Changes in microbial (Bacteria and Archaea) plankton community structure after artificial dispersal in grazer-free microcosms

Microbes are considered to have a global distribution due to their high dispersal capabilities. However, our knowledge of the way geographically distant microbial communities assemble after dispersal in a new environment is limited. In this study, we examined whether communities would converge because similar taxa would be selected under the same environmental conditions, or would diverge because of initial community composition, after artificial dispersal. To this aim, a microcosm experiment was performed, in which the temporal changes in the composition and diversity of different prokaryoplankton assemblages from three distant geographic coastal areas (Banyuls-sur-Mer in northwest Mediterranean Sea, Pagasitikos Gulf in northeast Mediterranean and Woods Hole, MA, USA in the northwest Atlantic), were studied. Diversity was investigated using amplicon pyrosequencing of the V1-V3 hypervariable regions of the 16S rRNA. The three assemblages were grown separately in particle free and autoclaved Banyuls-sur-mer seawater at 18 °C in the dark. We found that the variability of prokaryoplankton community diversity (expressed as richness, evenness and dominance) as well as the composition were driven by patterns observed in Bacteria. Regarding community composition, similarities were found between treatments at family level. However, at the OTU level microbial communities from the three different original locations diverge rather than converge during incubation. It is suggested that slight differences in the composition of the initial prokaryoplankton communities, resulted in separate clusters the following days even when growth took place under identical abiotic conditions

Plankton Microorganisms Coinciding with Two Consecutive Mass Fish Kills in a Newly Reconstructed Lake

Lake Karla, Greece, was dried up in 1962 and its refilling started in 2009. We examined the Cyanobacteria and unicellular eukaryotes found during two fish kill incidents, in March and April 2010, in order to detect possible causative agents. Both microscopic and molecular (16S/18S rRNA gene diversity) identification were applied. Potentially toxic Cyanobacteria included representatives of the Planktothrix and Anabaena groups. Known toxic eukaryotes or parasites related to fish kill events were Prymnesium parvum and Pfiesteria cf. piscicida, the latter being reported in an inland lake for the second time. Other potentially harmful microorganisms, for fish and other aquatic life, included representatives of Fungi, Mesomycetozoa, Alveolata, and Heterokontophyta (stramenopiles). In addition, Euglenophyta, Chlorophyta, and diatoms were represented by species indicative of hypertrophic conditions. The pioneers of L. Karla's plankton during the first months of its water refilling process included species that could cause the two observed fish kill events

Changes in Heterotrophic Picoplankton Community Structure after Induction of a Phytoplankton Bloom under Different Light Regimes

Bacterial and archaeal diversity and succession were studied during a mesocosm experiment that investigated whether changing light regimes could affect the onset of phytoplankton blooms. For this, 454-pyrosequencing of the bacterial V1-V3 and archaeal V3-V9 16S rRNA regions was performed in samples collected from four mesocosms receiving different light irradiances at the beginning and the end of the experiment and during phytoplankton growth. In total, 46 bacterial operational taxonomic units (OTUs) with ≥1% relative abundance occurred (22-34 OTUs per mesocosm). OTUs were affiliated mainly with Rhodobacteraceae, Flavobacteriaceae and Alteromonadaceae. The four mesocosms shared 11 abundant OTUs. Dominance increased at the beginning of phytoplankton growth in all treatments and decreased thereafter. Maximum dominance was found in the mesocosms with high irradiances. Overall, specific bacterial OTUs had different responses in terms of relative abundance under in situ and high light intensities, and an early phytoplankton bloom resulted in different bacterial community structures both at high (family) and low (OTU) taxonomic levels. Thus, bacterial community structure and succession are affected by light regime, both directly and indirectly, which may have implications for an ecosystem's response to environmental changes

Microbes and us: microbiology literacy in Greece

Microbes are ubiquitous and provide numerous services to humans and our planet. However, a query arises as to whether these microbial services are valued by the general public especially after unprecedented conditions like the COVID-19 pandemic. In this context a survey was conducted to investigate the concept of microbe in Greece. Thematic analysis of 672 anonymous responses (age range 4–75yo) received for the open-ended prompt “What is the first thing that comes to mind when you hear the word microbe?” revealed five thematic categories: Negative emotions, Fuzzy associations, Biology, Entities and Health. Almost 80% of responses fell under “Biology” and “Health” and the general pattern of answers was the same across all age groups. Microbes took a variety of forms in the minds of respondents, however, the concept of “microbe” seems to be more unshaped at younger ages (4–11yo), as revealed in children's language choices. Overall, the often-negative perception of microorganisms seems to be confirmed in this study. Although this research was limited to participants from Greece, it remains relevant to other countries around the world as well. We discuss the reasons behind this negative perception and offer suggestions for reversing it

Implementation of the Water Framework Directive: Lessons Learned and Future Perspectives for an Ecologically Meaningful Classification Based on Phytoplankton of the Status of Greek Lakes, Mediterranean Region

The enactment of the Water Framework Directive (WFD) initiated scientific efforts to develop reliable methods for comparing prevailing lake conditions against reference (or nonimpaired) states, using the state of a set biological elements. Drawing a distinction between impaired and natural conditions can be a challenging exercise. Another important aspect is to ensure that water quality assessment is comparable among the different Member States. In this context, the present paper offers a constructive critique of the practices followed during the WFD implementation in Greece by pinpointing methodological weaknesses and knowledge gaps that undermine our ability to classify the ecological quality of Greek lakes. One of the pillars of WDF is a valid lake typology that sets ecological standards transcending geographic regions and national boundaries. The national typology of Greek lakes has failed to take into account essential components. WFD compliance assessments based on the descriptions of phytoplankton communities are oversimplified and as such should be revisited. Exclusion of most chroococcal species from the analysis of cyanobacteria biovolume in Greek lakes/reservoirs and most reservoirs in Spain, Portugal, and Cyprus is not consistent with the distribution of those taxa in lakes. Similarly, the total biovolume reference values and the indices used in classification schemes reflect misunderstandings of WFD core principles. This hampers the comparability of ecological status across Europe and leads to quality standards that are too relaxed to provide an efficient target for the protection of Greek/transboundary lakes such as the ancient Lake Megali Prespa

Bacteria Release from Microplastics into New Aquatic Environments

Microplastics are considered the most common waste in aquatic ecosystems, and studying them along with their interactions with biota are considered a priority. Here, results on the role of microplastics in the dispersion of microbes from terrestrial to aquatic ecosystems are presented. Data were obtained from microcosm experiments in which microplastics (plastic bags (BA), polyethylene bottles (BO), acrylic beads (BE), and cigarette butts (BU)) with their attached natural bacterial communities were inoculated in filtered and autoclaved lake water. The bacterial abundance on microplastics was estimated before inoculation using a protocol for the enumeration of sediment bacteria and ranged between 1.63 (BA) and 203.92 (BE) × 103 cells mm−2. Bacteria were released in the new medium, and their growth rates reached 5.8 d−1. In the attached communities, Beta- (21.4%) and Alphaproteobacteria (18.6%) were the most abundant classes, while in the free-living communities Gammaproteobacteria dominated (48.07%). Abundant OTUs (≥1%) of the free-living communities were associated with the genera Acinetobacter, Pseudomonas, Ecidovorax, Delftia, Comamonas, Sphingopyxis, and Brevundimonas and members of the FCB group. Members of these genera are known to degrade natural or man-made organic compounds and have recently emerged as opportunistic pathogens. Thus, besides trophic transmission, microplastics can directly release bacteria in the environment, which could affect the health of humans, animals, and ecosystems

Metagenomic Characterization of Bacterial Communities on Ready-to-Eat Vegetables and Effects of Household Washing on their Diversity and Composition

Ready-to-eat (RTE) leafy salad vegetables are considered foods that can be consumed immediately at the point of sale without further treatment. The aim of the study was to investigate the bacterial community composition of RTE salads at the point of consumption and the changes in bacterial diversity and composition associated with different household washing treatments. The bacterial microbiomes of rocket and spinach leaves were examined by means of 16S rRNA gene high-throughput sequencing. Overall, 886 Operational Taxonomic Units (OTUs) were detected in the salads’ leaves. Proteobacteria was the most diverse high-level taxonomic group followed by Bacteroidetes and Firmicutes. Although they were processed at the same production facilities, rocket showed different bacterial community composition than spinach salads, mainly attributed to the different contributions of Proteobacteria and Bacteroidetes to the total OTU number. The tested household decontamination treatments proved inefficient in changing the bacterial community composition in both RTE salads. Furthermore, storage duration of the salads at refrigeration temperatures affected the microbiome, by decreasing the bacterial richness and promoting the dominance of psychrotropic bacteria. Finally, both salads were found to be a reservoir of opportunistic human pathogens, while washing methods usually applied at home proved to be inefficient in their removal

Diversity of Bacteria in Lakes with Different Chlorophyll Content and Investigation of Their Respiratory Activity through a Long-Term Microcosm Experiment

Bacterial community structure and metabolism are critical factors for ecosystem functioning since they affect remineralization of nutrients and carbon flow. We used Illumina sequencing of 16SrRNA V3-V4 regions to investigate whether bacterial assemblage composition differs between four samples from two lakes in the geographic region of Epirus (Greece) characterized by distinct oligotrophic to eutrophic/hypereutrophic conditions as revealed by chlorophyll-a values. We found high similarity (>60%) for bacterial assemblages recovered from the two lakes when eutrophic/hypereutrophic conditions prevailed. Distinct bacterial communities appeared in oligotrophic and mesotrophic waters. Low temperature was occasionally an important factor in shaping the bacterial community. In parallel, microcosm experiments were performed to estimate respiration rates of bacterioplankton at in situ temperature and under a 2 °C temperature increase scenario. Differently assembled communities were found to display similar rates except under hypereutrophic conditions when respiration increased significantly, leading to hypoxic conditions. Temperature increase did not affect respiration rates. Overall this study indicated a clear differentiation of bacterial communities between sites of different trophic state. However, different communities responded similarly under a specific range of chlorophyll-a values and resisted small scale temperature perturbations. Different results were found for hypereutrophic conditions and this has implications for ecosystems functioning, given the increasing occurrence of eutrophication events

Evaluation of double formalin—Lugol's fixation in assessing number and biomass of ciliates: an example of estimations at mesoscale in NE Atlantic

International audienceCiliated protozoa are potential grazers of primary and bacterial production and act as intermediaries between picoplankton and copepods and other large suspension feeders. Accurate determination of ciliate abundance and feeding mode is crucial in oceanic carbon budget estimations. However, the impact of different fixatives on the abundance and cell volume of ciliates has been investigated in only a few studies using either laboratory cultures or natural populations. Lugol's solution and formalin are the most commonly used fixatives for the preservation of ciliates samples. In the present study, the aim was to compare 0.4% Lugol's solution and 2% borated-formalin fixation and evaluate the need of counting duplicate samples each using a different fixative. For this, a large number of samples (n = 110) from the NE Atlantic was analyzed in the frame of POMME program (Multidisciplinary Mesoscale Ocean Program). We established a statistically significant relationship (p < 0.0001) between Lugol's and formalin fixed samples for both abundance (r 2 = 0.50) and biomass (r 2 = 0.76) of aloricate ciliates which showed that counts were higher in Lugol's solution by a factor of 2 and a non-taxon specific cell-loss in formalin. However, loricate ciliate abundance in our samples which were represented primarily by Tintinnus spp. did not show any difference between the two treatments. Abundance and biomass of mixotrophic ciliates (chloroplast-bearing cells) were for various reasons underestimated in both treatments. Our results show that unique fixation by formalin may severely underestimate ciliates abundance and biomass although their population may not alter. For this reason, Lugol's solution is best for the estimation of their abundance and biomass. However, for counts of mixotrophs and the evaluation of the ecological role of ciliates in carbon flux, double fixation is essential. Compromises regarding the fixatives have lead to severe underestimations of mixotrophs in studies conducted by now.

Influence of ciliated protozoa and heterotrophic nanoflagellates on the fate of primary production in NE Atlantic Ocean.

International audience[1] Heterotrophic nanoflagellates and ciliates and their herbivorous activity were studied within the framework of the Programme Océan Multidisciplinaire Méso Echelle (POMME) in the northeastern Atlantic between 16°–22°W and 38°–45°N during winter, spring, and late summer/autumn 2001. Ciliate ingestion rates of Synechococcus and eukaryotic algae were measured using fluorescently labeled prey. Heterotrophic nanoflagellate ingestion rates of Synechococcus and Prochlorococcus were also estimated. Heterotrophic nanoflagellate and ciliate standing stock within the surface layer (0–100 m) showed seasonal variation, with maximal values in spring (866 mg C m À2 and 637 mg C m À2 , respectively). Oligotrichs dominated the ciliate assemblages, except at one site visited during spring, where a tintinnid bloom was observed. Ingestion of photosynthetic cells less than 10 mm in size was positively correlated (r = 0.7, p < 0.05, n = 12) with primary production and accounted for 2–94% of this. Phytoplankton consumption reflected differences in the evolution of the phytoplankton bloom and in the structure of the microbial food web, both associated with the strong mesoscale hydrodynamic variability of the study area. In that context it is worthy to note that when tintinnids reached high abundances locally (1260 cells L À1), their impact as phytoplankton grazers was important and reached 69% of primary production. Generally, heterotrophic nanoflagellates and ciliates were relatively more important in determining the fate of phytogenic carbon during spring. Another interesting feature of primary production consumption was that during the autumn, when Prochlorococcus dominated the phytoplankton community, the protozoan grazing activity was ineffective in regulating the fate of primary producers. Citation: Karayanni, H., U. Christaki, F. Van Wambeke, M. Denis, and T. Moutin (2005), Influence of ciliated protozoa and heterotrophic nanoflagellates on the fate of primary production in the northeast Atlantic Ocean