Biology subjects

Shabarova, T.

Publications and source records attributed to Shabarova, T..

7 recordsLinked to original sources

bioRxiv2025

High-temporal resolution of microbial food web dynamics and structure during phytoplankton blooms in the Baltic Sea

Heterotrophic nanoflagellates (HNF) are a key component of the microbial food webs, playing an essential role in nutrient recycling and energy transfer in aquatic ecosystems. They have been typically considered to be bacterivores, but they can be also omnivorous (feeding on prokaryotes and other eukaryotes) and predatory grazers (feeding on other eukaryotes). Here, we combine CARD-FISH with both short and long-amplicon sequencing to resolve dynamics of key HNF groups during two high-frequency sampling campaigns in spring (March-May) and autumn (September-November) phytoplankton blooms in the coastal waters of the Baltic Sea. This approach allowed us to resolve the microbial food web dynamics within HNF communities at the phylotype level at time scales relevant to HNF duplication times. Omnivorous katablepharids and predatory MAST-2 dominated the HNF community, especially in spring. Bacterivorous groups (e.g., MAST-1, CRY1) were less abundant. Long-read sequencing revealed distinct seasonal shifts in dominant phylotypes, with Katablepharis sp. and MAST-2D peaking in spring, while other lineages became more prominent in summer and autumn. The high abundance of omnivorous HNF, compared to bacterivores, highlights their key role both as grazers of bacteria and flagellates and as a food source for predatory and omnivorous ciliates. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=193 SRC="FIGDIR/small/676335v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@c4ec55org.highwire.dtl.DTLVardef@77fd5dorg.highwire.dtl.DTLVardef@19b237borg.highwire.dtl.DTLVardef@368f39_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

bioRxiv2025

Season-specific responses of freshwater ciliate communities to top-down and bottom-up experimental manipulations

In aquatic microbial food webs, ciliates represent an important trophic link in the energy transfer from prokaryotes, algae, and heterotrophic nanoflagellates (HNF) to higher trophic levels. However, the trophic role of abundant small ciliates (< 20 {micro}m) is not clearly understood. To unveil their trophic linkages, we conducted two experiments manipulating both top-down and bottom-up controlling factors, thus modulating the trophic cascading and bacterial prey availability for protists during contrasting spring and summer seasons with samples collected from a freshwater meso-eutrophic reservoir. Water samples were size fractionated, to modify food web complexity, i.e. 10-{micro}m, 20-{micro}m and unfiltered control and amended with bacterial prey additions. The samples were analyzed by morphological and sequencing techniques. The bacterial amendments triggered strong ciliate growth following the peaks of HNF in the 10-{micro}m and 20-{micro}m treatments, reflecting a trophic cascading from HNF to raptorial prostome ciliates (Balanion planctonicum and Urotricha spp.) in spring. In summer, HNF and ciliates peaked simultaneously, suggesting the important trophic cascade from bacteria to bacterivorous scuticociliates (Cyclidium glaucoma and Cinetochilum margaritaceum) and HNF. In spring, unfiltered treatments showed stronger ciliate top-down control by zooplankton than in summer. The sequence analysis revealed season-specific manipulation-induced shifts in ciliate communities and their large cryptic diversity. However, morphological and molecular analyses also revealed considerable discrepancies in the abundance of major ciliate taxa. The ciliate communities responded to our experimental manipulations in season-specific fashion, thereby highlighting the different roles of ciliates as an intermediate trophic link between prokaryotes and higher trophic levels. IMPORTANCECiliates are an important trophic link in aquatic microbial food webs. In this study, we used the food web manipulation techniques to reveal their complex trophic interactions during seasonally different plankton scenarios occurring in spring and summer. Manipulating top-down controlling factors (grazing pressure of micro- and metazooplankton grazers) and bottom-up factors (an availability of bacterial prey) shaped distinctly the complexity and dynamics of natural plankton communities and thus yielded significant changes in ciliate community dynamics. The experimentally simplified plankton and ciliate communities responded to our manipulations in season-specific fashions, reflected in different roles of ciliates as an intermediate trophic link between prokaryotes and higher trophic levels. This study also demonstrates that the combination of morphological and molecular analyses is essential for providing robust and ecologically meaningful results due to the reliability in quantifying the major ciliate taxa and their trophic role.

ecology↗

bioRxiv2024

Depth-dependent dynamics of protist communities as an integral part of spring succession in a freshwater reservoir

BackgroundProtists are essential contributors to eukaryotic diversity and exert profound influence on carbon fluxes and energy transfer in freshwaters. Despite their significance, there is a notable gap in research on protistan dynamics, particularly in the deeper strata of temperate lakes. This study aimed to address this gap by integrating protists into the well-described spring dynamics of [R]imov reservoir, Czech Republic. Over a two-month period covering transition from mixing to established stratification, we collected water samples from three reservoir depths (0.5, 10 and 30 m) with a frequency of up to three times per week. Microbial eukaryotic and prokaryotic communities were analysed using SSU rRNA gene amplicon sequencing and dominant protistan groups were enumerated by Catalysed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH). Additionally, we collected samples for water chemistry, phyto- and zooplankton composition analyses. ResultsFollowing the rapid changes in environmental and biotic parameters during spring, protistan and bacterial communities displayed swift transition from a homogeneous community to distinct strata-specific communities. Epilimnion exhibited the prevalence of auto-, mixotrophic protists dominated by cryptophytes and associated with spring algal bloom-specialized bacteria. In contrast, meta- and hypolimnion showcased the development of protist community dominated by putative parasitic Perkinsozoa, detritus or particle-associated ciliates, cercozoans and excavate protists co-occurring with bacteria associated with lake snow. ConclusionsOur high-resolution sampling matching the typical dividing time of microbes along with the combined microscopic and molecular approach and inclusion of all the components of microbial food web allowed us to follow depth-specific populations successions and interactions in a deep lentic ecosystem.

ecology↗

bioRxiv2023

Direct and indirect effects of the increase in atmospheric CO2 and temperature on groundwater organisms

Atmospherically rising temperature and CO2 impact all freshwater systems, including groundwater. Increasing CO2 leads to more intense weathering of silicate rocks. Here, we tested whether the increased levels, the weathering, or rather the increasing temperature, impacted on fauna and prokaryotes in the groundwater ecosystem. We conducted the analyses separately for deep, i.e. secluded, and shallow, quaternary aquifers which exchange with the surface more intensely. Organism abundances and relative composition did not correlate with temperature or CO2 levels. While many organisms rely on silica, in contrast, we found negative correlations between silica and fauna. The increases in silica over time, i.e. temporal trends, also partly correlated negatively with organisms. We hypothesize that the unexpected negative correlations are not direct effects, but indirectly indicate that groundwater communities do not adapt rapidly enough to changes. This jeopardizes future drinking water production which relies on the self-cleaning ecosystem services in groundwater.

ecology↗

bioRxiv2023

Rickettsiales' deep evolutionary history sheds light on the emergence of intracellular lifestyles

Ancient bacteria largely lived and flourished as free-living cells till the rise of eukaryotes triggered their adaptation to a new habitat: the intracellular milieu. Rickettsiales bacteria are the most prevalent intracellular microorganisms discovered and the culprits behind some of mankinds worst pestilential diseases. Here, we show that intracellularity is not a defining feature of the group and describe the eco-evolutionary processes that transformed harmless free-living bacteria into obligate intracellular symbionts and parasites. We found that the evolution of free-living lineages towards enhanced cross-feeding interactions with microbial eukaryotes trapped them in a nutritional bind to their trophic partners. We discovered that the oldest Rickettsiales lineages are the closest relatives to modern eukaryotes and are enriched in proteins predicted to have been present in the mitochondrial ancestor. This study not only opens avenues for the detection and surveillance of emerging diseases but also expands our understanding of the origins of complex life. One-Sentence SummaryCross-feeding interactions shaped Rickettsiales genomic architectures along the parasite/free-living spectrum

microbiology↗

bioRxiv2020

Microbial drama in four acts - Extreme rain events cause cyclic succession in plankton communities

Highly abundant, small waterbodies contribute substantially to global freshwater shoreline and surface area. They are strongly interlinked with the terrestrial surrounding, thus controlling the flow of energy, nutrients and organisms through the landscape. Disturbance events can have severe consequences for these ecosystems and the entire downstream freshwater network and require more attention in the context of global change-induced increases in weather extremes. Here we show that extreme rain events (floods) cause cyclic successions in microbial communities and the planktonic food web of a small forest pond. We analyzed the dynamics of nutrients and the entire plankton community during two flood events and subsequent quasi-stable conditions. Floods induced a repeated washout of resident organisms and hundred-fold increases in nutrient load. However, within two weeks, the microbial community recovered to a pre-disturbance state through four well-defined succession phases. Reassembly of phyto- and especially zooplankton took considerably longer and displayed both repetitive and adaptive patterns. Release of dissolved nutrients from the pond was associated with inflow rates and state of community recovery, and it returned to pre-disturbance levels earlier than microbial composition. Our study exemplifies extraordinary compositional and functional resilience of small waterbodies and presents the detailed mechanism of the underlying processes.

ecology↗

bioRxiv2020

A freshwater radiation of diplonemids

Diplonemids are considered marine protists and have been reported among the most abundant and diverse eukaryotes in the world oceans. Recently we detected the presence of freshwater diplonemids in Lake Biwa, Japan. However, their distribution and abundances in freshwater ecosystems remain unknown. We assessed abundance and diversity of diplonemids from several geographically distant deep freshwater lakes of the world by amplicon-sequencing, shotgun metagenomics and CARD-FISH. We found diplonemids in all the studied lakes, albeit with low abundances and diversity. We assembled long 18S rRNA sequences from freshwater diplonemids and showed that they form a new lineage distinct from the diverse marine clades. Freshwater diplonemids are a sister-group to marine isolates from coastal and bay areas, suggesting a recent habitat transition from marine to freshwater habitats. Images of CARD-FISH targeted freshwater diplonemids suggest they feed on bacteria. Our analyses of 18S rRNA sequences retrieved from single cell genomes of marine diplonemids shows they encode multiple rRNA copies that may be very divergent from each other, suggesting that marine diplonemid abundance and diversity both have been overestimated. These results have wider implications on assessing eukaryotic abundances in natural habitats by using amplicon-sequencing alone.

microbiology↗