Biology subjects

Khadempour, L.

Publications and source records attributed to Khadempour, L..

8 recordsLinked to original sources

bioRxiv2026

Genomic insights into bacterial isolates dominating honeypot ant crop microbiomes reveal metabolically distinct Fructilactobacillus sp.

Honeypot ants engage in a convergently-evolved phenotype called repletism, where specialized workers expand their crops and gasters to store vast amounts of food internally. They then store that food for months to support colonies during times of food scarcity. This fascinating phenotype is not well-understood and very little is known about the microbial interactions happening within the fructose-rich replete crop. Previous research using amplicon sequencing showed that Fructilactobacillus makes up nearly 100% of the crop microbiomes of Myrmecocystus mexicanus repletes. This striking result and successful isolation of those strains led to the present investigation into the phylogenetic diversity of these strains and any clues to the nature of the symbiotic relationship between them and the ant host. We find that the isolates from these repletes represented two evolutionary lineages, both most closely related to F. fructivorans. One of those lineages was also found to be phylogenetically and metabolically distinct from all other Fructilactobacillus reference genomes used in this study. This discovery in a genus of bacteria that are highly relevant for fermented human foods and will also lay the groundwork for future understanding of the convergent evolutionary mechanisms of repletism in ants. 3. Impact statementThese analyses add to the literature by identifying a new microbe within a genus that is relevant to food systems. In addition, the host phenotype is convergently evolved and likely microbe-mediated (or at least highly exposed). Understanding this system allows for the testing of ideas of coevolutionary hypotheses with natural replicates. We expect interest to come from food safety and probiotics researchers, evolutionary biologists that think about the impacts of microbes, microbial ecologists interested in novel systems, and those interested in bacteria that may display unique metabolic possibilities. This output allows for the clear future examination of this system with many clear hypotheses. Our analysis allows for the creation of a new and unique model system of host-microbe symbiosis. 4. Data summaryNew genomes assembled in this work can be found under BioProject ID PRJNA1449409. https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA1449409. Reference bacterial genomes were obtained from NCBI at the following accession numbers: SAMN20557570, SAMN28081009, SAMN28081010, SAMN02597458, SAMN43111088, SAMN28081011, SAMN28535231, SAMN04505734, SAMN28081013, SAMN33452149, SAMN37926504, SAMN02849426, SAMN02470196, SAMN02369432, SAMN02797779, SAMN02797782, SAMN02797768, SAMN09762388, SAMN12785275, SAMEA117660288. The honeypot ant genome was obtained from SAMN37666067. Raw proteomics files will be uploaded to ProteomeXchange with a unique identifier upon manuscript acceptance.

genomics↗

bioRxiv2026

Myrmecocystus honeypot ants have species specific resident gut microbiome

Myrmecocystus honeypot ants rely on specialized workers, repletes, to store dissolved carbohydrates in their crops long term. The repletes store this liquid, which does not spoil in their crops, for many months at a time. When resources are scarce, repletes redistribute the stored nutrients to their colony members via trophallaxis. While we suspect that the gut microbiome of honeypot ants may aid in spoilage prevention, before we can investigate this, we must first characterize it. Here, we used 16S rRNA gene sequencing to determine the microbial community composition across six Myrmecocystus honeypot ant species, sampling multiple colonies, castes, and organs. We found that microbiome community composition was strongly shaped by species, with variation between colonies in M. arenarius, M. depilis, and M. mexicanus. Organ level differences were observed in the crop and midgut in M. mexicanus. Caste differences were observed in M. flaviceps and M. mexicanus. Replete crops of M. mexicanus and M. depilis were enriched in Fructilactobacillus, other lactic acid bacteria, and acetic acid bacteria, whereas halophiles were more prominent in the gut of species such as M. flaviceps and M. wheeleri. In this study we demonstrate that Myrmecocystus ants host species-specific gut microbiomes and identify an association between lactic acid bacteria, acetic acid bacteria, and halophiles within replete crops. While much work remains in understanding the roles of the microbes in the symbiosis with their host ants, the dominance of these particular taxonomic groups suggests an association with a high sugar environment and a potential microbial role in preventing spoilage of the crop contents.

microbiology↗

bioRxiv2026

Convergently-evolved honeypot ants show mixed signs of niche conservatism

O_LIHoneypot ants are a compelling system for studying convergent evolution. In these ants, specialized workers store liquid food in distended crops, a trait known as repletism, which has evolved independently across multiple genera worldwide. Seasonal resource scarcity and aridity are hypothesized drivers of this trait, yet the role of environmental factors in shaping the evolution of repletism has never been empirically tested. C_LIO_LIWe modeled suitable habitats for 49 honeypot ant species using ensemble distribution models, then used the most important environmental predictors to compare niche structure across and within biogeographic regions (Nearctic, Australasia, Afrotropic, Neotropic, Palearctic). To address uneven sampling density among species, we independently applied occurrence-based and Boolean (suitable-pixel) approaches, comparing each against environmental background using PERMANOVA and PERMADISP. Niche overlap was also assessed using Schoeners D. C_LIO_LIVariable importance profiles showed no consistent patterns across genera or regions, but we observed clear distinction on species occupied environmental space both within and across biogeographic regions. The relatively few cases of niche similarity and overlap occurred mainly among congeneric species and between Nearctic and Afrotropical taxa. Globally, species distributions were structured along a gradient opposing dry, thermally extreme environments and wetter, more vegetated conditions. While accumulated heat, climatic seasonality, and water-energy balance also contributed to niche differentiation. C_LIO_LIDespite honeypot ants being considered desert specialists, our results show considerable environmental heterogeneity among species. As a group, honeypot ants neither occupy the same environmental space nor experience the same contemporary climatic pressures. This suggests that repletism is not a response to a single, conserved environmental condition, but to an interaction of physiological, morphological and behavioral constraints under different climatic contexts. C_LIO_LIBy characterizing the contemporary environmental niches of honeypot ants, this study establishes a baseline for further research on the evolution of repletism. While our results suggest that contemporary environmental factors cannot explain the convergence of honeypot ants, future work should examine paleoclimatic conditions along with species-level ecological traits. C_LI

ecology↗

bioRxiv2022

The first fossil replete ant worker establishes living food storage in the Eocene

Worker specialization extends the behavioral and ecological repertoire of ant colonies. Specialization may relate to colony defense, brood care, foraging, and, in some taxa, storage. Replete workers swell the crop and gaster to store liquid food, which can be accessed by other colony members through trophallaxis. This storage ability, known as repletism, has independently evolved across several ant lineages, but the temporal history of this trait has not yet been investigated. Here, we describe the first fossil replete in the extinct species Leptomyrmex neotropicus Baroni Urbani, 1980 preserved in Miocene-age Dominican amber. Together with new evidence of repletism in L. neotropicus extant sister species, L. relictus Boudinot et al., 2016, we reconstruct the pattern of acquisition and descent in this storage-linked trait. Our ancestral state reconstruction suggests that Leptomyrmex acquired replete workers in the Eocene and may therefore represent the earliest instance of so-called "honeypot" ants among all known ants, both living and extinct.

evolutionary biology↗

bioRxiv2021

Prey identity affects fitness of a generalist consumer in a brown food web

The use of ever-advancing sequencing technologies has revealed incredible biodiversity at the microbial scale, and yet we know little about the ecological interactions in these communities. For example, in the phytotelmic community found in the purple pitcher plant, Sarrecenia purpurea, ecologists typically consider the bacteria as a functionally homogenous group. In this food web, bacteria decompose detritus and are consumed by protozoa that are considered generalist consumers. Here we tested whether a generalist consumer benefits from all bacteria equally. We isolated and identified 22 strains of bacteria, belonging to six genera, from S. purpurea plants. We grew the protozoa, Tetrahymena sp. with single isolates and strain mixtures of bacteria and measured Tetrahymena fitness. We found that different bacterial strains had different effects on protozoan fitness, both in isolation and in mixture. Our results demonstrate that not accounting for composition of prey communities may affect the predicted outcome of predator-prey interactions.

ecology↗

bioRxiv2020

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

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

systems biology↗

bioRxiv2019

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

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

ecology↗

bioRxiv2018

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

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

microbiology↗