Leaf Endophytes Relationship with Host Metabolome Expression in Tropical Gymnosperms

Plant-microbe interactions play a pivotal role in shaping host fitness, especially concerning chemical defense mechanisms. In cycads, establishing direct correlations between specific endophytic microbes and the synthesis of highly toxic defensive phytochemicals has been challenging. Our research delves into the intricate relationship between plant-microbe associations and the variation of secondary metabolite production in two closely related Zamia species that grow in distinct habitats; terrestrial and epiphytic. Employing an integrated approach, we combined microbial metabarcoding, which characterize the leaf endophytic bacterial and fungal communities, with untargeted metabolomics to test if the relative abundances of specific microbial taxa in these two Zamia species were associated with different metabolome profiles. The two species studied shared approximately 90% of the metabolites spanning diverse biosynthetic pathways: alkaloids, amino acids, carbohydrates, fatty acids, polyketides, shikimates, phenylpropanoids, and terpenoids. Co-occurrence networks revealed positive associations among metabolites from different pathways, underscoring the complexity of their interactions. Our integrated analysis demonstrated to some degree that the intraspecific variation in metabolome profiles of the two host species was associated with the abundance of bacterial orders Acidobacteriales and Frankiales, as well as the fungal endophytes belonging to the orders Chaetothyriales, Glomerellales, Heliotiales, Hypocreales, and Sordariales. We further associate individual metabolic similarity with four specific fungal endophyte members of the core microbiota, but no specific bacterial taxa associations were identified. This study represents a pioneering investigation to characterize leaf endophytes and their association with metabolomes in tropical gymnosperms, laying the groundwork for deeper inquiries into this complex domain.

Gut microbiomes of cycad-feeding insects tolerant to β-methylamino-L-alanine (BMAA) are rich in siderophore biosynthesis

Ingestion of the cycad toxins β-methylamino-L-alanine (BMAA) and azoxyglycosides is harmful to diverse organisms. However, some insects are specialized to feed on toxin-rich cycads with apparent immunity. Some cycad-feeding insects possess a common set of gut bacteria, which might play a role in detoxifying cycad toxins. Here, we investigated the composition of gut microbiota from a worldwide sample of cycadivorous insects and characterized the biosynthetic potential of selected bacteria. Cycadivorous insects shared a core gut microbiome consisting of six bacterial taxa, mainly belonging to the Proteobacteria, which we were able to isolate. To further investigate selected taxa from diverging lineages, we performed shotgun metagenomic sequencing of co-cultured bacterial sub-communities. We characterized the biosynthetic potential of four bacteria from Serratia, Pantoea, and two different Stenotrophomonas lineages, and discovered a suite of biosynthetic gene clusters notably rich in siderophores. Siderophore semi-untargeted metabolomics revealed a broad range of chemically related yet diverse iron-chelating metabolites, including desferrioxamine B, suggesting the occurrence of an unprecedented desferrioxamine-like biosynthetic pathway that remains to be identified. These results provide a foundation for future investigations into how cycadivorous insects tolerate diets rich in azoxyglycosides, BMAA, and other cycad toxins, including a possible role for bacterial siderophores.

Cycad phylogeny predicts host plant use of Eumaeus butterflies

Eumaeus butterflies are obligate herbivores of Zamia, the most diverse neotropical genus of cycads. Eumaeus-Zamia interactions have been characterized mainly for species distributed in North and Central America. However, larval host plant use by the southern Eumaeus clade remains largely unknown, precluding a comprehensive study of co-evolution between the genera. Here, we combine fieldwork with museum and literature surveys to expand herbivory records for Eumaeus from 21 to 38 Zamia species. We inferred a time-calibrated phylogeny of Eumaeus to test for distinct macroevolutionary scenarios of larval host plant conservatism and co-evolution. We found a remarkable coincidence between Eumaeus and Zamia diversification, with the butterfly stem group diverging at the same time as the most recent radiation of Zamia in the Miocene. Cophylogenetic reconciliation analyses show a strong cophylogenetic signal between cycads and their butterfly herbivores. Bipartite model-based approaches indicate that this is because closely related Zamia species are used by the same Eumaeus species, suggesting larval host plant resource tracking by the butterfly herbivores. Our results highlight a case of tight evolution between Eumaeus butterflies and cycads, pointing to the generality of correlated evolution and phylogenetic tracking in plant-herbivore interactions across seed plants.

Taxonomic, Genomic, and Functional Variation in the Gut Microbiomes of Wild Spotted Hyenas Across 2 Decades of Study

The gut microbiome provides vital functions for mammalian hosts, yet research on its variability and function across adult life spans and multiple generations is limited in large mammalian carnivores. Here, we used 16S rRNA gene and metagenomic high-throughput sequencing to profile the bacterial taxonomic composition, genomic diversity, and metabolic function of fecal samples collected from 12 wild spotted hyenas (Crocuta crocuta) residing in the Masai Mara National Reserve, Kenya, over a 23-year period spanning three generations. The metagenomic data came from four of these hyenas and spanned two 2-year periods. With these data, we determined the extent to which host factors predicted variation in the gut microbiome and identified the core microbes present in the guts of hyenas. We also investigated novel genomic diversity in the mammalian gut by reporting the first metagenome-assembled genomes (MAGs) for hyenas. We found that gut microbiome taxonomic composition varied temporally, but despite this, a core set of 14 bacterial genera were identified. The strongest predictors of the microbiome were host identity and age, suggesting that hyenas possess individualized microbiomes and that these may change with age during adulthood. The gut microbiome functional profiles of the four adult hyenas were also individual specific and were associated with prey abundance, indicating that the functions of the gut microbiome vary with host diet. We recovered 149 high-quality MAGs from the hyenas' guts; some MAGs were classified as taxa previously reported for other carnivores, but many were novel and lacked species-level matches to genomes in existing reference databases. IMPORTANCE There is a gap in knowledge regarding the genomic diversity and variation of the gut microbiome across a host's life span and across multiple generations of hosts in wild mammals. Using two types of sequencing approaches, we found that although gut microbiomes were individualized and temporally variable among hyenas, they correlated similarly to large-scale changes in the ecological conditions experienced by their hosts. We also recovered 149 high-quality MAGs from the hyena gut, greatly expanding the microbial genome repertoire known for hyenas, carnivores, and wild mammals in general. Some MAGs came from genera abundant in the gastrointestinal tracts of canid species and other carnivores, but over 80% of MAGs were novel and from species not previously represented in genome databases. Collectively, our novel body of work illustrates the importance of surveying the gut microbiome of nonmodel wild hosts, using multiple sequencing methods and computational approaches and at distinct scales of analysis.

Experimental evidence challenges the presumed defensive function of a "slow toxin" in cycads

[Formula: see text]-methylamino-L-alanine (BMAA) is a neurotoxic non-protein amino acid found in the tissues of cycad plants. The demonstrated toxicity of BMAA to diverse organisms, including humans, is widely assumed to imply a defensive function of BMAA against herbivores; however, this hypothesis has not previously been tested in an ecologically relevant system. We investigated the effects of dietary BMAA, across a range of dosages matching and exceeding levels typically present in cycad leaves, on the feeding preferences and performance of a generalist lepidopteran herbivore (Spodoptera littoralis).We observed no effects of dietary BMAA on the survival or development of S. littoralis larvae, nor any larval preference between BMAA-laced and control diets. These findings suggest that BMAA in cycad tissues does not deter feeding by insect herbivores, raising questions about other potential physiological or ecological functions of this compound.

No guts about it: captivity, but not neophobia phenotype, influences the cloacal microbiome of house sparrows (Passer domesticus)

Behavioral traits such as anxiety and depression have been linked to diversity of the gut microbiome in humans, domesticated animals, and lab-bred model species, but the extent to which this link exists in wild animals, and thus its ecological relevance, is poorly understood. We examined the relationship between a behavioral trait (neophobia) and the cloacal microbiome in wild house sparrows (Passer domesticus,n = 22) to determine whether gut microbial diversity is related to personality in a wild animal. We swabbed the cloaca immediately upon capture, assessed neophobia phenotypes in the lab, and then swabbed the cloaca again after several weeks in captivity to additionally test whether the microbiome of different personality types is affected disparately by captivity, and characterized gut microbiomes using 16S rRNA gene amplicon sequencing. We did not detect differences in cloacal alpha or beta microbial diversity between neophobic and non-neophobic house sparrows, and diversity for both phenotypes was negatively impacted by captivity. Although our results suggest that the adult cloacal microbiome and neophobia are not strongly linked in wild sparrows, we did detect specific OTUs that appeared more frequently and at higher abundances in neophobic sparrows, suggesting that links between the gut microbiome and behavior may occur at the level of specific taxa. Further investigations of personality and the gut microbiome are needed in more wild species to reveal how the microbiome-gut-brain axis and behavior interact in an ecological context.

Defining and quantifying the core microbiome: Challenges and prospects

The term "core microbiome" has become widely used in microbial ecology over the last decade. Broadly, the core microbiome refers to any set of microbial taxa, or the genomic and functional attributes associated with those taxa, that are characteristic of a host or environment of interest. Most commonly, core microbiomes are measured as the microbial taxa shared among two or more samples from a particular host or environment. Despite the popularity of this term and its growing use, there is little consensus about how a core microbiome should be quantified in practice. Here, we present a brief history of the core microbiome concept and use a representative sample of the literature to review the different metrics commonly used for quantifying the core. Empirical analyses have used a wide range of metrics for quantifying the core microbiome, including arbitrary occurrence and abundance cutoff values, with the focal taxonomic level of the core ranging from phyla to amplicon sequence variants. However, many of these metrics are susceptible to sampling and other biases. Developing a standardized set of metrics for quantifying the core that accounts for such biases is necessary for testing specific hypotheses about the functional and ecological roles of core microbiomes.

Vast (but avoidable) underestimation of global biodiversity

The number of species on Earth is highly uncertain. A recent study has suggested that there are less than 2 million prokaryotic species on Earth; this Formal Comment suggests instead that there are more likely hundreds of millions or billions of species, and that the majority of these are bacteria associated with insects and other animals.

The high adaptability of Hyphantria cunea larvae to cinnamic acid involves in detoxification, antioxidation and gut microbiota response

Hyphantria cunea is one of the most destructive invasive agricultural and forest pests worldwide. In order to better understand the adaptation mechanism of H. cunea larvae to secondary metabolites of their highly diversified host plants, the physiological function and detoxification ability of midgut, as well as the gut microbial community were investigated in H. cunea larvae fed with cinnamic acid-treated artificial diets. Our results showed that cinnamic acid treatment could not affect the growth and food utilization of H. cunea larvae, as evidenced by a non-significantly altered larval body weight and efficiency of conversion of ingested food. Evaluation of oxidative stress-related parameters (e.g. malondialdehyde and hydrogen peroxide) and midgut histopathology also clearly confirmed that cinnamic acid treatment caused no significant oxidative damage and pathological changes in the larval midgut. Variance analysis showed that cinnamic acid treatment significantly increased the content of non-enzymatic antioxidants (ascorbic acid and glutathione), the activity of antioxidant enzymes (superoxide dismutase and peroxidase) and detoxification enzyme (carboxylate esterase), as well as the abundance of several gut microbiota at the genus level (Hydrogenophaga and Acinetobacter) involved in the organic substance degradation in larval midgut. Further Pearson's correlation analysis revealed that these strongly altered gut microbiota at the genus level appeared to be significantly correlated with the detoxification and antioxidation parameters. These findings demonstrate the high adaptability of H. cunea larvae to cinnamic acid involves in detoxification, antioxidation and gut microbiota response, and indicate the existence of an extremely effective counter-defense mechanism for H. cunea larvae against the secondary metabolites of host plants.

Three antimicrobials alter gut microbial communities and causing different mortality of brown planthopper, Nilaparvata lugens Stål

The symbionts in the gut of brown planthopper play an important role in the nutrition utilization and growth of their host, Nilaparvata lugens Stål (Hemiptera: Delphacidae). Controlling the BPH infection on rice by inhibiting the symbionts using antimicrobials is feasible. However, the impact of antimicrobials on the microbiome in the gut has not been fully elucidated. In this study, we found the mortality reached 35.5%, 33.1% and 19.4%, when BPHs were exposed to toyocamycin, tebuconazole, and zhongshengmycin, respectively. Significant differences were found between the structures of gut microbial communities in adult BPHs treated with different antimicrobials and water. The antimicrobials reduced the fungal diversity by reducing the non-dominant fungi abundance, and increased bacterial diversity by inhibiting the dominant bacteria Acinetobacter in the gut. The diversification of taxonomic groups in gut depended on the different selective stress of antimicrobials. For the microbial absolute abundance, the total microbial gut community abundance decreased under antimicrobial exposure, but the absolute abundance of Serratia significantly increased in the antimicrobial treatment group. Overall, our study enriched the knowledge of microbiomes in the gut of BPH under the antimicrobial treatment and provided guidelines to enhance the pest management effect of BPH by using antimicrobials.

Ecology and evolution of cycad-feeding Lepidoptera

Cycads are an ancient group of tropical gymnosperms that are toxic to most animals - including humans - though the larvae of many moths and butterflies (order: Lepidoptera) feed on cycads with apparent immunity. These insects belong to distinct lineages with varying degrees of specialisation and diverse feeding ecologies, presenting numerous opportunities for comparative studies of chemically mediated eco-evolutionary dynamics. This review presents the first evolutionary evaluation of cycad-feeding among Lepidoptera along with a comprehensive review of their ecology. Our analysis suggests that multiple lineages have independently colonised cycads from angiosperm hosts, yet only a few clades appear to have radiated following their transitions to cycads. Defensive traits are likely important for diversification, as many cycad specialists are warningly coloured and sequester cycad toxins. The butterfly family Lycaenidae appears to be particularly predisposed to cycad-feeding and several cycadivorous lycaenids are warningly coloured and chemically defended. Cycad-herbivore interactions provide a promising but underutilised study system for investigating plant-insect coevolution, convergent and divergent adaptations, and the multi-trophic significance of defensive traits; therefore the review ends by suggesting specific research gaps that would be fruitfully addressed in Lepidoptera and other cycad-feeding insects.

Burrowing activity of coconut rhinoceros beetle on Guam cycads

Guam’s established population of non-native coconut rhinoceros beetle (CRB, Oryctes rhinoceros L.) began creating burrows in stem apices of several cycad species in a managed garden. We conducted an island-wide survey to determine the spatial patterns of CRB burrowing of stems of in situ Cycas micronesica. We also measured starch of healthy and unhealthy coconut leaf tissue and compared this with starch of cycad stem tissue. The starch concentration of the central unexpanded leaf in healthy Philippine coconut trees was ≈90 mg·g⁻¹, and that of unhealthy Guam coconut trees was ≈40 mg·g⁻¹. The starch concentration of the tissue within the CRB burrow locations on C. micronesica trees was 145 mg·g⁻¹. Burrowing of C. micronesica was restricted to female CRB adults and was found throughout the full latitudinal gradient of Guam. Our findings indicate Guam’s unhealthy coconut trees are no longer nutrient-dense, and the female CRB population may have exhibited a phylogenetically distant host shift to the abundant C. micronesica plants for a starch-rich diet within the concepts of the ‘ecological fitting’ hypothesis. We add proximity to coconut tree habitats as a new threat to Guam’s endangered C. micronesica population.

Avermectin stress varied structure and function of gut microbial community in Lymantria dispar asiatica (Lepidoptera: Lymantriidae) larvae

Lymantria dispar asiatica is a globally distributed herbivorous pest. Avermectin is a highly effective, broad-spectrum insecticide. In this study, fourth instar L. dispar asiatica larvae were exposed to a LC₃₀ dose of avermectin. The structure and function of larval gut microbial community was analyzed to examine how gut microbiota in L. dispar asiatica larvae responded to avermectin stress. Results showed that the structure and function of gut microbial community in L. dispar asiatica larvae were varied by avermectin stress. To be precise, more than half quantity of the observed Optical Taxonomic Units (OTUs) showed significantly different abundances under avermectin stress. Linear discriminant analysis effect size (LEfSe) suggested nine bacterial genera and 12 fungal genera contributed to the different gut microbial community structure in L. dispar asiatica larvae. Gut microbial function classification (PICRUSt and FUNGuild) suggested that three bacterial function categories and a fungal function guild were significantly increased, and two fungal function guilds were significantly decreased by avermectin stress. This study furthers our understanding of the physiology of L. dispar asiatica larvae under avermectin stress, and is an essential step towards future development of potential pesticide targets.

Combining stable isotope analysis with DNA metabarcoding improves inferences of trophic ecology

Knowing what animals eat is fundamental to our ability to understand and manage biodiversity and ecosystems, but researchers often must rely on indirect methods to infer trophic position and food intake. Using an approach that combines evidence from stable isotope analysis and DNA metabarcoding, we assessed the diet and trophic position of Anthene usamba butterflies, for which there are no known direct observations of larval feeding. An earlier study that analyzed adults rather than caterpillars of A. usamba inferred that this butterfly was aphytophagous, but we found that the larval guts of A. usamba and two known herbivorous lycaenid species contain chloroplast 16S sequences. Moreover, chloroplast barcoding revealed high sequence similarity between chloroplasts found in A. usamba guts and the chloroplasts of the Vachellia drepanolobium trees on which the caterpillars live. Stable isotope analysis provided further evidence that A. usamba caterpillars feed on V. drepanolobium, and the possibilities of strict herbivory versus limited omnivory in this species are discussed. These results highlight the importance of combining multiple approaches and considering ontogeny when using stable isotopes to infer trophic ecology where direct observations are difficult or impossible.