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The monitoring of phytoplankton is crucial to highlight changes in the marine ecosystems. In the present study, the phytoplankton community of an eLTER station in the Northern Adriatic Sea was analysed combining two approaches, i.e. microscopy and eDNA metabarcoding (targeting V4 and V9 regions of the 18S rRNA gene, and using PR2 and SILVA as reference databases), to highlight the strengths and weaknesses of these two methods. Metabarcoding revealed a so far unknown phytoplankton diversity (99 genera and 151 species), while microscopy detected 14 genera and 44 species not revealed by metabarcoding. Only a small percentage of genera and species were shared by the two methods (microscopy and metabarcoding), 18S regions (V4 and V9) and reference databases (PR2 and SILVA). Metabarcoding showed a community characterized by a higher number of phytoflagellate and dinoflagellate genera and species, in comparison with microscopy where diatom and dinoflagellate taxa were the most represented. Moreover, metabarcoding failed to reveal almost all the coccolithophores. The results confirmed metabarcoding as a powerful tool, but it should still be combined with microscopy to have a more detailed information on the community and to counteract the drawbacks of metabarcoding, such as gaps in the reference databases.

In 1981 I established kingdom Chromista, distinguished from Plantae because of its more complex chloroplast-associated membrane topology and rigid tubular multipartite ciliary hairs. Plantae originated by converting a cyanobacterium to chloroplasts with Toc/Tic translocons; most evolved cell walls early, thereby losing phagotrophy. Chromists originated by enslaving a phagocytosed red alga, surrounding plastids by two extra membranes, placing them within the endomembrane system, necessitating novel protein import machineries. Early chromists retained phagotrophy, remaining naked and repeatedly reverted to heterotrophy by losing chloroplasts. Therefore, Chromista include secondary phagoheterotrophs (notably ciliates, many dinoflagellates, Opalozoa, Rhizaria, heliozoans) or walled osmotrophs (Pseudofungi, Labyrinthulea), formerly considered protozoa or fungi respectively, plus endoparasites (e.g. Sporozoa) and all chromophyte algae (other dinoflagellates, chromeroids, ochrophytes, haptophytes, cryptophytes). I discuss their origin, evolutionary diversification, and reasons for making chromists one kingdom despite highly divergent cytoskeletons and trophic modes, including improved explanations for periplastid/chloroplast protein targeting, derlin evolution, and ciliary/cytoskeletal diversification. I conjecture that transit-peptide-receptor-mediated ‘endocytosis’ from periplastid membranes generates periplastid vesicles that fuse with the arguably derlin-translocon-containing periplastid reticulum (putative red algal trans-Golgi network homologue; present in all chromophytes except dinoflagellates). I explain chromist origin from ancestral corticates and neokaryotes, reappraising tertiary symbiogenesis; a chromist cytoskeletal synapomorphy, a bypassing microtubule band dextral to both centrioles, favoured multiple axopodial origins. I revise chromist higher classification by transferring rhizarian subphylum Endomyxa from Cercozoa to Retaria; establishing retarian subphylum Ectoreta for Foraminifera plus Radiozoa, apicomonad subclasses, new dinozoan classes Myzodinea (grouping Colpovora gen. n., Psammosa), Endodinea, Sulcodinea, and subclass Karlodinia; and ranking heterokont Gyrista as phylum not superphylum.

Macrolides are a significant family of natural products with diverse structures and bioactivities. Considerable effort has been made in recent decades to isolate additional macrolides and characterize their chemical and bioactive properties. The majority of macrolides are obtained from marine organisms, including sponges, marine microorganisms and zooplankton, cnidarians, mollusks, red algae, bryozoans, and tunicates. Sponges, fungi and dinoflagellates are the main producers of macrolides. Marine macrolides possess a wide range of bioactive properties including cytotoxic, antibacterial, antifungal, antimitotic, antiviral, and other activities. Cytotoxicity is their most significant property, highlighting that marine macrolides still encompass many potential antitumor drug leads. This extensive review details the chemical and biological diversity of 505 macrolides derived from marine organisms which have been reported from 1990 to 2020.

We investigated seasonal and spatial patterns of phytoplankton variability in the East China Sea in order to understand biomass and compositional responses to environmental factors in the contemporary ocean. We used satellite imagery from 2002 to 2013 to define the mean seasonal climatology of sea surface temperature and chlorophyll a. Phytoplankton and environmental measurements were synthesized for the study region and four seasons from 11 cruises conducted from 2006 to 2012. The results of CHEMTAX analyses on group-specific phytoplankton composition were consistent with those of microscopy and flow cytometry observations, revealing three patterns of seasonal variability. Canonical correspondence analysis and generalized additive models (GAMs) were used to resolve the spatiotemporal variations of major phytoplankton groups and their relationships to month, temperature, salinity, nutrients, mixed layer depth, and bottom depth. Monsoon forcing drove the distributional patterns of environmental factors and was critical to explaining phytoplankton dynamics at the seasonal scale. Compared to autumn and winter, significantly higher chlorophyll a concentrations were observed during spring and summer, associated with the spring bloom and the Changjiang (Yangtze) River plume, respectively. Diatoms dominated biomass over the East China Sea, especially during the summer months influenced by the Changjiang (Yangtze) River plume, whereas dinoflagellates were especially important during spring blooms. GAMs analysis showed the differences in their responses to environmental variability, with a clear mid-range salinity optimum (~31) and a more pronounced temperature effect for dinoflagellates. The photosynthetic bacteria, Prochlorococcus and Synechococcus, both increased strongly with warming, but Prochlorococcus showed stronger sensitivity to variations in physical environmental parameters, whereas Synechococcus was more responsive to chemical (nutrient) variability, with broader tolerance of low-salinity conditions.

Aim - Trends in spatial patterns of diversity in macroscopic organisms can be well predicted from correlative models, using topo‐climatic variables for plants and animals allowing inference over large scales. By contrast, diversity in soil microorganisms is generally considered as mostly driven by edaphic variables and, therefore, difficult to extrapolate on a large spatial scale based on predictive models. Here, we compared the power of topo‐climatic versus edaphic variables for predicting the diversity of various soil protist groups at the regional scale. Location - Swiss western Alps. Taxa - Full protist community and nine clades belonging respectively to three functional groups: parasites (Apicomplexa, Peronosporomycetes and Phytomyxea), phagotrophs (Sarcomonadea, Tubulinea and Spirotrichea) and phototrophs (Chlorophyta, Trebouxiophyceae and Diatomeae). Methods - We extracted soil DNA from 178 sites along a wide range of elevations with a random‐stratified sampling design. We defined protist Operational Taxonomic Units assemblages by metabarcoding of the V4 region of the rRNA small subunit gene. We assessed and modelled the diversity (Shannon index) patterns of all above‐mentioned taxonomic groups based on topo‐climatic (topography, slope southness, slope steepness and average summer temperature) and edaphic (soil temperature, relative humidity, pH, electroconductivity, phosphorus percentage, carbon/nitrogen, loss on ignition and shale percentage) variables in Generalized Additive Models (GAM). Results - The respective significance of topo‐climatic and edaphic variables varied among taxonomic and—to a certain extent—functional groups: while many variables explained significantly the diversity of the three phototrophs this was less the case for the three parasites. Topo‐climatic variables had a better predictive power than edaphic variables, yet predictive power varied among taxonomic groups. Main conclusions - Topo‐climatic variables (particularly slope steepness and summer temperature if we consider their significance in the GAMs) were, on average, better predictors of protist diversity at the landscape scale than edaphic variables. However, the predictive power of these variables on diversity differed considerably among taxonomic groups; such relationships may be due to direct and/or indirect (e.g. biotic) influences (like with parasitic taxa, where low predictive power is most likely explained by the absence of information on the hosts’ distribution). Future prospects include using such spatial models to predict hotspots of diversity and disease outbreaks.

Many phytoplankton species produce toxic substances, but their functional role is unclear. Specifically, it remains uncertain whether these compounds have a toxic or deterrent effect on grazers; only, the latter is consistent with toxins as defensive tools. Here, we show that 10 of 12 species or strains of toxic dinoflagellates were consumed at lower rates than a similarly sized nontoxic dinoflagellate by a copepod. Through video observations of individual prey–grazer interactions, we further demonstrate that the dominating mechanism is through capture, examination, and subsequent rejection of vital cells, that is, a true deterrent effect that offers a straightforward explanation to its evolution. We argue that the diversity of grazer responses to toxic phytoplankton reported in the literature, including toxic effects, and the high diversity of toxin profiles between strains of the same phytoplankton species reflect different stages of an ever-ongoing evolutionary arms race, facilitated by rapid adaptation of grazers to toxic substances. We further argue that defensive toxicity requires a chemical signal exterior to the cell that informs the grazer about the toxicity of the cell. The signal can be the toxin itself or just an aposematic signal of toxicity. In the former case, allelochemical effects may emerge at high cell concentrations as a nonadaptive side effect of a predator defenses.

Dinoflagellates are a major aquatic protist group with amphiesma, multiple cortical membranous “cell wall” layers that contain large circum-cortical alveolar sacs (AVs). AVs undergo extensive remodeling during cell- and life-cycle transitions, including ecdysal cysts (ECs) and resting cysts that are important in some harmful algal bloom initiation–termination. AVs are large cortical vesicular compartments, within which are elaborate cellulosic thecal plates (CTPs), in thecate species, and the pellicular layer (PL). AV-CTPs provide cellular mechanical protection and are targets of vesicular transport that are replaced during EC-swarmer cell transition, or with increased deposition during the cellular growth cycle. AV-PL exhibits dynamical-replacement with vesicular trafficking that are orchestrated with amphiesmal chlortetracycline-labeled Ca2+ stores signaling, integrating cellular growth with different modes of cell division cycle/progression. We reviewed the dynamics of amphiesma during different cell division cycle modes and life cycle stages, and its multifaceted regulations, focusing on the regulatory and functional readouts, including the coral–zooxanthellae interactions.

• Although most of the tens of thousands of diatom species are photoautotrophs, a small number of heterotrophic species no longer photosynthesize. We sequenced the genome of a nonphotosynthetic diatom, Nitzschia Nitz4, to determine how carbon metabolism was altered in the wake of this trophic shift. • Nitzschia Nitz4 has retained its plastid and plastid genome, but changes associated with the transition to heterotrophy were cellular-wide and included losses of photosynthesis-related genes from the nuclear and plastid genomes, elimination of isoprenoid biosynthesis in the plastid, and remodeling of mitochondrial glycolysis to maximize adenosine triphosphte (ATP) yield. The genome contains a β-ketoadipate pathway that may allow Nitzschia Nitz4 to metabolize lignin-derived compounds. • Diatom plastids lack an oxidative pentose phosphate pathway (oPPP), leaving photosynthesis as the primary source of NADPH to support essential biosynthetic pathways in the plastid and, by extension, limiting available sources of NADPH in nonphotosynthetic plastids. • The genome revealed similarities between nonphotosynthetic diatoms and apicomplexan parasites for provisioning NADPH in their plastids and highlighted the ancestral absence of a plastid oPPP as a potentially important constraint on loss of photosynthesis, a hypothesis supported by the higher frequency of transitions to parasitism or heterotrophy in lineages that have a plastid oPPP.

Coral reefs are the most biodiversity-rich ecosystems in the world’s oceans. Coral establishes complex interactions with various microorganisms that constitute an important part of the coral holobiont. The best-known coral endosymbionts are Symbiodiniaceae dinoflagellates. Each member of the coral microbiome contributes to its total lipidome, which integrates many molecular species. The present study summarizes available information on the molecular species of the plasma membrane lipids of the coral host and its dinoflagellates (phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylserine (PS), phosphatidylinositol (PI), ceramideaminoethylphosphonate, and diacylglyceryl-3-O-carboxyhydroxymethylcholine), and the thylakoid membrane lipids of dinoflagellates (phosphatidylglycerol (PG) and glycolipids). Alkyl chains of PC and PE molecular species differ between tropical and cold-water coral species, and features of their acyl chains depend on the coral’s taxonomic position. PS and PI structural features are associated with the presence of an exoskeleton in the corals. The dinoflagellate thermosensitivity affects the profiles of PG and glycolipid molecular species, which can be modified by the coral host. Coral microbiome members, such as bacteria and fungi, can also be the source of the alkyl and acyl chains of coral membrane lipids. The lipidomics approach, providing broader and more detailed information about coral lipid composition, opens up new opportunities in the study of biochemistry and ecology of corals.

Building on a summary of how turbulence influences biological systems, we reviewed key phytoplankton-turbulence laboratory experiments (after Peters and Redondo in Scientia Marina: Lectures on plankton and turbulence, International Centre for Coastal Resources, Barcelona, 1997) and Peters and Marrasé (Marine Ecology Progress Series 205:291–306, 2000) to provide a current overview of artificial turbulence generation methods and quantification techniques. This review found that most phytoplankton studies using artificial turbulence feature some form of quantification of turbulence; it is recommended to use turbulent dissipation rates (ε) for consistency with physical oceanographic and limnological observations. Grid-generated turbulence is the dominant method used to generate artificial turbulence with most experiments providing quantified ε values. Couette cylinders are also commonly used due to the ease of quantification, albeit as shear rates not ε. Dinoflagellates were the primary phytoplanktonic group studied due to their propensity for forming harmful algal blooms (HAB) as well as their apparent sensitivity to turbulence. This study found that a majority of experimental setups are made from acrylate plastics that could emit toxins as these materials degrade under UV light. Furthermore, most cosm systems studied were not sufficiently large to accommodate the full range of turbulent length scales, omitting larger vertical overturns. Recognising that phytoplankton-turbulence interactions are extremely complex, the continued promotion of more interdisciplinary studies is recommended.