Biology subjects

Eglit, Y.

Publications and source records attributed to Eglit, Y..

9 recordsLinked to original sources

bioRxiv2026

A hydrogen-producing mitochondrion in an anaerobic eukaryotrophic rhizarian

Diverse eukaryotes thrive under low oxygen conditions, in part through highly modified mitochondrion-related organelles (MROs) that use alternate metabolic pathways to support ATP production and cofactor recycling. Anaerobic lifestyles have evolved repeatedly across the eukaryotic tree of life, each providing an independent opportunity to understand how eukaryotes adapt to life in low oxygen conditions. Here, we use single-cell transcriptomics to reconstruct the MRO metabolism of PCE SSF, a benthic eukaryotrophic flagellate and the first cultivated representative of Novel Clade 12 (NC12; Rhizaria), an independently anaerobic rhizarian lineage. PCE SSF possesses an anaerobic hydrogen-producing mitochondrion capable of hydrogenosome-type substrate-level phosphorylation. It also retains a nearly complete but likely branched tricarboxylic acid pathway that lacks citrate synthase and malate dehydrogenase. The function of citrate synthase may instead be fulfilled by the typically cytosolic ATP citrate lyase, previously reported in this context only in the anaerobic cercozoan, Brevimastigomonas motovehiculus. Unlike B. motovehiculus, however, PCE SSF retains only Complex II and the NuoE/NuoF subunits of the electron transport chain and lacks a mitochondrial genome. Together, these features indicate an atypical and reduced mitochondrial metabolism, highlighting the diversity of evolutionary solutions to anaerobic energy metabolism in eukaryotes.

genomics↗

bioRxiv2026

DIVERGENT TRAJECTORIES FOR ANAEROBIC MITOCHONDRIAL EVOLUTION IN BREVIATE PROTISTS

Mitochondrion-related organelles (MROs) have evolved as adaptations to low oxygen conditions multiple times in the eukaryote tree of life. However, the evolutionary steps by which aerobic mitochondrial functions were replaced by anaerobic pathways are still poorly understood. The breviate Pygsuia biforma is particularly interesting because it is the only protist known to have replaced the canonical mitochondrial iron-sulfur cluster (ISC) system with a horizontally acquired SUF-like minimal system (SMS) protein. This functions within an MRO possessing a uniquely configured electron transport chain (ETC). To investigate the evolutionary path by which the P. biforma MRO evolved these features, we conducted a comparative transcriptomic study of eight diverse marine breviate species and predicted their MRO proteomes. We found three distinct patterns of iron-sulfur cluster biosynthesis machinery across the breviates where organisms would encode: the canonical ISC system alone, the ISC system and cytoplasmic SMS system, and a cytoplasmic and MRO-localized SMS system. Phylogenetic analyses suggests that the SMS system was acquired via lateral gene transfer in an ancestor of all breviates and later duplicated, with one copy gaining mitochondrial targeting and replacing the ISC system in a subset of breviates. We observed similarly divergent evolutionary trajectories for quinone-utilizing proteins. Two species have completely lost the ETC while the remaining lineages retain a partial ETC and mitochondrial contact site and cristae organizing system (MICOS), previously thought to be absent in breviates. These patterns reflect divergent biochemical configurations of MROs shaped by gene transfer, loss, and duplication within a single eukaryotic lineage and underscores dynamic remodeling of organellar metabolism in response to marine hypoxic environments.

evolutionary biology↗

bioRxiv2024

Two newly cultivated eukaryotrophic flagellates represent distinct anaerobic lineages

Endomyxans are a poorly sampled and incompletely resolved aggregate of Rhizarian lineages that fall outside Filosa and Retaria. Among them, "Novel Clade 12" (NC12; Bass et al. 2009) is an environmental clade comprised primarily of sequences derived from anoxic sediments, hitherto lacking a morphologically-characterised representative. We have cultivated a marine anaerobic eukaryotroph, SSF, that we identify as the first representative of NC12. SSF is a teardrop-shaped cell with two unequal flagella emerging a third of the way down the cell behind a distinctive row of refractile globules. The posterior end of the cell is filled with food vacuoles. There is a surface thickening discernible in light microscopy. We also describe another distinct anaerobe eukaryotrophic lineage, also cultivated from marine sediment: PG. It consists of large pyriform cells with a substantial trailing "tail" and two unequal flagella, the posterior exceptionally long. In small subunit ribosomal RNA gene phylogenies, it falls outside the characterised clades and forms a distinct novel rhizarian lineage in its own right. Together, SSF and PG represent two additional independent adaptations to anoxic conditions within Rhizaria.

microbiology↗

bioRxiv2024

Characterisation of Skoliomonas gen. nov., a haloalkaliphilic anaerobe related to barthelonids (Metamonada).

Metamonads are a large and exclusively anaerobic clade of protists. Additionally, metamonads are one of the three clades with a proposed excavate ancestral cell morphology, characterised by a conspicuous ventral groove often accompanied by a posterior flagellum with a vane. Here, we characterise four isolates of an anaerobic bacterivorous flagellate from hypersaline and alkaline soda lake environments, which represents a novel clade. Small subunit ribosomal RNA (SSU rRNA) gene phylogenies support recent phylogenomic analyses in placing this clade as the sister group to Barthelona spp., a lineage that is itself sister to or deeply branching within Fornicata (Metamonada). The cells have a distinctive morphology comprised of a hunchbacked cell body with a narrow twisting ventral groove ending in a large opening to a conspicuous cytopharynx curving up the dorsal side of the cell. The right margin of the groove is defined by a thin lip that twists slightly to the left towards the posterior. The posterior of the cell ends in a spike up to half a cell body long. The posterior flagellum bears a wide ventral-facing vane. One isolate forms cysts with a complex wall and a single plug. The narrow ventral groove and elongate cytopharynx are shared with barthelonids. We describe one isolate as Skoliomonas litria, gen. et sp. nov. Further investigation of mitochondrial-related organelles (MRO) in Skoliomonas spp. and detailed ultrastructural studies would be important to understanding the evolution of adaptation to anaerobic conditions in Metamonads--especially fornicates--as well as the evolution of the excavate groove.

evolutionary biology↗

bioRxiv2023

Amoebozoan testate amoebae illuminate the diversity of heterotrophs and the complexity of ecosystems throughout geological time

Heterotrophic protists are vital in Earths ecosystems, influencing carbon and nutrient cycles and occupying key positions in food webs as microbial predators. Fossils and molecular data suggest the emergence of predatory microeukaryotes and the transition to a eukaryote-rich marine environment by 800 million years ago (Ma). Neoproterozoic vase-shaped microfossils (VSMs) linked to Arcellinida testate amoebae represent the oldest evidence of heterotrophic microeukaryotes. This study explores the phylogenetic relationship and divergence times of modern Arcellinida and related taxa using a relaxed molecular clock approach. We estimate the origin of nodes leading to extant members of the Arcellinida Order to have happened during the latest Mesoproterozoic and Neoproterozoic (1054 - 661 Ma), while the divergence of extant infraorders postdates the Silurian. Our results demonstrate that at least one major heterotrophic eukaryote lineage originated during the Neoproterozoic. A putative radiation of eukaryotic groups (e.g. Arcellinida) during the early-Neoproterozoic sustained by favorable ecological and environmental conditions may have contributed to eukaryotic life endurance during the Cryogenian severe ice ages. Moreover, we infer that Arcellinida most likely already inhabited terrestrial habitats during the Neoproterozoic, coexisting with terrestrial Fungi and green algae, before land plant radiation. The most recent extant Arcellinida groups diverged during the Silurian Period, alongside other taxa within Fungi and flowering plants. These findings shed light on heterotrophic microeukaryotes evolutionary history and ecological significance in Earths ecosystems, using testate amoebae as a proxy. Significance StatementArcellinida shelled amoebae are heterotrophic microbial eukaryotes with an extensive Neoproterozoic fossil record represented by the vase-shaped microfossils (VSMs), a diverse group that is abundant and widespread in late Tonian rocks (VSMs). Here we combined phylogenomic sampling and the fossil record to generate time-calibrated trees. Our results illuminate key events in the history of life, including: i) the Tonian origin of extant microbial eukaryote lineages; ii) a speculative proposed radiation of eukaryotes before the Cryogenian, "Tonian revolution"; iii) the establishment of complex terrestrial habitats before the Cryogenian; iv) a post-Silurian divergence of modern Arcellinida sub-clades in terrestrial (including freshwater) habitats. Our results provide valuable insights into the evolution of life throughout geological time and are congruent with recent discoveries regarding the early diversification of eukaryotes, including the Precambrian history of eukaryotic protosteroids.

evolutionary biology↗

bioRxiv2023

Meteora sporadica, a protist with incredible cell architecture, is related to Hemimastigophora.

Kingdom-level branches are being added to the tree of eukaryotes at a rate approaching one per year, with no signs of slowing down1-4. Some are completely new discoveries, while others are morphologically unusual protists that were previously described but lacked molecular data. For example, Hemimastigophora are predatory protists with two rows of flagella that were known since the 19th century, but proved to represent a new deep-branching eukaryote lineage when phylogenomic analyses were conducted2. Meteora sporadica Hausmann et al. 20025 is a protist with a unique morphology and motility; cells glide over substrates along a long axis of anterior and posterior projections, and have a pair of lateral arms that swing back and forth. Originally, Meteora was described by light microscopy only, from a short-term enrichment of deep-sea sediment. A small subunit ribosomal RNA (SSU rRNA) sequence was reported recently, but the phylogenetic placement of Meteora remained unresolved6. Here, we investigated two cultivated Meteora sporadica isolates in detail. Transmission electron microscopy showed that the anterior-posterior projections are supported by microtubules originating from a cluster of subnuclear MTOCs. Likewise, the arms are supported by microtubules, and neither have a flagellar axoneme-like structure. Sequencing the mitochondrial genome showed this to be amongst the most gene-rich known, outside jakobids. Remarkably, phylogenomic analyses of 254 nuclear protein-coding genes robustly support a close relationship with Hemimastigophora. Our study suggests that Meteora and Hemimastigophora together represent a morphologically diverse supergroup, and thus are important for resolving the tree of eukaryote life and early eukaryote evolution.

evolutionary biology↗

bioRxiv2023

Extreme mitochondrial reduction in a novel group of free-living metamonads.

Metamonads are a diverse group of heterotrophic microbial eukaryotes adapted to living in hypoxic environments. All metamonads but one harbour metabolically altered mitochondrion-related organelles (MROs) with reduced functions relative to aerobic mitochondria, however the degree of reduction varies markedly over the metamonad tree. To further investigate metamonad MRO diversity, we generated high quality draft genomes, transcriptomes, and predicted proteomes for five recently discovered free-living metamonads. Phylogenomic analyses placed these organisms in a group we informally named the BaSk (Barthelonids+Skoliomonads) clade, which emerges as a deeply branching sister group to the Fornicata, a metamonad phylum that includes parasitic and free-living flagellates. Extensive bioinformatic analyses of the manually curated gene models showed that these organisms are predicted to have extremely reduced MRO proteomes in comparison to other free-living metamonads. Loss of the mitochondrial iron-sulfur cluster (ISC) assembly system in some organisms in this group appears to be linked to the acquisition in their common ancestral lineage of a SUF-like minimal system (SMS) Fe/S cluster pathway through lateral gene transfer (LGT). One of the isolates, Skoliomonas litria, appears to have undergone further mitochondrial reduction having lost all other known MRO pathways. No proteins were confidently assigned to the predicted MRO proteome of this organism suggesting that the organelle has been lost. The extreme mitochondrial reduction observed within this free-living anaerobic protistan clade is unprecedented and demonstrates that mitochondrial functions, under some conditions, may be completely lost even in free-living organisms.

genomics↗

bioRxiv2019

Barthelonids represent a deep-branching Metamonad clade with mitochondrion-related organelles generating no ATP.

We here report the phylogenetic position of barthelonids, small anaerobic flagellates previously examined using light microscopy alone. Barthelona spp. were isolated from geographically distinct regions and we established five laboratory strains. Transcriptomic data generated from one Barthelona strain (PAP020) was used for large-scale, multi-gene phylogenetic (phylogenomic) analyses. Our analyses robustly placed strain PAP020 at the base of the Fornicata clade, indicating that barthelonids represent a deep-branching Metamonad clade. Considering the anaerobic/microaerophilic nature of barthelonids and preliminary electron microscopy observations on strain PAP020, we suspected that barthelonids possess functionally and structurally reduced mitochondria (i.e. mitochondrion-related organelles or MROs). The metabolic pathways localized in the MRO of strain PAP020 were predicted based on its transcriptomic data and compared with those in the MROs of fornicates. Strain PAP020 is most likely incapable of generating ATP in the MRO, as no mitochondrial/MRO enzymes involved in substrate-level phosphorylation were detected. Instead, we detected the putative cytosolic ATP-generating enzyme (acetyl-CoA synthetase), suggesting that strain PAP020 depends on ATP generated in the cytosol. We propose two separate losses of substrate-level phosphorylation from the MRO in the clade containing barthelonids and (other) fornicates.

evolutionary biology↗

bioRxiv2019

Ecological and evolutionary patterns in the enigmatic protist genus Percolomonas (Heterolobosea; Discoba) from diverse habitats

The heterotrophic flagellate Percolomonas cosmopolitus (Heterolobosea) is often observed in saline habitats worldwide that range from coastal waters to saturated brines. However, only two cultures assigned to this morphospecies have been examined using molecular methods, and their 18S rRNA gene sequences are extremely different. Further the salinity tolerances of individual strains are unknown. Thus, our knowledge on the autecology and diversity in this morphospecies is deficient. Here, we report 18S rRNA gene data on seven strains similar to P. cosmopolitus from seven geographically remote locations (New Zealand, Kenya, Korea, Poland, Russia, Spain, and the USA) with sample salinities ranging from 4{per thousand} to 280{per thousand}, and compare morphology and salinity tolerance of the nine available strains. Percolomonas cosmopolitus-like strains show few-to-no consistent morphological differences, and form six clades separated by often extremely large 18S rDNA divergences (up to 42.4%). Some strains grew best at salinities from 75 to 125{per thousand} and represent halophiles. All but one of these belonged to two geographically heterogeneous clusters that formed a robust monophyletic group in phylogenetic trees; this likely represents an ecologically specialized subclade of halophiles. Our results suggest that P. cosmopolitus is a cluster of several cryptic species (at least), which are unlikely to be distinguished by geography. Interestingly, the 9 Percolomonas strains formed a clade in 18S rDNA phylogenies, unlike most previous analyses based on two sequences.

microbiology↗