Heterotrophic Flagellates from Freshwater and Soil Habitats in Subtropical China (Wuhan Area, Hubei Province)

We studied the diversity of heterotrophic flagellates from the sandy sediments of the Yangtze River, sandy and silty sediments of Donghu Lake, soil, moss and litter from the Luojiashan and Moshan hills as well as litter from the floodplain near Donghu Lake in April 2010. Sixty-seven heterotrophic flagellate species were identified by means of phase and interference contrast light microscopy and transmission electron microscopy. The majority of the observed flagellates were bacterivorous. Local species richness of river sediment communities was significantly lower than that of lake sediments and terrestrial habitats. The communities from the terrestrial habitats were more heterogeneous than those from freshwater sediments. Common species for the aquatic habitats were Rhynchomonas nasuta, Paraphysomonas sp., Neobodo designis, N. curvifilis, Bodo saltans and Spumella spp. In the soils only Spumella spp. was found in the majority of samples. Most characteristic taxa for the lake sediments were Helkesimastix faecicola, Petalomonas minuta, P. pusilla, Diphylleia rotans, Amastigomonas caudata. Amoeboflagellates such as Cercomonas angustus, C. granulifera, Paracercomonas crassicauda were specific for the terrestrial habitats. There were no specific taxa in the river sediments. The majority of the heterotrophic flagellates identified in this survey have been noted in China earlier. They are common (and usually predominant) for other regions in both freshwater and soil habitats

Gene expression during bacterivorous growth of a widespread marine heterotrophic flagellate

Phagocytosis is a fundamental process in marine ecosystems by which prey organisms are consumed and their biomass incorporated in food webs or remineralized. However, studies searching for the genes underlying this key ecological process in free-living phagocytizing protists are still scarce, in part due to the lack of appropriate ecological models. Our reanalysis of recent molecular datasets revealed that the cultured heterotrophic flagellate Cafeteria burkhardae is widespread in the global oceans, which prompted us to design a transcriptomics study with this species, grown with the cultured flavobacterium Dokdonia sp. We compared the gene expression between exponential and stationary phases, which were complemented with three starvation by dilution phases that appeared as intermediate states. We found distinct expression profiles in each condition and identified 2056 differentially expressed genes between exponential and stationary samples. Upregulated genes at the exponential phase were related to DNA duplication, transcription and translational machinery, protein remodeling, respiration and phagocytosis, whereas upregulated genes in the stationary phase were involved in signal transduction, cell adhesion, and lipid metabolism. We identified a few highly expressed phagocytosis genes, like peptidases and proton pumps, which could be used to target this ecologically relevant process in marine ecosystems

Divergent genomic trajectories predate the origin of animals and fungi

22 pages, 4 figures, supplementary information https://doi.org/10.1038/s41586-022-05110-4.-- Data availability: The raw sequence data and assembled genomes generated in this study have been deposited in the European Nucleotide Archive (ENA) at EMBL-EBI under accession number PRJEB52884 (https://www.ebi.ac.uk/ena/browser/view/PRJEB52884). The genome assemblies are also available in figshare (https://doi.org/10.6084/m9.figshare.19895962.v1). Protein sequences of the species used in this study were downloaded from the GenBank public databases (https://www.ncbi.nlm.nih.gov/protein/), Uniprot (https://www.uniprot.org/), JGI genome database (https://genome.jgi.doe.gov/portal/) and Ensembl genomes (https://www.ensembl.org). The following specific databases were also used in this study: Pfam A v29 (https://pfam.xfam.org/), EggNOG emapperdb-4.5.1 (http://eggnog5.embl.de) and UniProt reference proteomes release 2016_02 (https://www.uniprot.org/). The supporting data files of this study are available in the following repository: https://doi.org/10.6084/m9.figshare.13140191.v1.-- Code availability: The most relevant custom code developed for this study (the MAPBOS pipeline and the machine learning classifiers) is available at https://doi.org/10.5281/zenodo.6586559Animals and fungi have radically distinct morphologies, yet both evolved within the same eukaryotic supergroup: Opisthokonta1,2. Here we reconstructed the trajectory of genetic changes that accompanied the origin of Metazoa and Fungi since the divergence of Opisthokonta with a dataset that includes four novel genomes from crucial positions in the Opisthokonta phylogeny. We show that animals arose only after the accumulation of genes functionally important for their multicellularity, a tendency that began in the pre-metazoan ancestors and later accelerated in the metazoan root. By contrast, the pre-fungal ancestors experienced net losses of most functional categories, including those gained in the path to Metazoa. On a broad-scale functional level, fungal genomes contain a higher proportion of metabolic genes and diverged less from the last common ancestor of Opisthokonta than did the gene repertoires of Metazoa. Metazoa and Fungi also show differences regarding gene gain mechanisms. Gene fusions are more prevalent in Metazoa, whereas a larger fraction of gene gains were detected as horizontal gene transfers in Fungi and protists, in agreement with the long-standing idea that transfers would be less relevant in Metazoa due to germline isolation3,4,5. Together, our results indicate that animals and fungi evolved under two contrasting trajectories of genetic change that predated the origin of both groups. The gradual establishment of two clearly differentiated genomic contexts thus set the stage for the emergence of Metazoa and FungiE.O.-P. was supported by a predoctoral FPI grant from MINECO (BES-2015-072241) and by ESF Investing in your future. E.O.-P., D.L-E., A.S.A. and I.R.-T. received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP7-2007-2013) (Grant agreement No. 616960) and also from grants (BFU2014-57779-P and PID2020-120609GB-I00) by MCIN/AEI/10.13039/501100011033 and ‘ERDF A way of making Europe’. E.O.-P. and G.J.Sz. received funding from the European Research Council under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No. 714774). T.A.W. was supported by a Royal Society University Research Fellowship (URF\R\201024) and NERC standard grant NE/P00251X/1. This work was supported by the Gordon and Betty Moore Foundation through grant GBMF9741 to T.A.W. and G.J.Sz. J.S.P. and E.B. received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP7-2007-2013) (Grant agreement No. 615274). D.V.T. and cell culturing were supported by the Russian Science Foundation grant no. 18-14-00239, https://rscf.ru/project/18-14-00239/. Culture of P. vietnamica was obtained as the result of field work in Vietnam as part of the project ‘Ecolan 3.2’ of the Russian–Vietnam Tropical Center. P.J.K. is supported by an Investigator Award from the Gordon and Betty Moore Foundation (https://doi.org/10.37807/GBMF9201)With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)Peer reviewe

Extensive molecular tinkering in the evolution of the membrane attachment mode of the Rheb GTPase

Rheb is a conserved and widespread Ras-like GTPase involved in cell growth regulation mediated by the (m)TORC1 kinase complex and implicated in tumourigenesis in humans. Rheb function depends on its association with membranes via prenylated C-terminus, a mechanism shared with many other eukaryotic GTPases. Strikingly, our analysis of a phylogenetically rich sample of Rheb sequences revealed that in multiple lineages this canonical and ancestral membrane attachment mode has been variously altered. The modifications include: (1) accretion to the N-terminus of two different phosphatidylinositol 3-phosphate-binding domains, PX in Cryptista (the fusion being the first proposed synapomorphy of this clade), and FYVE in Euglenozoa and the related undescribed flagellate SRT308; (2) acquisition of lipidic modifications of the N-terminal region, namely myristoylation and/or S-palmitoylation in seven different protist lineages; (3) acquisition of S-palmitoylation in the hypervariable C-terminal region of Rheb in apusomonads, convergently to some other Ras family proteins; (4) replacement of the C-terminal prenylation motif with four transmembrane segments in a novel Rheb paralog in the SAR clade; (5) loss of an evident C-terminal membrane attachment mechanism in Tremellomycetes and some Rheb paralogs of Euglenozoa. Rheb evolution is thus surprisingly dynamic and presents a spectacular example of molecular tinkering

<i>Triangulopteris lacunata</i> gen. et sp. nov. (Centroplasthelida), a New Centrohelid Heliozoan from Soil

A new genus and species of centrohelid heliozoans, Triangulopteris lacunata gen. et sp. nov. (Pterocystidae Cavalier-Smith and Heyden, 2007), from four geographically remote locations (the Crimean Peninsula, the Dnieper Lowland (the East European Plain), Franz Josef Land, and the Kolyma Lowland (North–Eastern Siberia) was examined using light and electron microscopy. The novel centrohelid is characterized by round shape, 4.3–16.3 μm in diameter, covered with two types of scales: 1.06–4.54 μm long triangular spine scales and 1.22–2.05 μm oval plate scales. Studied centrohelid heliozoan possesses a unique spine scale morphology. The base of scales is represented by a horse hoof-shaped basal plate. The inner surface and lateral wings of spine scales have numerous radial ribs with two ‘pockets’ that are located on both sides of the spine shaft. These pockets are formed by the lateral wings and ends of the basal plate. The cyst formation and transition to a spicules-bearing stage were noted. Additionally, phylogenetic tree was constructed based on SSU rRNA sequences including the strain HF-25 from the permafrost of Kolyma Lowland. The resulting phylogeny recovered it within the clade Pterista, while forming a separate sister lineage to H2 clade, which only had included freshwater environmental sequences

First finding of free-living representatives of Prokinetoplastina and their nuclear and mitochondrial genomes

Abstract Kinetoplastids are heterotrophic flagellated protists, including important parasites of humans and animals (trypanosomatids), and ecologically important free-living bacterial consumers (bodonids). Phylogenies have shown that the earliest-branching kinetoplastids are all parasites or obligate endosymbionts, whose highly-derived state makes reconstructing the ancestral state of the group challenging. We have isolated new strains of unusual free-living flagellates that molecular phylogeny shows to be most closely related to endosymbiotic and parasitic Perkinsela and Ichthyobodo species that, together with unidentified environmental sequences, form the clade at the base of kinetoplastids. These strains are therefore the first described free-living prokinetoplastids, and potentially very informative in understanding the evolution and ancestral states of morphological and molecular characteristics described in other kinetoplastids. Overall, we find that these organisms morphologically and ultrastructurally resemble some free-living bodonids and diplonemids, and possess nuclear genomes with few introns, polycistronic mRNA expression, high coding density, and derived traits shared with other kinetoplastids. Their genetic repertoires are more diverse than the best-studied free-living kinetoplastids, which is likely a reflection of their higher metabolic potential. Mitochondrial RNAs of these new species undergo the most extensive U insertion/deletion editing reported so far, and limited deaminative C-to-U and A-to-I editing, but we find no evidence for mitochondrial trans-splicing

Monophyly of diverse Bigyromonadea and their impact on phylogenomic relationships within stramenopiles

Highlights: • Generation of transcriptomes from three new Pirsoniales species for the first time. • Generation of transcriptomes from four new Developea species, enriching the clade. • Phylogenomic recovery of a monophyletic Bigyromonadea: Pirsoniales and Developea. • Bigyormonads’ ability to aggregate and form pseudopod resembles oomycete zoospores. • Report of the first case of eukaryovory in the flagellated stages of Pirsoniales. Stramenopiles are a diverse but relatively well-studied eukaryotic supergroup with considerable genomic information available (Sibbald and Archibald, 2017). Nevertheless, the relationships between major stramenopile subgroups remain unresolved, in part due to a lack of data from small nanoflagellates that make up a lot of the genetic diversity of the group. This is most obvious in Bigyromonadea, which is one of four major stramenopile subgroups but represented by a single transcriptome. To examine the diversity of Bigyromonadea and how the lack of data affects the tree, we generated transcriptomes from seven novel bigyromonada species described in this study: Develocauda condao n. gen. n. sp., Develocanicus komovi n. gen. n. sp., Develocanicus vyazemskyi n. sp., Cubaremonas variflagellatum n. gen. n. sp., Pirsonia chemainus nom. prov., Feodosia pseudopoda nom. prov., and Koktebelia satura nom. prov. Both maximum likelihood and Bayesian phylogenomic trees based on a 247 genematrix recovered a monophyletic Bigyromonadea that includes two diverse subgroups, Developea and Pirsoniales, that were not previously related based on single gene trees. Maximum likelihood analyses show Bigyromonadea related to oomycetes, whereas Bayesian analyses and topology testing were inconclusive. We observed similarities between the novel bigyromonad species and motile zoospores of oomycetes in morphology and the ability to self-aggregate. Rare formation of pseudopods and fused cells were also observed, traits that are also found in members of labyrinthulomycetes, another osmotrophic stramenopiles. Furthermore, we report the first case of eukaryovory in the flagellated stages of Pirsoniales. These analyses reveal new diversity of Bigyromonadea, and altogether suggest their monophyly with oomycetes, collectively known as Pseudofungi, is the most likely topology of the stramenopile tree

Heterotrophic Flagellates from Freshwater and Soil Habitats in Subtropical China (Wuhan Area, Hubei Province)

We studied the diversity of heterotrophic flagellates from the sandy sediments of the Yangtze River, sandy and silty sediments of Donghu Lake, soil, moss and litter from the Luojiashan and Moshan hills as well as litter from the floodplain near Donghu Lake in April 2010. Sixty-seven heterotrophic flagellate species were identified by means of phase and interference contrast light microscopy and transmission electron microscopy. The majority of the observed flagellates were bacterivorous. Local species richness of river sediment communities was significantly lower than that of lake sediments and terrestrial habitats. The communities from the terrestrial habitats were more heterogeneous than those from freshwater sediments. Common species for the aquatic habitats were Rhynchomonas nasuta, Paraphysomonas sp., Neobodo designis, N. curvifilis, Bodo saltans and Spumella spp. In the soils only Spumella spp. was found in the majority of samples. Most characteristic taxa for the lake sediments were Helkesimastix faecicola, Petalomonas minuta, P. pusilla, Diphylleia rotans, Amastigomonas caudata. Amoeboflagellates such as Cercomonas angustus, C. granulifera, Paracercomonas crassicauda were specific for the terrestrial habitats. There were no specific taxa in the river sediments. The majority of the heterotrophic flagellates identified in this survey have been noted in China earlier. They are common (and usually predominant) for other regions in both freshwater and soil habitats

Unaltered microscopic photographs of Rhodelphis cells.

Raw photographs of Rhodelphis limneticus and R. marinus that correspond to photographs in Figure 1, along with Extended Data Figures 1 and 2 are presented