Ulrike Obertegger

The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna

Molecular tools have revolutionized the exploration of biodiversity, especially in organisms for which traditional taxonomy is difficult, such as for microscopic animals (meiofauna). Environmental (eDNA) metabarcode surveys of DNA extracted from sediment samples are increasingly popular for surveying biodiversity. Most eDNA surveys use the nuclear gene-encoding small-subunit rDNA gene (18S) as a marker; however, different markers and metrics used for delimiting species have not yet been evaluated against each other or against morphologically defined species (morphospecies). We assessed more than 12,000 meiofaunal sequences of 18S and of the main alternatively used marker [Cytochrome c oxidase subunit I (COI) mtDNA] belonging to 55 datasets covering three taxonomic ranks. Our results show that 18S reduced diversity estimates by a factor of 0.4 relative to morphospecies, whereas COI increased diversity estimates by a factor of 7.6. Moreover, estimates of species richness using COI were robust among three of four commonly used delimitation metrics, whereas estimates using 18S varied widely with the different metrics. We show that meiofaunal diversity has been greatly underestimated by 18S eDNA surveys and that the use of COI provides a better estimate of diversity. The suitability of COI is supported by cross-mating experiments in the literature and evolutionary analyses of discreteness in patterns of genetic variation. Furthermore its splitting of morphospecies is expected from documented levels of cryptic taxa in exemplar meiofauna. We recommend against using 18S as a marker for biodiversity surveys and suggest that use of COI for eDNA surveys could provide more accurate estimates of species richness in the future.

Water residence time as a driving force of zooplankton structure and succession

Abstract.We studied zooplankton dynamics in a groundwater-fed, montane lake during four consecutive years and assessed the importance of water residence time for zooplankton dynamics. Crustacean abundance and biomass were significantly correlated with water residence time and temperature, but showed no significant correlation with phytoplankton biovolume. We hypothesised that temperature depended on water residence time (τ), and therefore we further investigated the functional relationship of crustacean dominance with the latter by logistic regression analysis. Water residence time values above a threshold value (τ = 193 days) determined crustacean biomass dominance while values below determined rotiferan dominance. Our results indicated that water residence time was an important factor structuring zooplankton succession in this lake that showed large fluctuations of τ values (median 263 days; range 23 – 786 days for the four year period) compared to other lakes. We suggest that crustacean biomass was directly controlled through water residence time as found for riverine systems, whereas rotifer biomass was controlled through exploitative competition with crustaceans for phytoplankton. The importance of water residence time may have been underestimated in lakes when explaining zooplankton community structure and succession, because studies usually focus on other factors such as temperature, predation, or food limitation.

Microbiological Properties in Acidic Forest Soils with Special Consideration of KCl Extractable Al

To determine the importance of Al-availability for soil micro-organisms 95 forest soils from Tyrol/Austria with comparable topography, vegetation, climatic conditions, soil type and with low soil pH (median = 3.9) were investigated for their physical (percentage of stable aggregates, water holding capacity), chemical (pH, electrical conductivity, contents of organic matter, concentrations of easily extractable aluminium, calcium, potassium, magnesium and phosphorus) and microbiological characteristics (microbial biomass and respiration, metabolic quotient, content of ATP, activities of protease and CM-cellulase, cfu-values of total and Al-tolerant bacteria and fungi). A highly significant negative correlation was detected between concentrations of KCl-extractable aluminium and soil pH. By the application of multivariate statistical methods, the effect of the concentration of KCl-extractable aluminium on abundance and activities of soil micro-organisms could be revealed. Al turned out to be of great importance for micro-organisms and often outmatched the significance of other well known soil properties like organic matter, pH or water holding capacity. However, due to very healthy trees at the sites under investigation no effect of Al or soil acidification on forest decline could be detected.

Using the guild ratio to characterize pelagic rotifer communities

Ecological research is moving from a species-based to a functional-based approach to better understand the underlying principles that govern community dynamics. Studies of functional-based ecology, however, have been limited for zooplankton and particularly for rotifers. While rotifers show a variety of trophi types and coronal shapes, suggesting the importance of niche differentiation in their feeding strategy, relatively little is known of how this relates to rotifer dynamics. We used the guild ratio (GR′, a ratio of raptorial to microphagous species), an index based on a functional trait (i.e. feeding strategy), as a novel approach to rotifer dynamics. We extracted the seasonal GR′ by using seasonal trend decomposition and investigated similarities between study sites (Lake Washington, USA and Lake Caldonazzo, Italy) and its relation to cladocerans by cross-correlation analysis. Our study indicated that (i) raptorial and microphagous rotifers showed alternating dominance, and that raptorial rotifers and cladocerans had a synchronous pattern, (ii) the seasonal pattern of the GR′ was consistent across different sampling frequencies, and (iii) the GR′ was similar in both lakes. We interpreted these patterns as the general strength of the GR′: discernment of species–environment relationships and robustness across sampling regimes. The limitations of the GR′ (i.e. species identity is neglected, simplification of food preferences) can also be seen as its strong point: synthesis of multi-species patterns. In addition, the independence of GR′ from species-level identification and its potential to make use of datasets with infrequent sampling intervals and low taxon resolution could further support its innovative aspect.

Different diversification rates between sexual and asexual organisms

Patterns of diversity reflect the balance between speciation and extinction over time. Here we estimate net diversification rates for samples of sexual and asexual rotifers using phylogenetic reconstructions from sequence data of one mtDNA locus, cytochrome oxidase c subunit I. All four clades of bdelloid rotifers, obligate asexuals, had higher number of species per clade and significantly higher accumulation of diversification events towards the root of the trees than the four clades of their sexual relatives, the monogonont rotifers. Such differences were robust to confounding effects of number of analysed sequences, haplotype diversity, overall genetic divergence, age of the clades or geographic coverage. Our results support the idea that differences in diversification rates could thus be ascribed to different mechanisms of speciation, with ecological speciation as the most plausible mechanism for asexual organisms.

SEXUAL SPECIES ARE SEPARATED BY LARGER GENETIC GAPS THAN ASEXUAL SPECIES IN ROTIFERS

Why organisms diversify into discrete species instead of showing a continuum of genotypic and phenotypic forms is an important yet rarely studied question in speciation biology. Does species discreteness come from adaptation to fill discrete niches or from interspecific gaps generated by reproductive isolation? We investigate the importance of reproductive isolation by comparing genetic discreteness, in terms of intra‐ and interspecific variation, between facultatively sexual monogonont rotifers and obligately asexual bdelloid rotifers. We calculated the age (phylogenetic distance) and average pairwise genetic distance (raw distance) within and among evolutionarily significant units of diversity in six bdelloid clades and seven monogonont clades sampled for 4211 individuals in total. We find that monogonont species are more discrete than bdelloid species with respect to divergence between species but exhibit similar levels of intraspecific variation (species cohesiveness). This pattern arises because bdelloids have diversified into discrete genetic clusters at a faster net rate than monogononts. Although sampling biases or differences in ecology that are independent of sexuality might also affect these patterns, the results are consistent with the hypothesis that bdelloids diversified at a faster rate into less discrete species because their diversification does not depend on the evolution of reproductive isolation.

Phytoplankton functional response to spatial and temporal differences in a cold and oligotrophic lake

We explored phytoplankton communities from a functional perspective in two connected but hydro-morphologically distinct basins during the ice-free period in the cold and oligotrophic Lake Tovel, Italy. Despite the absence of dispersal barriers, we expected a clear separation of the phytoplankton communities between basins based on their physical distinctions: a shallow and a deep basin with low and high water residence time, respectively. To investigate seasonal succession and spatiality, taxa were classified according to their functional groups (FGs) and traits (FTs). Relationships between functional classifications and environmental parameters were assessed by non-metric multidimensional scaling integrated with cluster analysis. Clustering of FGs and FTs was complementary and reflected different hydrological conditions of each basin: (i) more stable conditions and higher functional variation across seasons in the deep basin and (ii) less stable conditions and lower functional variation across seasons in the shallow basin. Phytoplankton functional composition evidenced how local conditions selected for corresponding functional attributes adapted to each basin’s environment. These results, together with the presence of rare, cold-tolerant taxa such as Pseudotetraëdriella kamillae and Stephanocostis chantaicus, highlighted the need for long-term phytoplankton studies, and the creation of a FG that includes cold-adapted, oligotrophic taxa.

Changes in galactolipid composition of the cold freshwater dinoflagellate Borghiella dodgei in response to temperature

The freshwater dinoflagellate Borghiella dodgei is adapted to cold temperatures. We investigated the effects of small temperature changes on its galactolipid composition, choosing 3 and 7°C as deviations from its optimal growth temperature (5°C). The galactolipid profile, important for maintenance of membrane fluidity, was determined by liquid chromatography–mass spectrometry and the influence of temperature on galactolipids was investigated by one-way ANOVA. We found 24 different galactolipid species, including novel tri-galactosyldiacylglycerols (TGDGs). The overall amount of mono- (MGDG), di- (DGDG) and tri- (TGDG) galactosyldiacylglycerols remained stable while single galactolipids varied with temperature. Few changes were found from 3 to 5°C, instead 11 galactolipid species changed from 5 to 7°C. Concomitantly with the unsaturation index of MGDGs, the more unsaturated galactolipids decreased at higher temperature, and the less abundant and less unsaturated galactolipids in each lipid class accumulated. Changes in the galactolipid profile of Borghiella underlined its cold-stenothermal nature: it can adapt to relatively ‘higher’ temperatures by reducing the synthesis of the more unsaturated MGDGs, DGDGs and TGDGs, but remains restricted by its lower growth rate. Based on our results, we predict that with climate change the galactolipid profile of cold-stenothermal algae will change with important repercussions on their consumers.

Rotifer–crustacean interactions in a pseudokarstic lake: influence of hydrology

Zooplankton abundance was related to hydrological and environmental variables in a hydrologically dynamic lake fed by a pseudokarstic aquifer. The study period (2002–2006) in Lake Tovel covered different hydrological situations with water residence time (WRT) having the lowest values in 2002 and the highest values in 2003. WRT was negatively correlated with silica concentrations and algal biovolume. Furthermore, the biovolume of small algae was highest in spring and summer, while large algae did not show any pattern. In multivariate analysis, high abundance of crustacean species in autumn and winter was positively related to WRT and negatively to algal biovolume, while high abundance of rotifer species in spring and summer was negatively related to WRT and positively to algal biovolume. With the exception of Keratella cochlearis and Gastropus stylifer, rotifers showed a pattern of crustacean avoidance, and three groups were distinguished: (i) Ascomorpha ecaudis and Polyarthra dolichoptera, (ii) Asplanchna priodonta and Synchaeta spp., and (iii) Filinia terminalis and Keratella quadrata. These groups were associated with different food sources and depths. We suggest that WRT influenced the rotifer–crustacean relationship by wash-out effects and competition for food resources. The dynamics of single rotifer species were attributable to specific feeding requirements and adaptations. In summary, WRT determined the platform for abiotic and biotic interactions that influenced population dynamics of crustaceans and rotifers.

Comparative Analysis of Membrane Lipids in Psychrophilic and Mesophilic Freshwater Dinoflagellates.

Here we report the lipid profiles of ten dinoflagellate species originating from different freshwater habitats and grown at 4, 13, or 20°C akin to their natural occurrence. Lipids were determined by High Performance Liquid Chromatography-ElectroSpray Ionization-Mass Spectrometry in positive and negative ion modes. Besides the well-studied monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG) lipids, our study revealed the presence of intact molecular lipid species of trigalactosyldiacylglycerols, betaine diacylglyceryl-carboxyhydroxymethylcholine, sulfolipid sulfoquinovosyldiacylglycerols (SQDG) and phospholipids, in particular phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol. In multivariate ordination, the freshwater dinoflagellates studied could be distinguished into two groups based on their lipid profiles. Peridinium aciculiferum, Borghiella dodgei, B. tenuissima and Tovellia coronata belonged to group 1 while Ceratium cornutum, Gymnodinium palustre, Jadwigia applanata, P. cinctum, P. willei, and P. gatunense belonged to group 2. Indicator species analysis evidenced that group 1 was characterized by 36:9 MGDG and 36:9 DGDG and group 2 by 38:9 and 38:10 MGDG, 38:9 and 38:10 DGDG and 34:1 SQDG. We suggest that the grouping of dinoflagellates indicated their range of temperature tolerance. Furthermore, non-thylakoid lipids were linked to dinoflagellate phylogeny based on the large ribosomal sub-unit (28S LSU) rather than their temperature tolerance. Thus certain lipids better reflected habitat adaptation while other lipids better reflected genetic diversity.