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Testate amoebae are valuable indicators of peatland hydrology and have been used in many palaeoclimatic studies in peatlands. Because the species' ecological optima may vary around the globe, the development of transfer function models is an essential prerequisite for regional palaeoclimatic studies using testate amoebae. We investigated testate amoebae ecology in nine peatlands covering a 250-km north-south transect in south-central Alaska. Redundancy analysis and Mantel tests were used to establish the relationship between the measured environmental variables (water-table depth and pH) and testate amoebae communities. Transfer-function models were developed using weighted averaging, weighted average partial least squares and maximum likelihood techniques. Model prediction error was initially 15.8 cm for water-table depth and 0.3 for pH but this was reduced to 9.7 cm and 0.2 by selective data exclusion. The relatively poor model performance compared with previous studies may be explained by the limitations of one-off water-table measurements, the very large environmental gradients covered and by recent climatic change in the study area. The environmental preferences of testate amoebae species agree well with previous studies in other regions. This study supports the use of testate amoebae in palaeoclimate studies and provides the first testate amoebae transfer function from Alaska.

The two main methods for partitioning crude methanolic extract from Amphidinium carterae biomass were compared. The objective was to obtain three enriched fractions containing amphidinols (APDs), carotenoids, and fatty acids. Since the most valuable bioproducts are APDs, their recovery was the principal goal. The first method consisted of a solid-phase extraction (SPE) in reverse phase that, for the first time, was optimized to fractionate organic methanolic extracts from Amphidinium carterae biomass using reverse-phase C18 as the adsorbent. The second method consisted of a two-step liquid-liquid extraction coupled with SPE and, alternatively, with solvent partitioning. The SPE method allowed the recovery of the biologically-active fraction (containing the APDs) by eluting with methanol (MeOH): water (H[sub.2] O) (80:20 v/v). Alternatively, an APD purification strategy using solvent partitioning proved to be a better approach for providing APDs in a clear-cut way. When using n-butanol, APDs were obtained at a 70% concentration (w/w), whereas for the SPE method, the most concentrated fraction was only 18% (w/w). For the other fractions (carotenoids and fatty acids), a two-step liquid-liquid extraction (LLE) method coupled with the solvent partitioning method presented the best results.

The use of chitosan as a flocculant has become a topic of interest over the years due to its positively charged polymer and biodegradable and non-toxic properties. However, most studies only focus on microalgae and wastewater treatment. This study provides crucial insight into the potential of using chitosan as an organic flocculant to harvest lipids and docosahexaenoic acid (DHA-rich Aurantiochytrium sp. SW1 cells by examining the correlation of flocculation parameters (chitosan concentration, molecular weight, medium pH, culture age, and cell density) toward the flocculation efficiency and zeta potential of the cells. A strong correlation between the pH and harvesting efficiency was observed as the pH increased from 3, with the optimal flocculation efficiency of >95% achieved at a chitosan concentration of 0.5 g/L at pH 6 where the zeta potential was almost zero (3.26 mV). The culture age and chitosan molecular weight have no effect on the flocculation efficiency but increasing the cell density decreases the flocculation efficiency. This is the first study to reveal the potential of chitosan to be used as a harvesting alternative for thraustochytrid cells.

Abstract We tracked temporal changes in protist diversity at the Long Term Ecological Research (LTER) station MareChiara in the Gulf of Naples (Mediterranean Sea) on eight dates in 2011 using a metabarcoding approach. Illumina analysis of the V4 and V9 fragments of the 18S rDNA produced 869 522 and 1 410 071 sequences resulting in 6517 and 6519 OTUs, respectively. Marked compositional variations were recorded across the year, with less than 2% of OTUs shared among all samples and similar patterns for the two marker tags. Alveolata, Stramenopiles and Rhizaria were the most represented groups. A comparison with light microscopy data indicated an over-representation of Dinophyta in the sequence dataset, whereas Bacillariophyta showed comparable taxonomic patterns between sequence and light microscopy data. Shannon diversity values were stable from February to September, increasing thereafter with a peak in December. Community variance was mainly explained by seasonality (as temperature), trophic status (as chlorophyll a), and influence of coastal waters (as salinity). Overall, the background knowledge of the system provided a sound context for the result interpretation, showing that LTER sites provide an ideal setting for high-throughput sequencing (HTS) metabarcoding characterisation of protist assemblages and their relationships with environmental variations. Temporal diversity and community structure of the entire protist assemblage from the Gulf of Naples assessed using high throughput sequencing and light microscopy.

Coenzyme Q (CoQ; ubiquinone) is an essential component of the respiratory chain. It is also a potent antioxidant that prevents oxidative damage to DNA, biological membranes, and lipoproteins. CoQ comprises a six-carbon ring with polar substituents that interact with electron acceptors and donors, and a hydrophobic polyisoprenoid chain that allows for its localization in cellular membranes. Human CoQ has 10 isoprenoid units (CoQ[sub.10] ) within the polyisoprenoid chain. Few microorganisms produce CoQ[sub.10] . This work shows that Thraustochytrium sp. RT2316-16 produces CoQ[sub.10] and CoQ[sub.9] . The CoQ[sub.10] content in RT2316-16 depended strongly on the composition of the growth medium and the age of the culture, whereas the CoQ[sub.9] content was less variable probably because it served a different function in the cell. Adding p-hydroxybenzoic acid to the culture media positively influenced the CoQ[sub.10] content of the cell. The absence of some B vitamins and p-aminobenzoic acid in the culture medium negatively affected the growth of RT2316-16, but reduced the decline in CoQ[sub.10] that otherwise occurred during growth. The highest content of CoQ[sub.9] and CoQ[sub.10] in the biomass were 855 μg g[sup.−1] and 10 mg g[sup.−1] , respectively. The results presented here suggest that the thraustochytrid RT2316-16 can be a potential vehicle for producing CoQ[sub.10] . Metabolic signals that trigger the synthesis of CoQ[sub.10] in RT2316-16 need to be determined for optimizing culture conditions.

An in situ imaging technique has been used to show that large rhizarian plankton represent a much larger biomass than previously thought, meaning that they are likely to make an important contribution to ocean ecosystems. Rhizaria are major players in ocean ecology Ocean ecosystems are inhabited by planktonic organisms spanning a wide size range, with large zooplankton feeding on smaller species and thereby contributing to the marine food web and carbon cycling. However, our understanding of the role and contribution of fragile and large zooplankton to the marine ecosystem is limited. Using data collected by an in situ imaging system during the Tara Oceans global survey, Tristan Biard et al . quantified the respective contributions of Rhizaria (a broad phylogenetic group of marine protists) and other zooplankton larger than 600 μm, finding that they represent a much larger biomass than previously appreciated, contributing up to 5.2% of the total oceanic biota carbon reservoir. These findings highlight the important contribution of Rhizaria to plankton biomass, primary productivity and other biogeochemical processes in the oceans. Planktonic organisms play crucial roles in oceanic food webs and global biogeochemical cycles 1 , 2 . Most of our knowledge about the ecological impact of large zooplankton stems from research on abundant and robust crustaceans, and in particular copepods 3 , 4 . A number of the other organisms that comprise planktonic communities are fragile, and therefore hard to sample and quantify, meaning that their abundances and effects on oceanic ecosystems are poorly understood. Here, using data from a worldwide in situ imaging survey of plankton larger than 600 μm, we show that a substantial part of the biomass of this size fraction consists of giant protists belonging to the Rhizaria, a super-group of mostly fragile unicellular marine organisms that includes the taxa Phaeodaria and Radiolaria (for example, orders Collodaria and Acantharia). Globally, we estimate that rhizarians in the top 200 m of world oceans represent a standing stock of 0.089 Pg carbon, equivalent to 5.2% of the total oceanic biota carbon reservoir 5 . In the vast oligotrophic intertropical open oceans, rhizarian biomass is estimated to be equivalent to that of all other mesozooplankton (plankton in the size range 0.2–20 mm). The photosymbiotic association of many rhizarians with microalgae may be an important factor in explaining their distribution. The previously overlooked importance of these giant protists across the widest ecosystem on the planet 6 changes our understanding of marine planktonic ecosystems.

The Shallow Benthic Zonation is one of the most important achievements of biostratigraphy in the last twenty years. Here we summarize the state of the art in the field of Larger Benthic Foraminifera (LBF) and sketch the main lines of research that are improving the precision and usefulness of this scale. The goal of updating the zonation requires a wealth of data coming not only from biostratigraphic investigations but also from paleoenvironmental analyses, biological knowledge, rigorous taxonomic determination, and understanding of paleobiogeography. The papers collected for this special issue are contributions to this broad research program.

Although macroscopic plants, animals, and fungi are the most familiar eukaryotes, the bulk of eukaryotic diversity is microbial. Elucidating the timing of diversification among the more than 70 lineages is key to understanding the evolution of eukaryotes. Here, we use taxon-rich multigene data combined with diverse fossils and a relaxed molecular clock framework to estimate the timing of the last common ancestor of extant eukaryotes and the divergence of major clades. Overall, these analyses suggest that the last common ancestor lived between 1866 and 1679 Ma, consistent with the earliest microfossils interpreted with confidence as eukaryotic. During this interval, the Earth's surface differed markedly from today; for example, the oceans were incompletely ventilated, with ferruginous and, after about 1800 Ma, sulfidic water masses commonly lying beneath moderately oxygenated surface waters. Our time estimates also indicate that the major clades of eukaryotes diverged before 1000 Ma, with most or all probably diverging before 1200 Ma. Fossils, however, suggest that diversity within major extant clades expanded later, beginning about 800 Ma, when the oceans began their transition to a more modern chemical state. In combination, paleontological and molecular approaches indicate that long stems preceded diversification in the major eukaryotic lineages.

Thraustochytrids are aquatic unicellular protists organisms that represent an important reservoir of a wide range of bioactive compounds, such as essential polyunsaturated fatty acids (PUFAs) such as arachidonic acid (ARA), docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA), which are involved in the regulation of the immune system. In this study, we explore the use of co-cultures of Aurantiochytrium sp. and bacteria as a biotechnological tool capable of stimulating PUFA bioaccumulation. In particular, the co-culture of lactic acid bacteria and the protist Aurantiochytrium sp. T66 induce PUFA bioaccumulation, and the lipid profile was evaluated in cultures at different inoculation times, with two different strains of lactic acid bacteria capable of producing the tryptophan dependent auxins, and one strain of Azospirillum sp., as a reference for auxin production. Our results showed that the Lentilactobacillus kefiri K6.10 strain inoculated at 72 h gives the best PUFA content (30.89 mg g[sup.−1] biomass) measured at 144 h of culture, three times higher than the control (8.87 mg g[sup.−1] biomass). Co-culture can lead to the generation of complex biomasses with higher added value for developing aquafeed supplements.