A ridge-to-reef ecosystem microbial census reveals environmental reservoirs for animal and plant microbiomes.

Microbes are found in nearly every habitat and organism on the planet, where they are critical to host health, fitness, and metabolism. In most organisms, few microbes are inherited at birth; instead, acquiring microbiomes generally involves complicated interactions between the environment, hosts, and symbionts. Despite the criticality of microbiome acquisition, we know little about where hosts' microbes reside when not in or on hosts of interest. Because microbes span a continuum ranging from generalists associating with multiple hosts and habitats to specialists with narrower host ranges, identifying potential sources of microbial diversity that can contribute to the microbiomes of unrelated hosts is a gap in our understanding of microbiome assembly. Microbial dispersal attenuates with distance, so identifying sources and sinks requires data from microbiomes that are contemporary and near enough for potential microbial transmission. Here, we characterize microbiomes across adjacent terrestrial and aquatic hosts and habitats throughout an entire watershed, showing that the most species-poor microbiomes are partial subsets of the most species-rich and that microbiomes of plants and animals are nested within those of their environments. Furthermore, we show that the host and habitat range of a microbe within a single ecosystem predicts its global distribution, a relationship with implications for global microbial assembly processes. Thus, the tendency for microbes to occupy multiple habitats and unrelated hosts enables persistent microbiomes, even when host populations are disjunct. Our whole-watershed census demonstrates how a nested distribution of microbes, following the trophic hierarchies of hosts, can shape microbial acquisition.

In situ lipid profiling of insect pheromone glands by direct analysis in real time mass spectrometry.

Lipid pheromones play a significant role in the behavior and ecology of many insects. The characterization of pheromone structures is a significant challenge due to their low abundance and ephemeral nature. Here we present a method for the analysis of lipid molecules from single pheromone glands of Drosophila melanogaster (fruit fly) using Direct Analysis in Real Time mass spectrometry (DART MS). Our results reveal that DART MS analysis of single tissues generates reproducible, species-specific lipid profiles comprised of fatty acids, wax esters, diacylglycerides and triacylglycerides. In addition, the ion source temperature and application of a solvent wash can cause significant qualitative and quantitative changes in the mass spectral profile. Lastly, we show that untargeted chemical fingerprinting of the gland can be used to accurately categorize species according to phylogenetic subgroup or genotype. Collectively, our findings indicate that DART MS is a rapid and powerful method for characterizing a broad range of lipids in tissues with minimal preparation. The application of direct tissue DART MS will expand the "secretome" of molecules produced by pheromone glands. In addition to its direct relevance to chemical ecology, the method could potentially be used in pharmaceutical studies for the screening and detection of tissue-specific drug metabolites.

Carbon-carbon double bond position elucidation in fatty acids using ozone-coupled direct analysis in real time mass spectrometry.

The carbon-carbon double bond positions of unsaturated fatty acids can have markedly different effects on biological function and also serve as biomarkers of disease pathology, dietary history, and species identity. As such, there is great interest in developing methods for the facile determination of double bond position for natural product chemistry, the pharmaceutical industry, and forensics. We paired ozonolysis with direct analysis in real time mass spectrometry (DART MS) to cleave and rapidly identify carbon-carbon double bond position in fatty acids, fatty alcohols, wax esters, and crude fatty acid extracts. In addition, ozone exposure time and DART ion source temperature were investigated to identify optimal conditions. Our results reveal that brief, offline exposure to ozone-generated aldehyde and carboxylate products that are indicative of carbon-carbon double bond position. The relative abundance of diagnostic fragments quantitatively reflects the ratios of isobaric fatty acid positional isomers in a mixture with a correlation coefficient of 0.99. Lastly, the unsaturation profile generated from unfractionated, fatty acid extracts can be used to differentiate insect species and populations. The ability to rapidly elucidate lipid double bond position by combining ozonolysis with DART MS will be useful for lipid structural elucidation, assessing isobaric purity, and potentially distinguishing between animals fed on different diets or belonging to different ecological populations.

The evolution of a series of behavioral traits is associated with autism-risk genes in cavefish.

BACKGROUND: An essential question in evolutionary biology is whether shifts in a set of polygenic behaviors share a genetic basis across species. Such a behavioral shift is seen in the cave-dwelling Mexican tetra, Astyanax mexicanus. Relative to surface-dwelling conspecifics, cavefish do not school (asocial), are hyperactive and sleepless, adhere to a particular vibration stimulus (imbalanced attention), behave repetitively, and show elevated stress hormone levels. Interestingly, these traits largely overlap with the core symptoms of human autism spectrum disorder (ASD), raising the possibility that these behavioral traits are underpinned by a similar set of genes (i.e. a repeatedly used suite of genes). RESULT: Here, we explored whether modification of ASD-risk genes underlies cavefish evolution. Transcriptomic analyses revealed that > 58.5% of 3152 cavefish orthologs to ASD-risk genes are significantly up- or down-regulated in the same direction as genes in postmortem brains from ASD patients. Enrichment tests suggest that ASD-risk gene orthologs in A. mexicanus have experienced more positive selection than other genes across the genome. Notably, these positively selected cavefish ASD-risk genes are enriched for pathways involved in gut function, inflammatory diseases, and lipid/energy metabolism, similar to symptoms that frequently coexist in ASD patients. Lastly, ASD drugs mitigated cavefish's ASD-like behaviors, implying shared aspects of neural processing. CONCLUSION: Overall, our study indicates that ASD-risk genes and associated pathways (especially digestive, immune and metabolic pathways) may be repeatedly used for shifts in polygenic behaviors across evolutionary time.

Microbes control Drosophila germline stem cell increase and egg maturation through hormonal pathways.

Reproduction is highly dependent on environmental and physiological factors including nutrition, mating stimuli and microbes. Among these factors, microbes facilitate vital functions for host animals such as nutritional intake, metabolic regulation, and enhancing fertility under poor nutrition conditions. However, detailed molecular mechanisms by which microbes control germline maturation, leading to reproduction, remain largely unknown. In this study, we show that environmental microbes exert a beneficial effect on Drosophila oogenesis by promoting germline stem cell (GSC) proliferation and subsequent egg maturation via acceleration of ovarian cell division and suppression of apoptosis. Moreover, insulin-related signaling is not required; rather, the ecdysone pathway is necessary for microbe-induced increase of GSCs and promotion of egg maturation, while juvenile hormone contributes only to increasing GSC numbers, suggesting that hormonal pathways are activated at different stages of oogenesis. Our findings reveal that environmental microbes can enhance host reproductivity by modulating host hormone release and promoting oogenesis.

Plant part and a steep environmental gradient predict plant microbial composition in a tropical watershed.

Plant microbiomes are shaped by forces working at different spatial scales. Environmental factors determine a pool of potential symbionts while host physiochemical factors influence how those microbes associate with distinct plant tissues. These scales are seldom considered simultaneously, despite their potential to interact. Here, we analyze epiphytic microbes from nine Hibiscus tiliaceus trees across a steep, but short, environmental gradient within a single Hawaiian watershed. At each location, we sampled eight microhabitats: leaves, petioles, axils, stems, roots, and litter from the plant, as well as surrounding air and soil. The composition of bacterial communities is better explained by microhabitat, while location better predicted compositional variance for fungi. Fungal community compositional dissimilarity increased more rapidly along the gradient than did bacterial composition. Additionally, the rates of fungal community compositional dissimilarity along the gradient differed among plant parts, and these differences influenced the distribution patterns and range size of individual taxa. Within plants, microbes were compositionally nested such that aboveground communities contained a subset of the diversity found belowground. Our findings indicate that both environmental context and microhabitat contribute to microbial compositional variance in our study, but that these contributions are influenced by the domain of microbe and the specific microhabitat in question, suggesting a complicated and potentially interacting dynamic.