Biology subjects

Piwosz, K.

Publications and source records attributed to Piwosz, K..

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

Phylogeny-aware comparative genomics of Vibrio vulnificus links genetic traits to pathogenicity

Vibrio vulnificus is a natural inhabitant of coastal brackish waters worldwide and an opportunistic pathogen that can cause severe infections and septicemia through seafood consumption or wound exposure. Due to global warming, its abundance is increasing at high latitudes. While the species harbors diverse virulence factors, its precise disease mechanisms remain unclear. Comparative genomics between clinical and environmental isolates can help identify key virulence genes, but the limited availability of genomes from environmental isolates has hindered progress. In this study, we sequenced the genomes of 82 V. vulnificus isolates from water, sediment, and seagrass along the Baltic Sea coast and complemented with published genomes from 208 clinical and 117 globally distributed isolates for comparative analysis. Phylogenetic reconstruction confirmed four major lineages, with Baltic Sea strains confined to lineage L2 and L4, while clinical and environmental strains were distributed across all lineages. This suggests that the phylogenetic structure of V. vulnificus reflects adaptation to environmental conditions rather than pathogenicity. Using the PhyloBOTL pipeline developed here, we identified 128 orthologs significantly enriched in clinical isolates, grouped into 36 co-localization clusters based on proximity in the genomes. These included genes linked to virulence, such as those for capsular polysaccharide synthesis and biofilm formation, as well as previously unrecognized candidates, including chaperone-usher pilus biosynthesis, spermidine synthesis, Type VI secretion effectors, and an RTX toxin-like protein. Several of the clinically enriched gene clusters have been independently lost in three V. vulnificus clades, suggesting convergent evolution and a distinct ecological niche shared by these claded. Finally, we used the clinically enriched genes to design PCR primers for detecting and monitoring pathogenic V. vulnificus strains, providing a valuable tool for surveillance and public health efforts.

microbiology↗

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

Effects of excess phosphate on a coastal plankton community

Eutrophication in the Baltic Sea has caused an imbalance in the inorganic nitrogen (N) to phosphorus (P) ratio, leaving excess phosphate (PO4) after the phytoplankton spring bloom that terminates after N-depletion. Using monitoring data, we demonstrated that the PO4 concentration has continued to increase in the outermost Gulf of Finland during past decades. We further investigated the fate of such excess PO4 in a two-week mesocosm (1.2 m3) experiment. The starting concentration of PO4 was 0.66 {micro}M, and treatments included a non-treated control (control), nitrate addition (N-add; 3.6 {micro}M), glucose addition (C-add; 25 {micro}M) and combined nitrate and glucose addition (N+C-add). The addition of N both in N-add and N+C-add treatments stimulated nano- and microphytoplankton, while the picophytoplankton abundance increased only after N-depletion. Also, the copepod biomass was positively affected by the N-addition. N2-fixing cyanobacteria were present but in low abundance. Carbon addition did not enhance heterotrophic bacterial uptake of PO4 contrary to our expectations, nor did it affect the phyto- or zooplankton community composition. The PO4 concentration was reduced to [~]0.4 {micro}M in the control and C-add treatments and to 0.16 {micro}M in the two N-amended treatments, with an inorganic N:P uptake ratio of 6.7. These results underscore the role of picophytoplankton in reducing the excess PO4 pool after the spring bloom, a function traditionally ascribed to bloom-forming diazotrophic cyanobacteria in the Baltic Sea.

microbiology↗

bioRxiv2024

Microbial remineralization processes during post-spring-bloom excess phosphate in the northern Baltic Sea

In the northern Baltic, post-spring-bloom low dissolved inorganic nitrogen to phosphorus conditions, degradation of N-rich organic matter potentially supports the drawdown of excess phosphate. During a 17-day-long mesocosm experiment in the south-west Finnish archipelago, we examined nitrogen, phosphorus and carbon acquiring extracellular enzyme activities in three size fractions (<0.2 {micro}m, 0.2-3 {micro}m, and >3 {micro}m), bacterial abundance, production, community composition and its predicted metabolic functions. The mesocosms received different carbon and nitrogen amendments to test for the effect of inorganic nutrient stoichiometry on enzymatic degradation processes that ultimately determine the export potential of organic matter. Alkaline phosphatase activity occurred mainly in the dissolved form and likely contributed to the excess phosphate conditions. In the beginning of the experiment, peptidolytic and glycolytic enzymes were predicted to be produced by free-living bacteria identified within the classes Actinobacteria and Alphaproteobacteria, whereas the contribution of picocyanobacteria increased towards the end. Our results imply that heterotrophic bacteria lost the competition to picocyanobacteria due to the lack of suitable energy sources. The high hydrolytic rates in fractions <0.2 {micro}m and 0.2-3 {micro}m, found in this study, could potentially retain inorganic nutrients in the surface layer and suppress downward fluxes of organic matter and hence carbon sequestration.

microbiology↗

bioRxiv2023

Winners in good times and bad times: Aerobic anoxygenic phototrophic bacteria profit from photoheterotrophy under carbon-rich and poor conditions

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC="FIGDIR/small/572764v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@1e52797org.highwire.dtl.DTLVardef@18a568forg.highwire.dtl.DTLVardef@138e2c5org.highwire.dtl.DTLVardef@1b0224c_HPS_FORMAT_FIGEXP M_FIG C_FIG Aerobic Anoxygenic Phototrophic (AAP) bacteria are an important component of freshwater bacterioplankton. They can support their heterotrophic metabolism with energy from light, and by that enhance their growth efficiency. Based on results from cultures, it was hypothesized that photoheterotrophy provides an advantage under carbon limitation and facilitates access to recalcitrant or low-energy carbon sources. However, verification of these hypotheses for natural AAP communities has been lacking. Here, we conducted whole community manipulation experiments and compared the growth of AAP bacteria under carbon limited and with recalcitrant or low-energy carbon sources under dark and light conditions to elucidate how they profit from photoheterotrophy. We found that it depends on the season. In spring, AAP bacteria induce photoheterotrophic metabolism under carbon limitation but they outperform heterotrophic bacteria when carbon is available. This effect seems to be driven by physiological responses rather than changes at the community level. In autumn photoheterotrophy is less beneficial. In both seasons, AAP bacteria responded negatively to recalcitrant or low-energy carbon sources in light. This unexpected observation may have ecosystem-level consequences as lake browning continues. In general, our findings contribute to the understanding of the dynamics of AAP bacteria observed in pelagic environments.

ecology↗

bioRxiv2023

Phenology and ecological role of Aerobic Anoxygenic Phototrophs in fresh waters

Aerobic anoxygenic phototrophic (AAP) bacteria are heterotrophic bacteria that supply their metabolism with light energy harvested by bacteriochlorophyll-a-containing reaction centres. Despite their substantial contribution to bacterial biomass, microbial food webs and carbon cycle, their phenology in freshwater lakes remains unknown. Hence, we investigated seasonal variations of AAP abundance and community composition biweekly across three years in a temperate, meso-oligotrophic freshwater lake. AAP bacteria displayed a clear seasonal trend with a spring maximum following the bloom of phytoplankton and a secondary maximum in autumn. As the AAP bacteria represent a highly diverse assemblage of species, we followed their seasonal succession using the amplicon sequencing of the pufM marker gene. To enhance the accuracy of the taxonomic assignment, we developed new pufM primers that generate longer amplicons and compiled the currently largest database of pufM gene, comprising 3633 reference sequences spanning all phyla known to contain AAP species. With this novel resource we demonstrated recurrent and dynamic seasonal succession of the AAP community. The majority of the species appeared during specific phases of the seasonal cycle, with less than 2% of AAP species detected during the whole year. Our results document the indigenous freshwater nature of the AAP community, characterized by high resilience and heterogenic adaptations to varying conditions of the freshwater environment. By integrating this information with the indicator of primary production (Chlorophyll-a) and existing ecological models, we show that AAP bacteria play a pivotal role in the recycling of dissolved organic matter released during spring phytoplankton bloom, contributing significantly to the ecological dynamics of lakes.

microbiology↗