Biology subjects

Kamenova, S.

Publications and source records attributed to Kamenova, S..

6 recordsLinked to original sources

bioRxiv2025

Arctic plant species display contrasting levels of chloroplast DNA copy numbers

DNA metabarcoding has revolutionised our ability to characterise biodiversity at unprecedented spatial and temporal scales, outperforming most traditional methods for biodiversity monitoring. However, DNA metabarcoding is not without limitations, in particular regarding the quantitative relationship between sequence read abundances and species numerical abundances or biomass (i.e., quantitative performance). Variation in DNA copy numbers has been often pinpointed as a potentially important factor biasing DNA metabarcoding quantitative performance but empirical comparisons of DNA copy number variation across species remain rare. Here, we identify chloroplast DNA copy number variation (cpDNA CNV) in plants as a potentially important factor that could impact quantitative performance in DNA metabarcoding studies. Using digital droplet PCR, we quantified chloroplast copy number variation in four common high Arctic plant species and between two plant tissue types (green tissues and roots). The amount of cpDNA per unit of dry mass varied by a factor of 3 (for roots) to 7.6 (for green tissues) among species, and up to 67 when comparing cpDNA copy numbers between green and root tissues from the same species. Despite significant differences in cpDNA copy numbers among species for both green tissues and roots, the most pronounced differences in cpDNA copy numbers were clearly between the two tissue types tested. These findings suggest that variation in cpDNA copy numbers among plant species and particularly plant tissue types can be an important but underestimated factor impacting plant sequence reads abundance in DNA metabarcoding datasets. We call for more extensive cpDNA CNV referencing efforts from wild-ranging plants to improve the use of DNA metabarcoding for research and biodiversity monitoring.

ecology↗

bioRxiv2024

Arctic greening drives changes in the diet and gut microbiome of a resident herbivore with consequences for fitness

Rapid climate warming is "greening" the tundra due to higher plant productivity, particularly of deciduous shrubs and grasses, potentially changing the nutritional base for herbivores. However, the consequences for herbivores are unclear. Although the gut microbiome is an essential factor, mediating the capacity to adapt to dietary change, few studies have investigated the effect of annual changes in the diet-gut microbiome nexus on fitness traits. In a model system, the Svalbard reindeer, a species experiencing the greatest rate of climate warming on Earth, we investigate how climate-induced changes in diet and the gut microbiome impact reindeer body mass. Using high-resolution DNA metabarcoding, we quantified diet and microbiome composition in rumen samples from 97 animals culled in October from 1998 to 2004 in four different valleys. Overall diet diversity and grass consumption were significantly higher following warmer summers, while intake of the dwarf shrub Salix polaris increased with the maximum normalised difference vegetation index (NDVI). The proportion of Salix had a significant positive effect on autumn body mass, which in turn increases ovulation rates and overwinter survival. There was a significant positive effect of Salix on the microbiome diversity, while between-year variation in Bacteroidota, the most common bacteria phylum, was also significantly, positively related to maximum NDVI. However, a structural equation model revealed that the direct "path" effect of the proportion of Salix in the diet on reindeer body mass was stronger than the indirect path effect, mediated through the gut microbiome. Our results suggest a positive impact of climate-driven Arctic greening on Svalbard reindeer fitness, operating through a change in diet composition, partially mediated by the changes in the gut microbiome. These findings advance our understanding of the mechanistic underpinnings of Arctic warming on herbivore populations and contribute to the debate about the importance of the diet-gut microbiome nexus in facilitating species resilience in the face of climate change.

ecology↗

bioRxiv2024

DNA metabarcoding diet analysis in ruminants is quantitative and integrates feeding over several weeks

Dietary DNA metabarcoding is an established method, especially useful for resolving the diverse diets of large mammalian herbivores (LMH). However, despite longstanding research interest on the topic, we still lack unequivocal evidence on the potential of DNA metabarcoding to reflect proportions of ingested dietary plants in LMH. One major aspect to consider is the time window during which ingested diet remains detectable in faecal samples. This parameter is currently unknown for LMH, thus potentially hindering the scope of ecological conclusions. Another unknown factor is quantitative performance, i.e. the extent to which the amount of ingested biomass can be assessed based on sequence read abundances. We assessed DNA metabarcoding quantitative performance and DNA half-life detectability for plants with different digestibilities in a controlled feeding experiment with three female Eurasian tundra reindeer (Rangifer tarandus tarandus). Reindeer were fed birch twigs (Betula pubescens) and increasing biomass of lichen (mainly Cladonia stellaris). Relative read abundance positively correlated with ingested lichen biomass, suggesting potential for deriving dietary proportions in free-ranging reindeer on natural pastures. Dietary DNA was consistently detected within a few hours upon ingestion, with a mean half-life detectability of 30 and 14 hours for birch and lichen, respectively. However, dietary DNA remained detectable in faeces for at least 26 days post-feeding, indicating that a single faecal sample can provide an unsuspectedly integrative estimate of diet in ruminants. Together, our findings provide novel empirical validation of DNA metabarcoding as a tool for diet analysis in LMH.

ecology↗

bioRxiv2023

Within-species variation in the gut microbiome of fish is driven by the interaction of light intensity and genetic background

Unravelling evolution-by-environment interactions on the gut microbiome is particularly relevant considering the unprecedented level of human-driven disruption of the ecological and evolutionary trajectories of species. Here, we aimed to evaluate whether an evolutionary response to size-selective mortality influences the gut microbiome of medaka (Oryzias latipes), how environmental conditions interact with the genetic background of medaka on their microbiota, and the association between microbiome diversity and medaka growth-related traits. To do so, we studied two lineages of medaka with known divergence in foraging efficiency and life history raised under antagonistic size-selective regimes for 10 generations (i.e. the largest or the smallest breeders were removed to mimic fishing-like or natural mortality). In pond mesocosms, the two lineages were subjected to contrasting population density and light intensity (used as proxies of resource availability). We observed significant differences in the gut microbiome composition and richness between the two lines, and this effect was mediated by light intensity. The bacterial richness of fishing-like medaka (small-breeder line) was reduced by 34% under low-light conditions compared to high-light conditions, while it remained unchanged in natural mortality-selected medaka (large-breeder line). However, the observed changes in bacterial richness did not correlate with changes in adult growth rate or body condition. Given the growing evidence about the gut microbiomes importance to host health, more in-depth studies are required to fully understand the role of the microbiome in size-selected organisms and the possible ecosystem-level consequences.

ecology↗

bioRxiv2018

DNA metabarcoding diet analysis reveals dynamic feeding behaviour and biological control potential of carabid farmland communities

Maximizing the delivery of key ecosystem services such as biological control through the management of natural enemy communities is one of the major challenges for modern agriculture. The main obstacle lies in our yet limited capacity of identifying the factors that drive the dynamics of trophic interactions within multi-species assemblages. Invertebrate generalist predators like carabid beetles are known for their dynamic feeding behaviour. Yet, at what extent different carabid species contribute to the regulation of animal and plant pests within agroecosystems is currently unknown. Here, we developed a DNA metabarcoding approach for characterizing the full diet spectrum of a community of fourteen very common carabid species inhabiting an intensively managed Western-European agroecosystem. We then investigated how diet and biological control potential within the carabid community varies with the sampling field location and the crop type (wheat vs oilseed rape). DNA metabarcoding diet analysis allowed to detect a wide variety of animal and plant taxa from carabid gut contents thus confirming their generalist feeding behaviour. The most common prey categories detected were arachnids, insects, earthworms and several plant families potentially including many weed species. Our results also show that the field location and the crop type are much stronger determinants then the species regarding carabid dietary choice: significantly more trophic links involving dipteran prey were observed in wheat, whereas more collembolan and plant prey was consumed in oilseed rape by the same carabid community. We speculate that structural differences in the habitats provided by these two crop types drive differences in resource availability cascading up the trophic chain, and we assume that specific carabid taxa could hardly be used to infer levels of ecosystem services (biological control) or disservices (e.g. intraguild predation). However, as this is the first study to report the use of DNA metabarcoding diet analysis in predatory carabid beetles we urge caution over the interpretation of our results. For instance, overall detection rates were rather low (31% of the individuals analysed tested positive for at least one prey category) most likely due to the overwhelming amplification of the carabid host DNA. Therefore, we acknowledge that more studies are required in order to confirm our observations and conclude with few recommendations for further improvements of the community-level DNA metabarcoding analysis of carabid diet.

ecology↗

bioRxiv2017

Comparing three types of dietary samples for prey DNA decay in an insect generalist predator

The rapidly growing field of molecular diet analysis is becoming increasingly popular among ecologists, especially when investigating methodologically challenging groups such as invertebrate generalist predators. Prey DNA detection success is known to be affected by multiple factors, however the type of dietary sample has rarely been considered. Here, we address this knowledge gap by comparing prey DNA detection success from three types of dietary samples. In a controlled feeding experiment, using the carabid beetle Pterostichus melanarius as a model predator, we collected regurgitates, feces and whole consumers (including their gut contents) at different time points post-feeding. All dietary samples were analyzed using multiplex PCR targeting three different length DNA fragments (128 bp, 332 bp and 612 bp). Our results show that both the type of dietary sample and the size of the DNA fragment contribute to a significant part of the variation found in the detectability of prey DNA. Specifically, we observed that in both regurgitates and whole consumers prey DNA was detectable significantly longer for all fragment sizes than for feces. Based on these observations, we conclude that prey DNA detected from regurgitates and whole consumers DNA extracts are comparable, whereas prey DNA detected from feces, though still sufficiently reliable for ecological studies, will not be directly comparable to the former. Therefore, regurgitates and feces constitute an interesting, non-lethal source for dietary information that could be applied to field studies in situations when invertebrate predators should not be killed.

ecology↗