The application of next‐generation sequencing (NGS) technologies for the development of simple sequence repeat (SSR) or microsatellite loci for genetic research in the botanical sciences is described. Microsatellite markers are one of the most informative and versatile DNA‐based markers used in plant genetic research, but their development has traditionally been a difficult and costly process. NGS technologies allow the efficient identification of large numbers of microsatellites at a fraction of the cost and effort of traditional approaches. The major advantage of NGS methods is their ability to produce large amounts of sequence data from which to isolate and develop numerous genome‐wide and gene‐based microsatellite loci. The two major NGS technologies with emergent application in SSR isolation are 454 and Illumina. A review is provided of several recent studies demonstrating the efficient use of 454 and Illumina technologies for the discovery of microsatellites in plants. Additionally, important aspects during NGS isolation and development of microsatellites are discussed, including the use of computational tools and high‐throughput genotyping methods. A data set of microsatellite loci in the plastome and mitochondriome of cranberry (Vaccinium macrocarpon Ait.) is provided to illustrate a successful application of 454 sequencing for SSR discovery. In the future, NGS technologies will massively increase the number of SSRs and other genetic markers available to conduct genetic research in understudied but economically important crops such as cranberry.

Food webs are known to have myriad trophic links between resource and consumer species. While herbivores have well‐understood trophic tendencies, the difficulties associated with characterizing the trophic positions of higher‐order consumers have remained a major problem in food web ecology. To better understand trophic linkages in food webs, analysis of the stable nitrogen isotopic composition of amino acids has been introduced as a potential means of providing accurate trophic position estimates. In the present study, we employ this method to estimate the trophic positions of 200 free‐roaming organisms, representing 39 species in coastal marine (a stony shore) and 38 species in terrestrial (a fruit farm) environments. Based on the trophic positions from the isotopic composition of amino acids, we are able to resolve the trophic structure of these complex food webs. Our approach reveals a high degree of trophic omnivory (i.e., noninteger trophic positions) among carnivorous species such as marine fish and terrestrial hornets.This information not only clarifies the trophic tendencies of species within their respective communities, but also suggests that trophic omnivory may be common in these webs.

In most ecosystems, microbes are the dominant consumers, commandeering much of the heterotrophic biomass circulating through food webs. Characterizing functional diversity within the microbiome, therefore, is critical to understanding ecosystem functioning, particularly in an era of global biodiversity loss. Using isotopic fingerprinting, we investigated the trophic positions of a broad diversity of heterotrophic organisms. Specifically, we examined the naturally occurring stable isotopes of nitrogen (¹⁵N:¹⁴N) within amino acids extracted from proteobacteria, actinomycetes, ascomycetes, and basidiomycetes, as well as from vertebrate and invertebrate macrofauna (crustaceans, fish, insects, and mammals). Here, we report that patterns of intertrophic ¹⁵N-discrimination were remarkably similar among bacteria, fungi, and animals, which permitted unambiguous measurement of consumer trophic position, independent of phylogeny or ecosystem type. The observed similarities among bacterial, fungal, and animal consumers suggest that within a trophic hierarchy, microbiota are equivalent to, and can be interdigitated with, macrobiota. To further test the universality of this finding, we examined Neotropical fungus gardens, communities in which bacteria, fungi, and animals are entwined in an ancient, quadripartite symbiosis. We reveal that this symbiosis is a discrete four-level food chain, wherein bacteria function as the apex carnivores, animals and fungi are meso-consumers, and the sole herbivores are fungi. Together, our findings demonstrate that bacteria, fungi, and animals can be integrated within a food chain, effectively uniting the macro- and microbiome in food web ecology and facilitating greater inclusion of the microbiome in studies of functional diversity. Significance We report evidence that microbes are trophically equivalent to animals. When bacteria or fungi are fed the same diets as animals, the microbes register the same trophic position as animals. This discovery reframes how microbes can be viewed within food chains and facilitates the inclusion of the microbiome in functional diversity studies. To demonstrate the broad applicability of our approach, we investigated the ancient symbioses represented by leaf-cutter ant fungus gardens, revealing four discrete trophic levels within this community and providing evidence that fungi, not ants, are the dominant herbivores of the Neotropics. Altogether, we show that microbes can be integrated with plants and animals in a food chain, thereby unifying the macro- and microbiome in studies of trophic ecology.

Growing evidence reveals strong overlap between microbiomes of flowers and bees, suggesting that flowers are hubs of microbial transmission. Whether floral transmission is the main driver of bee microbiome assembly, and whether functional importance of florally sourced microbes shapes bee foraging decisions are intriguing questions that remain unanswered. We suggest that interaction network properties, such as nestedness, connectedness, and modularity, as well as specialization patterns can predict potential transmission routes of microbes between hosts. Yet microbial filtering by plant and bee hosts determines realized microbial niches. Functionally, shared floral microbes can provide benefits for bees by enhancing nutritional quality, detoxification, and disintegration of pollen. Flower microbes can also alter the attractiveness of floral resources. Together, these mechanisms may affect the structure of the flower-bee interaction network.