Utricularia are rootless aquatic carnivorous plants which have recently attracted the attention of researchers due to the peculiarities of their miniaturized genomes. Here, we focus on a novel aspect of Utricularia ecophysiology—the interactions with and within the complex communities of microorganisms colonizing their traps and external surfaces. Bacteria, fungi, algae, and protozoa inhabit the miniature ecosystem of the Utricularia trap lumen and are involved in the regeneration of nutrients from complex organic matter. By combining molecular methods, microscopy, and other approaches to assess the trap-associated microbial community structure, diversity, function, as well as the nutrient turn-over potential of bacterivory, we gained insight into the nutrient acquisition strategies of the Utricularia hosts. We conclude that Utricularia traps can, in terms of their ecophysiological function, be compared to microbial cultivators or farms, which center around complex microbial consortia acting synergistically to convert complex organic matter, often of algal origin, into a source of utilizable nutrients for the plants.

The rootless, aquatic Utricularia species belong to the largest and most cosmopolitan carnivorous plant genus. Populations of Utricularia plants are an important component of many standing, nutrient-poor, and humic waters. Carbon (C) allocation is an aspect of Utricularia’s ecophysiology that has not been studied previously and there is considerable uncertainty about the functional and ecological benefit of the trap-associated microbial community and the potential role played by C exudation in enhancing plant–microbe interactions. A ¹³C-labelling experiment was conducted in greenhouse conditions to determine the C allocation between plant tissues of increasing age and trap fluid in two Utricularia species. Both species allocated a majority of the newly fixed C into the fast growing shoot apex (46.1±8.6% in U. vulgaris and 56.1% in U. australis). Carbon allocation rapidly decreased with increasing age of the shoot, constituting only 8.0±4.0% and 6.7% of the total newly fixed C in the oldest analysed segments in U. vulgaris and U. australis, respectively. In the trap-bearing shoot segments, the ratio of C exuded into the trap fluid to that in plant tissues increased markedly with age—in the oldest analysed segments twice as much newly fixed C was allocated into the trap fluid than the plant tissue. Overall, a significant amount of the newly fixed C, approximately 25% (U. vulgaris) and 20% (U. australis), was allocated to the trap fluid. The importance of C exudation for the development of the microbial community associated with the traps as well as for the growth and ecology of aquatic Utricularia is discussed.

Rootless carnivorous plants of the genus Utricularia are important components of many standing waters worldwide, as well as suitable model organisms for studying plant–microbe interactions. In this study, an investigation was made of the importance of microbial dinitrogen (N₂) fixation in the N acquisition of four aquatic Utricularia species and another aquatic carnivorous plant, Aldrovanda vesiculosa. 16S rRNA amplicon sequencing was used to assess the presence of micro-organisms with known ability to fix N₂. Next-generation sequencing provided information on the expression of N₂ fixation-associated genes. N₂ fixation rates were measured following ¹⁵N₂-labelling and were used to calculate the plant assimilation rate of microbially fixed N₂. Utricularia traps were confirmed as primary sites of N₂ fixation, with up to 16 % of the plant-associated microbial community consisting of bacteria capable of fixing N₂. Of these, rhizobia were the most abundant group. Nitrogen fixation rates increased with increasing shoot age, but never exceeded 1·3 μmol N g^–1 d. mass d^–1. Plant assimilation rates of fixed N₂ were detectable and significant, but this fraction formed less than 1 % of daily plant N gain. Although trap fluid provides conditions favourable for microbial N₂ fixation, levels of nif gene transcription comprised <0·01 % of the total prokaryotic transcripts. It is hypothesized that the reason for limited N₂ fixation in aquatic Utricularia, despite the large potential capacity, is the high concentration of NH₄-N (2·0–4·3 mg L^–1) in the trap fluid. Resulting from fast turnover of organic detritus, it probably inhibits N₂ fixation in most of the microorganisms present. Nitrogen fixation is not expected to contribute significantly to N nutrition of aquatic carnivorous plants under their typical growth conditions; however, on an annual basis the plant–microbe system can supply nitrogen in the order of hundreds of mg m^–2 into the nutrient-limited littoral zone, where it may thus represent an important N source.

Rootless aquatic carnivorous Utricularia exude up to 25% of their photosynthates into the trap lumen, which also harbours a complex microbial community thought to play a role in enhancing Utricularia nutrient acquisition. We investigated the composition of organic carbon in the trap fluid, its availability for microbial uptake, the influence of plant nutrient status and trap age on its biodegradability, and the composition of prokaryotic assemblages within the traps of three aquatic Utricularia species. Using ion chromatography and basal respiration rate measurements we confirmed that up to 30% of total dissolved organic carbon in Utricularia trap fluid in oligotrophic conditions was easily biodegradable compounds commonly found in plant root exudates (mainly glucose, fructose and lactate). The proportion of these compounds and their microbial utilisation decreased with increasing mineral nutrient supply and trap age. Fluorescence in situ hybridisation analyses showed that microbial trap assemblages are dominated by alpha and beta Proteobacteria, and that the assemblage composition is affected by changes in the ambient mineral nutrient supply. We suggest that organic carbon dynamics within the traps, involving both the plant and associated microbial assemblages, underlies the acquisition of key nutrients by Utricularia and may help explain the evolutionary success of the genus.

The species of Utricularia attract attention not only owing to their carnivorous lifestyle, but also due to an elevated substitution rate and a dynamic evolution of genome size leading to its dramatic reduction. To better understand the evolutionary dynamics of genome size and content as well as the great physiological plasticity in this mostly aquatic carnivorous genus, we analyzed the transcriptome of Utricularia vulgaris, a temperate species with well characterized physiology and ecology. We compared its transcriptome, namely gene content and overall transcript profile, with a previously described transcriptome of Utricularia gibba, a congener possessing one of the smallest angiosperm genomes. We sequenced a normalized cDNA library prepared from total RNA extracted from shoots of U. vulgaris including leaves and traps, cultivated under sterile or outdoor conditions. 454 pyrosequencing resulted in more than 1,400,000 reads which were assembled into 41,407 isotigs in 19,522 isogroups. We observed high transcript variation in several isogroups explained by multiple loci and/or alternative splicing. The comparison of U. vulgaris and U. gibba transcriptomes revealed a similar distribution of GO categories among expressed genes, despite the differences in transcriptome preparation. We also found a strong correspondence in the presence or absence of root-associated genes between the U. vulgaris transcriptome and U. gibba genome, which indicated that the loss of some root-specific genes had occurred before the divergence of the two rootless species. The species-rich genus Utricularia offers a unique opportunity to study adaptations related to the environment and carnivorous habit and also evolutionary processes responsible for considerable genome reduction. We show that a transcriptome may approximate the genome for gene content or gene duplication estimation. Our study is the first comparison of two global sequence data sets in Utricularia.