Scale evolution, sequence phylogeny, and taxonomy of thaumatomonad Cercozoa: 11 new species and new genera Scutellomonas, Cowlomonas, Thaumatospina and Ovaloplaca

Silica-scaled heterotrophic protists: Rotosphaerida, Thaumatomonadida and Centroplasthelida in Arctic waters of Russia

Maintaining high levels of biological diversity in various ecosystems is necessary for stable functioning of the Earth's biosphere. The article describes diversity and ecology of heterotrophic siliceous protists - rotosphaerids, colourless free-living thaumatomonad flagellates, and centrohelid heliozoans - in Arctic waters located of Asian Russia. Samples were collected in the mouths of the Olenyok, Yana, Indigirka, Kolyma Rivers - and small freshwater ponds near Settlement of Tiksi in Yakutia. Based on electron microscopy, 35 centrohelids (Heliozoa), 11 rotosphaerid species as well as four thaumatomonad flagellate species were found in the region. Seven species were recorded in Russia for the first time: Rabdiaster multicosta, Rabdiaster reticulata, Turriplaca denticulata, Choanocystis cf. cordiformis parvula, Raineriophrys pteromorphos, Pseudoraphidocystis glutinosa and Pseudoraphidiophrys formosa. For 43 species, the study area is the most northern location they were described. Morphological details of scales are discussed for selected species, particularly for widespread species of rotosphaerids - Pinaciophora fluviatilis. The literature on hydrochemical conditions was analyzed to find taxa with high sensitivity towards environmental changes. Such species could be further used for monitoring plankton, recovering evolutionary changes, and reconstructing past environments.

Year-Long Microbial Succession on Microplastics in Wastewater: Chaotic Dynamics Outweigh Preferential Growth

Microplastics are a globally-ubiquitous aquatic pollutant and have been heavily studied over the last decade. Of particular interest are the interactions between microplastics and microorganisms, especially the pursuit to discover a plastic-specific biome, the so-called plastisphere. To follow this up, a year-long microcosm experimental setup was deployed to expose five different microplastic types (and silica beads control) to activated aerobic wastewater in controlled conditions, with microbial communities being measured four times over the course of the year using 16S rDNA (bacterial) and ITS (fungal) amplicon sequencing. The biofilm community shows no evidence of a specific plastisphere, even after a year of incubation. Indeed, the microbial communities (particularly bacterial) show a clear trend of increasing dissimilarity between plastic types as time increases. Despite little evidence for a plastic-specific community, there was a slight grouping observed for polyolefins (PE and PP) in 6–12-month biofilms. Additionally, an OTU assigned to the genus Devosia was identified on many plastics, increasing over time while showing no growth on silicate (natural particle) controls, suggesting this could be either a slow-growing plastic-specific taxon or a symbiont to such. Both substrate-associated findings were only possible to observe in samples incubated for 6–12 months, which highlights the importance of studying long-term microbial community dynamics on plastic surfaces.

Description of Phaeobola aeris gen. nov., sp. nov (Rhizaria, Cercozoa, Euglyphida) Sheds Light on Euglyphida's Dark Matter

The majority of Euglyphida species are characterised by shells with imbricated silica scales. Environmental surveys indicate a large unexplored diversity and recent efforts hinted at a certain diversity of yet undescribed, inconspicuous, scale-lacking Euglyphida. Here we describe Phaeobola aeris gen. nov., sp. nov. that shows a variety of morphological characters typical for the Euglyphida but lacks silica scales-instead, this species bears an agglutinated test. Neither its morphology nor phylogenetic placement allows its assignment to any currently described family. We erected the yet monospecific genus Phaeobola gen. nov., which with yet available data remain Euglyphida incertae sedis.

Fish and crustacean biodiversity in an outer maritime estuary of the Pearl River Delta revealed by environmental DNA

Understanding the faunal community structure in the estuary would be crucial in assessing the health of the ecosystem. The poor visibility in the estuarine area due to the outflow from the Pearl River hinders the conventional visual census in assessing the megafaunal biodiversity. In this study, the fish and crustacean biodiversity of Hong Kong's western waters, i.e. the outer maritime estuary of the PRD, were studied through the metabarcoding of environmental DNA (eDNA). eDNA from the seawater and sediment samples was extracted from five sites in the region. After testing the performance of two genetic markers, amplicons of the cytochrome oxidase I, amplified by polymerase chain reaction, were subjected to Illumina high-throughput sequencing (MiSeq) analysis. A total of 22 fish species from 17 families and 34 crustacean species from 27 families were identified by blasting the sequences against the NCBI GenBank database, demonstrating segregation between samples from different sites. This study provides insight on the detail distribution of fish assembly in PRD, when compared with a previous eDNA study in the inner brackish PRD.

Heterotrophic flagellates and centrohelid heliozoans from marine waters of Curacao, the Netherlands Antilles

Recent progress in understanding the early evolution of eukaryotes was tied to morphological identification of flagellates and heliozoans from natural samples, isolation of their culture and genomic and ultrastructural investigations. These protists are the smallest and least studied microbial eukaryotes but play an important role in the functioning of microbial food webs. Using light and electron microscopy, we have studied the diversity of heterotrophic flagellates and centrohelid heliozoans from marine waters of Curacao (The Netherlands Antilles), and provide micrographs and morphological descriptions of observed species. Among 86 flagellates and 3 centrohelids encountered in this survey, five heterotrophic flagellates and one сentrohelid heliozoan were not identified even to the genus. Some flagellate protists have a unique morphology, and may represent undescribed lineages of eukaryotes of high taxonomic rank. The vast majority (89%) of identified flagellates is characterized by wide geographical distribution and have been reported previously from all hemispheres and various climatic regions. More than half of the species were previously observed not only from marine, but also from freshwater habitats. The parameters of the species accumulation curve indicate that our species list obtained for the Curacao study sites is far from complete, and each new sample should yield new species.

Amoeboid protist systematics: A report on the "Systematics of amoeboid protists" symposium at the VIIIth ECOP/ISOP meeting in Rome, 2019

Amoeboid protists are extremely abundant and diverse in natural systems where they often play outstanding ecological roles. They can be found in almost all major eukaryotic divisions, and genomic approaches are bringing major changes in our perception of their deep evolutionary relationships. At fine taxonomic levels, the generalization of barcoding is revealing a considerable and unsuspected specific diversity that can be appreciated with careful morphometric analyses based on light and electron microscopic observations. We provide examples on the difficulties and advances in amoeboid protists systematics in a selection of groups that were presented at the VIIIth ECOP/ISOP meeting in Rome, 2019. We conclude that, in all studied groups, important taxonomical rearrangements will certainly take place in the next few years, and systematics must be adapted to incorporate these changes. Notably, nomenclature should be flexible enough to integrate many new high level taxa, and a unified policy must be adopted to species description and to the establishment of types.

Morphology, Ultrastructure, and Phylogeny of Two Novel Species of Ventrifissura (V. oblonga n. sp. and V. velata n. sp., Thecofilosea, Cercozoa)

Ventrifissura is a group of poorly studied heterotrophic biflagellates in the phylum Cercozoa. Despite a phylogenetic placement with only weak support and a lack of ultrastructural data, Ventrifissura was assigned to Thecofilosea. In the presented study, we established cultures of two novel species of Ventrifissura (V. oblonga n. sp. and V. velata n. sp.) isolated from coastal marine environments in Japan, and performed light and electron microscopy observations and molecular phylogenetic analysis. Transmission electron microscopy revealed that V. oblonga shares several ultrastructural characteristics with thecofilosean flagellates, including permanently condensed chromosomes, a extracellular theca, and slender extrusomes. Molecular phylogenetic analysis could not resolve the phylogenetic position, but the possibility that Ventrifissura clusters into Ventrifilosa was supported by approximately unbiased tests. Based on both morphological and phylogenetic findings, we concluded that Ventrifissura is a basal lineage of Thecofilosea.

Multigene phylogeny and cell evolution of chromist infrakingdom Rhizaria: contrasting cell organisation of sister phyla Cercozoa and Retaria

Infrakingdom Rhizaria is one of four major subgroups with distinct cell body plans that comprise eukaryotic kingdom Chromista. Unlike other chromists, Rhizaria are mostly heterotrophic flagellates, amoebae or amoeboflagellates, commonly with reticulose (net-like) or filose (thread-like) feeding pseudopodia; uniquely for eukaryotes, cilia have proximal ciliary transition-zone hub-lattices. They comprise predominantly flagellate phylum Cercozoa and reticulopodial phylum Retaria, whose exact phylogenetic relationship has been uncertain. Given even less clear relationships amongst cercozoan classes, we sequenced partial transcriptomes of seven Cercozoa representing five classes and endomyxan retarian Filoreta marina to establish 187-gene multiprotein phylogenies. Ectoreta (retarian infraphyla Foraminifera, Radiozoa) branch within classical Cercozoa as sister to reticulose Endomyxa. This supports recent transfer of subphylum Endomyxa from Cercozoa to Retaria alongside subphylum Ectoreta which embraces classical retarians where capsules or tests subdivide cells into organelle-containing endoplasm and anastomosing pseudopodial net-like ectoplasm. Cercozoa are more homogeneously filose, often with filose pseudopodia and/or posterior ciliary gliding motility: zooflagellate Helkesimastix and amoeboid Guttulinopsis form a strongly supported clade, order Helkesida. Cercomonads are polyphyletic (Cercomonadida sister to glissomonads; Paracercomonadida deeper). Thecofilosea are a clade, whereas Imbricatea may not be; Sarcomonadea may be paraphyletic. Helkesea and Metromonadea are successively deeper outgroups within cercozoan subphylum Monadofilosa; subphylum Reticulofilosa (paraphyletic on site-heterogeneous trees) branches earliest, Granofilosea before Chlorarachnea. Our multiprotein trees confirm that Rhizaria are sisters of infrakingdom Halvaria (Alveolata, Heterokonta) within chromist subkingdom Harosa (= SAR); they further support holophyly of chromist subkingdom Hacrobia, and are consistent with holophyly of Chromista as sister of kingdom Plantae. Site-heterogeneous rDNA trees group Kraken with environmental DNA clade 'eSarcomonad', not Paracercomonadida. Ectoretan fossil dates evidence ultrarapid episodic stem sequence evolution. We discuss early rhizarian cell evolution and multigene tree coevolutionary patterns, gene-paralogue evidence for chromist monophyly, and integrate this with fossil evidence for the age of Rhizaria and eukaryote cells, and revise rhizarian classification.

Diversity of Cercomonad Species in the Phyllosphere and Rhizosphere of Different Plant Species with a Description of Neocercomonas epiphylla (Cercozoa, Rhizaria) a Leaf-Associated Protist

Cercomonads are among the most abundant and diverse groups of heterotrophic flagellates in terrestrial systems and show an affinity to plants. However, we still lack basic knowledge of plant-associated protists. We isolated 75 Cercomonadida strains from the phyllosphere and rhizosphere of plants from three functional groups: grasses (Poa sp.), legumes (Trifolium sp.) and forbs (Plantago sp.), representing 28 OTUs from the genera Cercomonas, Neocercomonas and Paracercomonas. The community composition differed clearly between phyllosphere and rhizosphere, but was not influenced by plant species identity. From these isolates we describe three novel cercomonad species including Neocercomonas epiphylla that was consistently and exclusively isolated from the phyllosphere. For each new species we provide a detailed morphological description as well as an 18S rDNA gene sequence as a distinct marker of species identity. Our data contribute to a better resolution of the systematics of cercomonads and their association with plants, by describing three novel species and adding gene sequences of 10 new cercomonad genotypes and of nine previously described species. In view of the functional importance of cercozoan communities in the phyllosphere and rhizosphere of plants, a more detailed understanding of their composition, function and predator-prey interactions are clearly required.