Biology subjects

Fadeev, E.

Publications and source records attributed to Fadeev, E..

7 recordsLinked to original sources

bioRxiv2025

Distinct functional potential of bacterial extracellular vesicles across biogeographic provinces of the South Pacific Ocean

Bacterial extracellular vesicles (BEVs) are nanoscale membranous structures released by diverse types of bacteria. Laboratory model systems indicate that these nanoparticles may play several roles in the ecophysiology of marine bacteria. However, their actual functionality in the environment remains unclear. Here we describe the proteomic composition of marine BEVs over more than 5,000 nautical miles of surface waters in the South Pacific, linking BEV cargoes to the bacterial communities producing them. BEVs were consistently present across a range of biogeochemical conditions, with an overall abundance comparable to that of bacterial cells. However, the protein content of the BEVs varied significantly between different ocean regions. The BEVs were enriched in carbohydrate transporters under phytoplankton bloom conditions, and contained iron and phosphate uptake-related proteins in nutrient-limited waters. This suggests that BEVs could enable cells to perform key extracellular functions in the marine environment. Our observations further highlight the prevalence of BEVs and the biogeographic patterns of their functional potential across oceanic scales.

microbiology↗

bioRxiv2023

Bacterial degradation of ctenophore Mnemiopsis leidyi organic matter

Blooms of gelatinous zooplankton, an important source of protein-rich biomass in coastal waters, often collapse rapidly, releasing large amounts of labile detrital organic matter (OM) into the surrounding water. Although these blooms have the potential to cause major perturbations in the marine ecosystem, their effects on the microbial community and hence on the biogeochemical cycles have yet to be elucidated. We conducted microcosm experiments simulating the scenario experienced by coastal bacterial communities after the decay of a ctenophore (Mnemiopsis leidyi) bloom in the northern Adriatic Sea. Within 24 h, a rapid response of bacterial communities to the M. leidyi OM was observed, characterized by elevated bacterial biomass production and respiration rates. Compared to our previous microcosm study of jellyfish (Aurelia aurita s.l.), M. leidyi OM degradation revealed that, despite the fundamental genetic and biochemical differences between the two species, a similar pattern in the bacterial community response was observed. Combined metagenomic and metaproteomic analysis indicated that the degradation activity was mainly performed by Pseudoalteromonas, producing a large amount of proteolytic exoenzymes and exhibiting high metabolic activity. Interestingly, the reconstructed metagenome-assembled genome (MAG) of Pseudoalteromonas phenolica was almost identical (average nucleotide identity >99%) to the MAG previously reconstructed in our A. aurita microcosm study. Taken together our data suggest that blooms of different gelatinous zooplankton are likely triggering a consistent response from natural bacterial communities, with specific bacterial lineages driving the remineralization of the gelatinous OM. ImportanceJellyfish blooms are increasingly becoming a recurring seasonal event in marine ecosystems, characterised by a rapid build-up of gelatinous biomass that collapses rapidly. Although these blooms have the potential to cause major perturbations, their impact on marine microbial communities is largely unknown. We conducted an incubation experiment simulating a bloom of the ctenophore Mnemiopsis leidyi in the Northern Adriatic, where we investigated the bacterial response to the gelatinous biomass. We found that the bacterial communities actively degraded the gelatinous organic matter, and overall showed a striking similarity to the dynamics previously observed after a simulated bloom of the jellyfish Aurelia aurita s.l. In both cases we found that a single bacterial species, Pseudoalteromonas phenolica, was responsible for most of the degradation activity. This suggests that blooms of different jellyfish are likely to trigger a consistent response from natural bacterial communities, with specific bacterial species driving the remineralisation of gelatinous biomass.

microbiology↗

bioRxiv2022

Selecting 16S rRNA primers for microbiome analysis in a host-microbe system: the case of the jellyfish Rhopilema nomadica

Amplicon sequencing of the 16S rRNA gene is extensively used to characterize bacterial communities, including those living in association with eukaryotic hosts. Deciding which region of the 16S rRNA gene to analyze and selecting the appropriate PCR primers remained a major decision when initiating any new microbiome study. Here, we compared three commonly used primers targeting different hypervariable regions of the 16S rRNA gene, V1V2, V3V4, and V4V5, using the jellyfish Rhopilema nomadica as a model. Although all primers exhibit a similar pattern in bacterial community composition, the performance of the V3V4 primer set was superior to V1V2 and V4V5. The V1V2 primers misclassified bacteria from the Bacilli class and exhibited low classification resolution for Rickettsiales, which represent the second most abundant 16S rRNA gene sequence in all the primers. The V4V5 primer set detected almost the same community composition as the V3V4, but the ability of these primers to also amplify eukaryotic 18S rRNA gene may hinder bacterial community observations. However, after overcoming the challenges possessed by each one of those primers, we found that all three of them show very similar bacterial community dynamics and composition. Nevertheless, based on our results, we propose that the V3V4 primer set is the most suitable for studying jellyfish-associated bacterial communities. Our results suggest that, at least for jellyfish samples, it may be feasible to directly compare microbial community estimates from different studies, each using different primers but otherwise similar experimental protocols. More generally, we recommend specifically testing different primers as a prelude to large-scale 16S rRNA gene amplicon analyses, especially of previously unstudied host-microbe associations.

microbiology↗

bioRxiv2022

Characterization of membrane vesicles in Alteromonas macleodii indicates potential roles in their copiotrophic lifestyle

Bacterial membrane vesicles (MVs) are likely abundant in the oceans. Based on observations from non-marine bacteria, MVs are involved in a range of physiological processes and play important roles in interactions between microbial cells. In this study we characterized MV production of six different strains of Alteromonas macleodii, a cosmopolitan marine bacterium. A. macleodii strains produced MVs at rates of up to 30 MVs cell-1 generation-1. The produced MVs had high morphological diversity that could potentially define their functional roles. Proteomic characterization revealed that MVs are rich in membrane proteins related to iron and phosphate uptake, as well as proteins with potential functions in biofilm formation. Furthermore, MVs were harboring hydrolytic enzymes. Taken together, our results suggest that in the largely oligotrophic oceans, A. macleodii MVs may support its growth through generation of extracellular "hotspots" that facilitate access to essential substrates. This study provides an important basis for further investigation of the ecological relevance of MVs in heterotrophic marine bacteria.

microbiology↗

bioRxiv2021

Seasonal dynamics are the major driver of microbial diversity and composition in intensive freshwater aquaculture

Aquaculture facilities such as fishponds are one of the most anthropogenically impacted freshwater ecosystems. The high fish biomass reared in aquaculture is associated with an intensive input into the water of fish-feed and fish excrements. This nutrients load may affect the microbial community in the water, which in turn can impact the fish health. To determine to what extent aquaculture practices and natural seasonal cycles affect the microbial populations, we characterized the microbiome of an inter-connected aquaculture system at monthly resolution, over three years. The system comprised two fishponds, where fish are grown, and a "control" operational water reservoir in which fish are not actively stocked. Clear natural seasonal cycles of temperature and inorganic nutrients concentration, as well as recurring cyanobacterial blooms during summer, were observed in both the fishponds and the reservoir. The structure of the aquatic bacterial communities in the system, characterized using 16S rRNA sequencing, was explained primarily by the natural seasonality, whereas aquaculture-related parameters had only a minor explanatory power. However, the cyanobacterial blooms were characterized by different cyanobacterial clades dominating at each fishpond, possibly in response to distinct nitrogen and phosphate ratios. In turn, nutrient ratios may have been by the magnitude of fish feed input. Taken together, our results show that, even in strongly anthropogenically impacted aquatic ecosystems, the structure of bacterial communities is mainly driven by the natural seasonality, with more subtle effects if aquaculture-related factors. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=114 SRC="FIGDIR/small/433039v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@154d693org.highwire.dtl.DTLVardef@d35ae9org.highwire.dtl.DTLVardef@1f5a7a2org.highwire.dtl.DTLVardef@d07fbc_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIWe present three years of monthly microbiome data from an aquaculture facility. C_LIO_LIThe microbiome changes seasonally, likely driven by temperature and rainwater runoff. C_LIO_LISummer blooms of toxin-producing cyanobacteria are repeatedly observed. C_LIO_LIFish food may impact microbiome through changes in nutrient ratios. C_LI

ecology↗

bioRxiv2020

Submesoscale dynamics directly shape bacterioplankton community structure in space and time

Submesoscale eddies and fronts are recognized as important components of oceanic mixing and energy fluxes. These submesoscale phenomena occur in the surface ocean for a period of a few days on scales between several hundred meters and a few tens of kilometers. Remote sensing and modeling suggest that they may influence marine ecosystem dynamics, but their limited temporal and spatial scales make them challenging for observation and in situ sampling. Here, the study of a submesoscale filament in summerly Arctic waters (depth 0 - 400 m) revealed enhanced vertical mixing of Polar and Atlantic water masses, resulting in a ca. 4 km wide and ca. 50 km long filament with distinct physical and biogeochemical conditions. Compared to the surrounding waters the filament was characterized by a distinct phytoplankton bloom dominated by diatoms and two-fold higher bacterioplankton cell densities. High-throughput 16S rRNA gene sequencing of both bacterioplankton communities revealed 3-4 orders of magnitude higher sequence abundance of Synechococcus inside the filament, as well as tenfold higher sequence abundance of taxonomic groups typically found during summertime in aging phytoplankton blooms (e.g., Flavobacteriales). In contrast, the surrounding waters contained severalfold higher sequence abundance of winterly taxonomic groups that are also associated with polar water masses (e.g., SAR202 clade). Altogether, our results show that physical submesoscale processes in the ocean can shape distinct biogeochemical conditions and microbial communities within a few kilometers. Furthermore, our results underline the importance of such submesoscale features for our understanding of surface ocean diversity and biogeochemical processes.

ecology↗

bioRxiv2020

Spatial dynamics in Arctic bacterioplankton community densities are strongly linked to distinct physical and biological processes (Fram Strait, 79°N)

The Arctic is impacted by climate warming faster than any other oceanic region on Earth. Assessing the baseline of microbial communities in this rapidly changing ecosystem is vital for understanding the implications of ocean warming and sea ice retreat on ecosystem functioning. Using CARD-FISH and semi-automated counting, we quantified 14 ecologically relevant taxonomic groups of bacterioplankton (Bacteria and Archaea) from surface (0-30 m) down to deep waters (2500 m) in summerly ice-covered and ice-free regions of the Fram Strait, the main gateway for Atlantic inflow into the Arctic Ocean. Cell abundances of the bacterioplankton communities in surface waters varied from 105 cells mL-1 in ice-covered regions to 106 cells mL-1 in the ice-free regions, and were overall driven by variations in phytoplankton bloom conditions across the Strait. The bacterial classes Bacteroidia and Gammaproteobacteria showed several-fold higher cell abundances under late phytoplankton bloom conditions of the ice-free regions. Other taxonomic groups, such as the Rhodobacteraceae, revealed a distinct association of cell abundances with the surface Atlantic waters. With increasing depth (>500 m), the total cell abundances of the bacterioplankton communities decreased by up to two orders of magnitude, while largely unknown taxonomic groups (e.g., SAR324 and SAR202 clades) maintained constant cell abundances throughout the entire water column (ca. 103 cells mL-1). This suggests that these enigmatic groups may occupy a specific ecological niche in the entire water column. Our results provide the first quantitative spatial variations assessment of bacterioplankton in the summerly ice-covered and ice-free Arctic water column, and suggest that further shift towards ice-free Arctic summers with longer phytoplankton blooms can lead to major changes in the associated standing stock of the bacterioplankton communities.

microbiology↗