Veljo Kisand

Background: Aquatic macrophytes shape microbial habitats in shallow coastal systems, yet the relative influence of plant-driven effects versus local hydrology and seasonal environmental variation remains poorly resolved. We investigated how Phragmites australis influences sediment, water, and phyllosphere bacterial communities in two shallow Baltic Sea bays, Haapsalu and Pärnu, that are approximately 83 km from each other. Results: Bacterial communities clustered strongly by substrate (sediment, water, and phyllosphere). Sediments exhibited higher 𝛼-diversity and stronger site specificity than water or phyllosphere habitats, with bulk sediments harboring greater richness than Phragmites -associated sediments. Seasonal 𝛼-diversity peaked in summer–autumn and reached minima in spring across sediments, whereas water communities showed weaker seasonality. β-diversity analyses revealed that sediments maintained lower seasonal turnover (i.e., more temporally stable) and site-specific communities compared to water and phyllosphere habitats, which showed rapid compositional shifts and higher seasonal dissimilarity. Pärnu Bay, which experiences stronger riverine influence, exhibits larger temporal shifts in both 𝛼- and β-diversity than Haapsalu Bay. Taxonomic differences between bays included the dominance of Cyanobium in Haapsalu Bay and Synechococcus in Pärnu Bay, most likely driven by site-specific hydrology and nutrient regimes. After accounting for environmental gradients, P. australis had only modest, context-dependent effects on the bacterial community composition. Conclusions: Local hydrology and seasonal variation, particularly riverine inputs and salinity dynamics, exert stronger control over coastal bacterial community composition in top-layer sediment and water than the presence of P. australis . While sediments act as relatively stable, site-specific reservoirs, water, and phyllosphere communities were more labile and seasonally dynamic. These findings underscore the importance of site-specific assessments in shallow coastal studies and caution against generalizing results across bays.

Microeukaryotic communities in brackish coastal ecosystems are structured by complex interactions between environmental conditions and habitat heterogeneity. This study examines how moderate salinity levels (ranging from freshwater to salinity 6) and habitat type (water column, sediment, and biofilm) influence microeukaryotic diversity and community composition in shallow coastal waters of the Gulf of Finland, the Baltic Sea. Combining field surveys with controlled short-term aquarium experiments, we analyzed taxonomic responses using 18S rRNA gene amplicon sequencing. Alpha diversity differed significantly across habitats but showed only minor shifts across shallow coastal salinity gradients, with the water column showing the highest richness, followed by biofilm and sediment. However, no substantial shift in alpha diversity was observed across the natural salinity gradient. In contrast, short-term exposure to increased salinity significantly reduced alpha diversity in the water column, while sediment communities remained more stable, likely due to their buffering capacity and microhabitat complexity. Redundancy analysis revealed that habitat type had a stronger effect on beta diversity than salinity, explaining 15% of the variation in natural samples. In experimental aquaria, incubation time exerted the greatest influence. This highlights the strong influence of ecological succession, trophic interactions, and stochastic processes in controlled environments. Several less-documented taxa, such as Gregarinomorphea, Perkinsida, Filosa−Imbricatea, and Filosa−Thecofilosea, were abundant in both natural and experimental samples, highlighting underexplored diversity in Baltic Sea microeukaryotes. These results suggest that stochastic processes, habitat-specific factors, and temporal dynamics dominate over moderate salinity effects in shaping shallow coastal microeukaryotic communities.

Protists play important roles in food chains and symbioses in soil and aquatic environments, displaying an enormous morphological and functional diversity ^1,2 . While most commonly found protist species are well known to science, our global-scale environmental DNA survey across soil, water, and sediments reveals dozens of novel, phylum-level phylogenetic lineages that remain to be characterized for basic morphology and function. A vast majority of these undescribed taxa occur in marine water and sediments, but some are common in soil. Most of these novel taxa have distinct substrate and habitat preferences and biogeographic patterns. To accord these lineages scientific agency and enable unambiguous scientific communication, we propose formal names for 150 species to phylum-level taxa from 25 deep lineages based on eDNA and rRNA gene long-read sequence information.

The environmental impact of amines utilized in processes involving CO ₂ -absorption has been evaluated towards bacteria, plants and invertebrates.

Parasites often occupy specific sites within their host, which has important implications for host performance and parasite transmission. Nonetheless, parasitic infections can occur beyond their typical location within a host, significantly altering host–parasite interactions. Yet, the causes behind the atypical tissue tropism are poorly understood. Here, we focus on a ubiquitous group of diplostomid parasites that form diverse communities in fish eyes. We used targeted DNA metabarcoding (cytochrome c oxydase subunit 1, COX1, 250 bp) to evaluate potential mechanisms underlying eye parasite atypical tissue tropism to the brain of two widespread fish species (Eurasian perch and common roach). We found that the most common eye-infecting species ( Tylodelphys clavata , Diplostomum baeri ) are present in the brains of perch but not in roach. The bipartite network comprising 5 species and 24 mitochondrial haplotypes revealed no brain-specific haplotypes, indicating an apparent lack of genetic divergence between brain- and eye-infecting parasites. Instead, the prevalence, intensity and diversity of eye infections were positively correlated with brain infections. Thus, our results suggest that the most parsimonious mechanism underlying brain infection is density-dependent spillover rather than parasite divergence-driven niche expansion. We anticipate that ‘off-target’ infections are likely to be severely underestimated in nature with important ecological, evolutionary and medical implications.

High relative abundance of yeast (Vishniacozyma, Papiliotrema, and Filobasidium) and bacterial (Massilia) genera found in spinach seeds correlates with suppression of Globisporangium ultimum damping-off infection.

Grazing by zooplankton can regulate bloom-forming cyanobacteria but can also transfer toxin-producing cells, as well as toxic metabolites, to the food web. While laboratory investigations have provided extensive knowledge on zooplankton and toxic cyanobacteria interactions, information on zooplankton feeding on toxin-producing cyanobacteria in natural water bodies remains scarce. In this study, we quantified Microcystis-specific mcyE synthase genes from the gut contents of various cladoceran and copepod taxa to assess the in situ crustacean community and taxon-specific ingestion of potentially toxic Microcystis in Lake Peipsi, a large eutrophic lake in Estonia, Northern Europe. Microcystis cells with mcyE genes were found in all crustaceans examined. However, some species, such as the cyclopoid copepod Mesocyclops leuckarti, were more efficient in ingesting potentially toxic Microcystis than other co-occurring cladocerans (Daphnia spp., Bosmina spp., Chydorus sphaericus) and copepods (Eudiaptomus gracilis). The amount of toxigenic Microcystis cells grazed by crustacean population changed temporarily, and copepods were the predominant consumers of toxigenic Microcystis during several months of the 5-month study period. Crustacean ingestion of toxigenic Microcystis was not related to Microcystis biomass or mcyE gene copy numbers in the environment but was instead related to the abundance of major crustacean grazers. Our findings emphasize the close interaction between crustacean zooplankton and toxigenic Microcystis, indicating that some species may play a more significant role in linking toxic cells within the food web than others.

While the prudent and reasonable use of veterinary antimicrobial agents in food-producing animals is necessary, researchers over the decades have shown that these antimicrobial agents can spread into the environment through livestock manure and wastewater. The analysis of the occurrence of antimicrobial compounds in soil samples is of a great importance to determine potential impacts on human and animal health and the environment. In this study, an affordable, rugged and simple analytical method has been developed for the determination of twenty-nine antimicrobial compounds from five different classes (tetracyclines, fluoro(quinolones), macrolides, sulfonamides and diaminopirimidines). Liquid–liquid extraction (LLE) with extract filtration combined with ultra-high performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) was the best strategy for the simultaneous determination of all analytes. The developed method was validated according to the Commission Implementing Regulation (EU) 2021/808. The limit of detections (LODs) ranged from 0.5 to 2.0 µg/kg, while the limit of quantitation (LOQ) was established at 1.0 to 20.0 µg/kg. The developed method was successfully applied for the determination of antimicrobial residues in one hundred and eighteen soil samples obtained from four European countries (Austria, Czech Republic, Estonia and Portugal). Doxycycline in the concentration levels of 9.07 µg/kg–20.6 µg/kg was detected in eight of the analysed samples. Samples were collected from areas where natural fertilizers (swine or cow manure) were applied. Our method can be efficiently used to monitor anti-microbial compounds in soil samples.

Environmental impact of isosorbide-based monomers and polymers have been evaluated towards bacteria, plants and invertebrates. Isosorbide acrylates show toxicity towards higher organisms while other tested mono- and polymeric compounds are harmless.