccal cavities. In vitro assays further indicated that Escovopsis strains isolated from evolutionarily derived leaf-cutting ants are less sensitive to PAA than strains from phylogenetically more basal fungus-farming ants, consistent with the dynamics of an evolutionary arms race between virulence and control for Escovopsis, but not Metarhizium. Atta ants form larger colonies with more extreme caste differentiation relative to other attines, in societies characterized by an almost complete absence of reproductive conflicts. We hypothesize that these changes are associated with unique evolutionary innovations in chemical pest management that appear robust against selection pressure for resistance by specialized mycopathogens.

Quality and quantity: transitions in antimicrobial gland use for parasite defense.

Parasites are a major force in evolution, and understanding how host life history affects parasite pressure and investment in disease resistance is a general problem in evolutionary biology. The threat of disease may be especially strong in social animals, and ants have evolved the unique metapleural gland (MG), which in many taxa produce antimicrobial compounds that have been argued to have been a key to their ecological success. However, the importance of the MG in the disease resistance of individual ants across ant taxa has not been examined directly. We investigate experimentally the importance of the MG for disease resistance in the fungus-growing ants, a group in which there is interspecific variation in MG size and which has distinct transitions in life history. We find that more derived taxa rely more on the MG for disease resistance than more basal taxa and that there are a series of evolutionary transitions in the quality, quantity, and usage of the MG secretions, which correlate with transitions in life history. These shifts show how even small clades can exhibit substantial transitions in disease resistance investment, demonstrating that host-parasite relationships can be very dynamic and that targeted experimental, as well as large-scale, comparative studies can be valuable for identifying evolutionary transitions.

Dynamic disease management in Trachymyrmex fungus-growing ants (Attini: Formicidae).

Multipartner mutualisms have potentially complex dynamics, with compensatory responses when one partner is lost or relegated to a minor role. Fungus-growing ants (Attini) are mutualistic associates of basidiomycete fungi and antibiotic-producing actinomycete bacteria; the former are attacked by specialized fungi (Escovopsis) and diverse generalist microbes. Ants deploy biochemical defenses from bacteria and metapleural glands (MGs) and express different behaviors to control contaminants. We studied four Trachymyrmex species that differed in relative abundance of actinomycetes to understand interactions among antimicrobial tactics that are contingent on the nature of infection. MG grooming rate and actinomycete abundance were negatively correlated. The two species with high MG grooming rates or abundant actinomycetes made relatively little use of behavioral defenses. Conversely, the two species with relatively modest biochemical defenses relied heavily on behavior. Trade-offs suggest that related species can evolutionarily diverge to rely on different defense mechanisms against the same threat. Neither bacterial symbionts nor MG secretions thus appear to be essential for mounting defenses against the specialized pathogen Escovopsis, but reduced investment in one of these defense modes tends to increase investment in the other.

An evaluation of the possible adaptive function of fungal brood covering by Attine ants.

Fungus-growing ants (Myrmicinae: Attini) live in an obligate symbiotic relationship with a fungus that they rear for food, but they can also use the fungal mycelium to cover their brood. We surveyed colonies from 20 species of fungus-growing ants and show that brood-covering behavior occurs in most species, but to varying degrees, and appears to have evolved shortly after the origin of fungus farming, but was partly or entirely abandoned in some genera. To understand the evolution of the trait we used quantitative phylogenetic analyses to test whether brood-covering behavior covaries among attine ant clades and with two hygienic traits that reduce risk of disease: mycelial brood cover did not correlate with mutualistic bacteria that the ants culture on their cuticles for their antibiotics, but there was a negative relationship between metapleural gland grooming and mycelial cover. A broader comparative survey showed that the pupae of many ant species have protective cocoons but that those in the subfamily Myrmicinae do not. We therefore evaluated the previously proposed hypothesis that mycelial covering of attine ant brood evolved to provide cocoon-like protection for the brood.

Ephemeral windows of opportunity for horizontal transmission of fungal symbionts in leaf-cutting ants.

Evolutionary theory predicts that hosts are selected to prevent mixing of genetically different symbionts when competition among lineages reduces the productivity of a mutualism. The symbionts themselves may also defend their interests: recent studies of Acromyrmex leaf-cutting ants showed that somatic incompatibility enforces single-clone gardens within mature colonies, thereby constraining horizontal transmission of fungal symbionts. However, phylogenetic analyses indicate that symbiont switches occur frequently enough to remove most signs of host-symbiont cocladogenesis. Here we resolve this paradox by showing that transmission among newly founded Acromyrmex colonies is not constrained. All tested queens of sympatric A. octospinosus and A. echinatior offered a novel fragment of fungus garden accepted the new symbiont. The outcome was unaffected by genetic distance between the novel and the original symbiont, and by the ant species the novel symbiont came from. The colony founding stage may thus provide an efficient but transient window for horizontal transmission, in which the fungus is unable to actively defend its partnership position before the host feeds on it, so that host fecal droplets remain compatible with alternative strains during the early stage of colony founding. We discuss how brief stages of low commitment between partners may increase the evolutionary stability of ancient coevolved mutualisms.

Two fungal symbioses collide: endophytic fungi are not welcome in leaf-cutting ant gardens.

Interactions among the component members of different symbioses are not well studied. For example, leaf-cutting ants maintain an obligate symbiosis with their fungal garden, while the leaf material they provide to their garden is usually filled with endophytic fungi. The ants and their cultivar may interact with hundreds of endophytic fungal species, yet little is known about these interactions. Experimental manipulations showed that (i) ants spend more time cutting leaves from a tropical vine, Merremia umbellata, with high versus low endophyte densities, (ii) ants reduce the amount of endophytic fungi in leaves before planting them in their gardens, (iii) the ants' fungal cultivar inhibits the growth of most endophytes tested. Moreover, the inhibition by the ants' cultivar was relatively greater for more rapidly growing endophyte strains that could potentially out-compete or overtake the garden. Our results suggest that endophytes are not welcome in the garden, and that the ants and their cultivar combine ant hygiene behaviour with fungal inhibition to reduce endophyte activity in the nest.