In the last two decades, the widespread application of genetic and genomic approaches has revealed a bacterial world astonishing in its ubiquity and diversity. This review examines how a growing knowledge of the vast range of animal–bacterial interactions, whether in shared ecosystems or intimate symbioses, is fundamentally altering our understanding of animal biology. Specifically, we highlight recent technological and intellectual advances that have changed our thinking about five questions: how have bacteria facilitated the origin and evolution of animals; how do animals and bacteria affect each other’s genomes; how does normal animal development depend on bacterial partners; how is homeostasis maintained between animals and their symbionts; and how can ecological approaches deepen our understanding of the multiple levels of animal–bacterial interaction. As answers to these fundamental questions emerge, all biologists will be challenged to broaden their appreciation of these interactions and to include investigations of the relationships between and among bacteria and their animal partners as we seek a better understanding of the natural world

Most aphids possess intracellular bacteria of the genus Buchnera. The bacteria are transmitted vertically via the aphid ovary, and the association is obligate for both partners: Bacteria-free aphids grow poorly and produce few or no offspring, and Buchnera are both unknown apart from aphids and apparently unculturable. The symbiosis has a nutritional basis. Specifically, bacterial provisioning of essential amino acids has been demonstrated. Nitrogen recycling, however, is not quantitatively important to the nutrition of aphid species studied, and there is strong evidence against bacterial involvement in the lipid and sterol nutrition of aphids. Buchnera have been implicated in various non-nutritional functions. Of these, just one has strong experimental support: promotion of aphid transmission of circulative viruses. It is argued that strong parallels may exist between the nutritional interactions (including the underlying mechanisms) in the aphid-Buchnera association and other insect symbioses with intracellular microorganisms.

All insects are colonized by microorganisms on the insect exoskeleton, in the gut and hemocoel, and within insect cells. The insect microbiota is generally different from microorganisms in the external environment, including ingested food. Specifically, certain microbial taxa are favored by the conditions and resources in the insect habitat, by their tolerance of insect immunity, and by specific mechanisms for their transmission. The resident microorganisms can promote insect fitness by contributing to nutrition, especially by providing essential amino acids, B vitamins, and, for fungal partners, sterols. Some microorganisms protect their insect hosts against pathogens, parasitoids, and other parasites by synthesizing specific toxins or modifying the insect immune system. Priorities for future research include elucidation of microbial contributions to detoxification, especially of plant allelochemicals in phytophagous insects, and resistance to pathogens; as well as their role in among-insect communication; and the potential value of manipulation of the microbiota to control insect pests.

Summary 1.Many insects derive nutritional advantage from persistent associations with microorganisms that variously synthesize essential nutrients or digest and detoxify ingested food. These persistent relationships are symbioses. 2. There is strong experimental evidence that symbiotic microorganisms provide plant sap-feeding insects with essential amino acids and contribute to the digestion of cellulose in some wood-feeding insects, including lower termites. Basic nutritional information is, however, lacking for many associations, including the relative roles of microbial and intrinsic sources of cellulose degradation in many insects and B-vitamin provisioning by microorganisms in blood-feeding insects.3. Some nutritional interactions between insects and their symbiotic microorganisms vary among conspecifics and closely related species. This variation can, in principle, contribute to nutritional explanations for variation in the abundance and distribution of insects. For example, the plant utilization traits of phloem-feeding aphids and stinkbugs have been demonstrated to depend on the identity of microbial partners. Evidence that associations can evolve rapidly comes from the demonstration that the impact of the bacterium Wolbachia on natural populations of its insect host can change from deleterious to beneficial within two decades. 4. Developing genomic tools, especially massively parallel sequencing and metagenomic analyses, offer the opportunity to explore the metabolic capabilities of symbiotic microorganisms and their insect hosts, from which defined hypotheses of nutritional function can be constructed. Nutritional ecology provides the appropriate framework to test these hypotheses in the relevant ecological context.

The incidence of phloem sap feeding by animals appears paradoxical. Although phloem sap is nutrient-rich compared with many other plant products and generally lacking in toxins and feeding deterrents, it is consumed as the dominant or sole diet by a very restricted range of animals, exclusively insects of the order Hemiptera. These insects display two sets of adaptations. First, linked to the high ratio of non-essential:essential amino acids in phloem sap, these insects contain symbiotic micro-organisms which provide them with essential amino acids. For example, bacteria of the genus Buchnera contribute up to 90% of the essential amino acids required by the pea aphid Acyrthosiphon pisum feeding on Vicia faba. Second, the insect tolerance of the very high sugar content and osmotic pressure of phloem sap is promoted by their possession in the gut of sucrase-transglucosidase activity, which transforms excess ingested sugar into long-chain oligosaccharides voided via honeydew. Various other animals consume phloem sap by proxy, through feeding on the honeydew of phloem-feeding hemipterans. Honeydew is physiologically less extreme than phloem sap, with a higher essential:non-essential amino acid ratio and lower osmotic pressure. Even so, ant species strongly dependent on honeydew as food may benefit from nutrients derived from their symbiotic bacteria Blochmannia.