CARD-FISH and prey tracer techniques reveal the role of overlooked flagellate groups as major bacterivores in freshwater hypertrophic shallow lakes.

Heterotrophic nanoflagellates (HNF) and ciliates are major protistan planktonic bacterivores. The term HNF, however, describes a functional guild only and, in contrast to the morphologically distinguishable ciliates, does not reflect the phylogenetic diversity of flagellates in aquatic ecosystems. Associating a function with taxonomic affiliation of key flagellate taxa is currently a major task in microbial ecology. We investigated seasonal changes in the HNF and ciliate community composition as well as taxa-specific bacterivory in four hypertrophic freshwater lakes. Taxa-specific catalyzed reporter deposition-fluorescence in situ hybridization probes assigned taxonomic affiliations to 51%-96% (average ±SD, 75 ± 14%) of total HNF. Ingestion rates of fluorescently labelled bacteria unveiled that HNF contributed to total protist-induced bacterial mortality rates more (56%) than ciliates (44%). Surprisingly, major HNF bacterivores were aplastidic cryptophytes and their Cry1 lineage, comprising on average 53% and 24% of total HNF abundance and 67% and 21% of total HNF bacterivory respectively. Kinetoplastea were important consumers of bacteria during summer phytoplankton blooms, reaching 38% of total HNF. Katablepharidacea (7.5% of total HNF) comprised mainly omnivores, with changing contributions of bacterivorous and algivorous phylotypes. Our results show that aplastidic cryptophytes, accompanied by small omnivorous ciliate genera Halteria/Pelagohalteria, are the major protistan bacterivores in hypertrophic freshwaters.

The Ability of Tetrahymena utriculariae (Ciliophora, Oligohymenophorea) to Colonize Traps of Different Species of Aquatic Carnivorous Utricularia.

The host specificity of the recently described ciliate species Tetrahymena utriculariae was tested in a greenhouse growth experiment, which included 14 different species of aquatic Utricularia as potential host plants. We confirmed the high specificity of the interaction between U. reflexa and T. utriculariae, the former being the only tested host species able to maintain colonization for prolonged time periods. We conclude that this plant-microbe relationship is a unique and specialized form of digestive mutualism and the plant-microbe unit a suitable experimental system for future ecophysiological studies.

The Green Tetrahymena utriculariae n. sp. (Ciliophora, Oligohymenophorea) with Its Endosymbiotic Algae (Micractinium sp.), Living in Traps of a Carnivorous Aquatic Plant.

The genus Tetrahymena (Ciliophora, Oligohymenophorea) probably represents the best studied ciliate genus. At present, more than forty species have been described. All are colorless, i.e. they do not harbor symbiotic algae, and as aerobes they need at least microaerobic habitats. Here, we present the morphological and molecular description of the first green representative, Tetrahymena utriculariae n. sp., living in symbiosis with endosymbiotic algae identified as Micractinium sp. (Chlorophyta). The full life cycle of the ciliate species is documented, including trophonts and theronts, conjugating cells, resting cysts and dividers. This species has been discovered in an exotic habitat, namely in traps of the carnivorous aquatic plant Utricularia reflexa (originating from Okavango Delta, Botswana). Green ciliates live as commensals of the plant in this anoxic habitat. Ciliates are bacterivorous, however, symbiosis with algae is needed to satisfy cell metabolism but also to gain oxygen from symbionts. When ciliates are cultivated outside their natural habitat under aerobic conditions and fed with saturating bacterial food, they gradually become aposymbiotic. Based on phylogenetic analyses of 18S rRNA and mitochondrial cox1 genes T. utriculariae forms a sister group to Tetrahymena thermophila.

Ecological Traits of the Algae-Bearing Tetrahymena utriculariae (Ciliophora) from Traps of the Aquatic Carnivorous Plant Utricularia reflexa.

Trap fluid of aquatic carnivorous plants of the genus Utricularia hosts specific microbiomes consisting of commensal pro- and eukaryotes of largely unknown ecology. We examined the characteristics and dynamics of bacteria and the three dominant eukaryotes, i.e. the algae-bearing ciliate Tetrahymena utriculariae (Ciliophora), a green flagellate Euglena agilis (Euglenophyta), and the alga Scenedesmus alternans (Chlorophyta), associated with the traps of Utricularia reflexa. Our study focused on ecological traits and life strategies of the highly abundant ciliate whose biomass by far exceeds that of other eukaryotes and bacteria independent of the trap age. The ciliate was the only bacterivore in the traps, driving rapid turnover of bacterial standing stock. However, given the large size of the ciliate and the cell-specific uptake rates of bacteria we estimated that bacterivory alone would likely be insufficient to support its apparent rapid growth in traps. We suggest that mixotrophy based on algal symbionts contributes significantly to the diet and survival strategy of the ciliate in the extreme (anaerobic, low pH) trap-fluid environment. We propose a revised concept of major microbial interactions in the trap fluid where ciliate bacterivory plays a central role in regeneration of nutrients bound in rapidly growing bacterial biomass.

The transcriptome of Utricularia vulgaris, a rootless plant with minimalist genome, reveals extreme alternative splicing and only moderate sequence similarity with Utricularia gibba.

BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: 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.

Dinitrogen fixation associated with shoots of aquatic carnivorous plants: is it ecologically important?

BACKGROUND AND AIMS: 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. METHODS: 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 (15)N2-labelling and were used to calculate the plant assimilation rate of microbially fixed N2. KEY RESULTS: 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. CONCLUSIONS: 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.

Patterns of activities of root phosphomonoesterase and phosphodiesterase in wetland plants as a function of macrophyte species and ambient phosphorus regime.

Phosphorus (P)-limited plants produce higher amounts of root phosphatases, but research has mostly focused on phosphomonoesterases (PMEs). Because phosphate diesters can form a significant proportion of organic P in wetlands, we aimed to determine whether wetland plants produce both root PMEs and root phosphodiesterases (PDEs), and, if so, what factors influence activities of these enzymes. We measured the activities of root PMEs and PDEs colorimetrically in a wide range of macrophytes from natural and P-enriched wetlands. Hydrolyzable P in sediments was analyzed using commercially available PMEs and PDEs. In all species, both root PMEs and PDEs were always present, and their activities were closely correlated. Sedges and broadleaved emergents had the highest activity of both enzymes, while those of floating-leaved plants were the lowest. Redundancy analysis revealed close association between root enzymes and the proportion of monoesterase- and diesterase-hydrolyzable dissolved unreactive P. Both enzymes were positively correlated with root tissue N : P ratio. Both plant and sediment traits were important when explaining differences in enzyme activities. Although the activities are related to ambient P regime, the relationship was not close enough to use root enzymes as reliable predictors of dissolved unreactive P that is hydrolyzed by sediment phosphomono- and diesterases.

Utricularia carnivory revisited: plants supply photosynthetic carbon to traps.

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.

Fluorescently Labeled Bacteria as a Tracer to Reveal Novel Pathways of Organic Carbon Flow in Aquatic Ecosystems.

Elucidating trophic interactions, such as predation and its effects, is a frequent task for many researchers in ecology. The study of microbial communities has many limitations, and determining a predator, prey, and predatory rates is often difficult. Presented here is an optimized method based on the addition of fluorescently labelled prey as a tracer, which allows for reliable quantitation of the grazing rates in aquatic predatory eukaryotes and estimation of nutrient transfer to higher trophic levels.

Correction to: Hunters or farmers? Microbiome characteristics help elucidate the diet composition in an aquatic carnivorous plant.

AbstractFollowing publication of the original article [1], the author reported an error in Fig. 3.

Heterotrophic N2-fixation contributes to nitrogen economy of a common wetland sedge, Schoenoplectus californicus.

A survey of the ecological variability within 52 populations of Schoenoplectus californicus (C.A. Mey.) Soják across its distributional range revealed that it is commonly found in nitrogen (N) limited areas, but rarely in phosphorus limited soils. We explored the hypothesis that S. californicus supplements its nitrogen demand by bacterial N2-fixation processes associated with its roots and rhizomes. We estimated N2-fixation of diazotrophs associated with plant rhizomes and roots from several locations throughout the species' range and conducted an experiment growing plants in zero, low, and high N additions. Nitrogenase activity in rhizomes and roots was measured using the acetylene reduction assay. The presence of diazotrophs was verified by the detection of the nifH gene. Nitrogenase activity was restricted to rhizomes and roots and it was two orders of magnitude higher in the latter plant organs (81 and 2032 nmol C2H4 g DW-1 d-1, respectively). Correspondingly, 40x more nifH gene copies were found on roots compared to rhizomes. The proportion of the nifH gene copies in total bacterial DNA was positively correlated with the nitrogenase activity. In the experiment, the contribution of fixed N to the plant N content ranged from 13.8% to 32.5% among clones from different locations. These are relatively high values for a non-cultivated plant and justify future research on the link between N-fixing bacteria and S. californicus production.

Iron and nitrogen cycling, bacterioplankton community composition and mineral transformations involving phosphorus stabilisation in the ferruginous hypolimnion of a post-mining lake.

Lake Medard is an oligotrophic post-mining lake characterised by ferruginous bottom waters, with marked redox gradients resulting from iron (Fe) and nitrogen (N) speciation and accompanying depth-dependent variations in the abundance of volatile fatty acids (VFAs), pH and alkalinity. The lacustrine system is meromictic, featuring a dysoxic hypolimnion and an anoxic monimolimnion with relatively high concentrations of sulfate (SO42-, 19 ± 2 mM) and Fe(ii) (127 ± 17 µM). An increase in dissolved manganese is also observed with increasing depth, together with a general lack of sulfide, which can only be detected at the sediment-water interface at concentrations of ∼0.30 µM. In the hypolimnion, nitrate (NO3-) becomes progressively depleted and ammonium (NH4+) dominates the dissolved N inventory (up to 185 ± 13 µM). Here we describe the biogeochemical disequilibrium conditions governing critical mineralogical transformations involving Fe and phosphorus (P) co-precipitation in the dysoxic-to-anoxic bottom water column. A combination of mineral equilibrium modelling and synchrotron-based diffraction and spectroscopic techniques was applied to investigate the minerals comprising the upper anoxic sediments. The combined dataset indicates that elemental recycling on and below the hypolimnion promote the precipitation of FeOOH polymorphs that accumulate as heterogeneous mineral clusters. Changes in the relative abundance of bacterioplankton taxa with increasing water depth point to a link between the activity of certain members of Proteobacteria and the co-recycling of carbon (C), N, and Fe stocks. Such a redox recycling process seems to lead to P stabilisation into organic-rich Fe-(oxyhydr)oxides near and above the anoxic sediment-water interface (SWI).

Hunters or farmers? Microbiome characteristics help elucidate the diet composition in an aquatic carnivorous plant.

BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: 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.

Is biomass a reliable estimate of plant fitness?

The measurement of fitness is critical to biological research. Although the determination of fitness for some organisms may be relatively straightforward under controlled conditions, it is often a difficult or nearly impossible task in nature. Plants are no exception. The potential for long-distance pollen dispersal, likelihood of multiple reproductive events per inflorescence, varying degrees of reproductive growth in perennials, and asexual reproduction all confound accurate fitness measurements. For these reasons, biomass is frequently used as a proxy for plant fitness. However, the suitability of indirect fitness measurements such as plant size is rarely evaluated. This review outlines the important associations between plant performance, fecundity, and fitness. We make a case for the reliability of biomass as an estimate of fitness when comparing conspecifics of the same age class. We reviewed 170 studies on plant fitness and discuss the metrics commonly employed for fitness estimations. We find that biomass or growth rate are frequently used and often positively associated with fecundity, which in turn suggests greater overall fitness. Our results support the utility of biomass as an appropriate surrogate for fitness under many circumstances, and suggest that additional fitness measures should be reported along with biomass or growth rate whenever possible.

Enzymatic activities in traps of four aquatic species of the carnivorous genus Utricularia.

• Here, enzymatic activity of five hydrolases was measured fluorometrically in the fluid collected from traps of four aquatic Utricularia species and in the water in which the plants were cultured. • In empty traps, the highest activity was always exhibited by phosphatases (6.1-29.8 µmol l-1  h-1 ) and ß-glucosidases (1.35-2.95 µmol l-1  h-1 ), while the activities of α-glucosidases, ß-hexosaminidases and aminopeptidases were usually lower by one or two orders of magnitude. Two days after addition of prey (Chydorus sp.), all enzymatic activities in the traps noticeably decreased in Utricularia foliosa and U. australis but markedly increased in Utricularia vulgaris. • Phosphatase activity in the empty traps was 2-18 times higher than that in the culture water at the same pH of 4.7, but activities of the other trap enzymes were usually higher in the water. Correlative analyses did not show any clear relationship between these activities. • Trap comensals (Euglena) could be partly responsible for production of some trap enzymes. The traps can produce phosphatases independently of catching prey. Taking into account the enzymatic activities in traps, phosphorus uptake from prey might be more important than that of nitrogen for the plants.