Characterization of a Deep-Branching Heterolobosean, Pharyngomonas turkanaensis n. sp., Isolated from a Non-Hypersaline Habitat, and Ultrastructural Comparison of Cysts and Amoebae Among Pharyngomonas Strains

Gut protozoa of wild rodents - a meta-analysis

Protozoa are well-known inhabitants of the mammalian gut and so of the gut microbiome. While there has been extensive study of a number of species of gut protozoa in laboratory animals, particularly rodents, the biology of the gut protozoa of wild rodents is much less well-known. Here we have systematically searched the published literature to describe the gut protozoa of wild rodents, in total finding records of 44 genera of protozoa infecting 228 rodent host species. We then undertook meta-analyses that estimated the overall prevalence of gut protozoa in wild rodents to be 24%, with significant variation in prevalence among some host species. We investigated how host traits may affect protozoa prevalence, finding that for some host lifestyles some protozoa differed in their prevalence. This synthesis of existing data on wild rodent gut protozoa provides a better understanding of the biology of these common gut inhabitants and suggests directions for their future study.

Lighting lantern above Psalteriomonadidae: Unveiling novel diversity within the genus Psalteriomonas (Discoba: Heterolobosea)

Psalteriomonadidae are a small family of anaerobic free-living protists belonging to Heterolobosea, Discoba. We cultured 74 new strains of mostly amoeboid Psalteriomonadidae obtained from mainly freshwater habitats and sequenced their 18S rRNA gene. Based on the phylogenetic analysis and genetic distances, we report multiple novel species, four of which we formally describe based on the light-microscopic morphology (Psalteriomonas minuta, P. australis, P. fimbriata, and P. parva). We also examined the ultrastructure of two Psalteriomonas species using transmission electron microscopy. We transfer Sawyeria marylandensis into the genus Psalteriomonas and synonymize Sawyeria with Psalteriomonas. In addition, we studied the flagellate stage of P. marylandensis comb. nov. for the first time, using light and scanning electron microscopy.

Characterisation and Cultivation of New Lineages of Colponemids, a Critical Assemblage for Inferring Alveolate Evolution

There are several alveolate groups outside the well-studied trio - ciliates, dinoflagellates, and apicomplexans - that are crucial for understanding the evolution of this major taxon. One such assemblage is the "colponemids", which are eukaryotrophic biflagellates, usually with a ventral groove associated with the posterior flagellum. Previous phylogenetic studies show colponemids forming up to three distinct deep branches within alveolates (e.g. sister groups to Myzozoa or all other alveolates). We have developed dieukaryotic (predator-prey) cultures of four colponemid isolates. One represents the first stable culture of the halophile Palustrimonas (feeding on Pharyngomonas), while SSU rDNA phylogenies show the other isolates as two distinct new lineages. Neocolponema saponarium gen. et sp. nov. is a swimming alkaliphile with a large groove, which feeds on a kinetoplastid. Loeffela hirca gen. et sp. nov. is halophilic, has a subtle groove, usually moves along surfaces, and feeds on Pharyngomonas and Percolomonas. Prey capture in both new genera is raptorial, involves a specialized structure/region to the right of the proximal posterior flagellum, and presumed extrusomes. The relationships amongst Myzozoa, ciliates, and the (now) five described colponemid clades are unresolved, signaling that colponemid diversity represents both a challenge and important resource for tracing deep alveolate evolution.

The Diversity Patterns of Rare to Abundant Microbial Eukaryotes Across a Broad Range of Salinities in a Solar Saltern

Solar salterns are excellent artificial systems for examining species diversity and succession along salinity gradients. Here, the eukaryotic community in surface water of a Korean solar saltern (30 to 380 practical salinity units) was investigated from April 2019 to October 2020 using Illumina sequencing targeting the V4 and V9 regions of 18S rDNA. A total of 926 operational taxonomic units (OTUs) and 1,999 OTUs were obtained with the V4 and V9 regions, respectively. Notably, most of the OTUs were microbial eukaryotes, and the high-abundance groups (> 5% relative abundance (RA), Alveolata, Stramenopila, Archaeplastida, and Opisthokonta) usually accounted for > 90% of the total cumulative read counts and > 80% of all OTUs. Moreover, the high-abundance Alveolata (larger forms) and Stramenopila (smaller forms) groups displayed a significant inverse relationship, probably due to predator-prey interactions. Most of the low-abundance (0.1-5% RA) and rare (< 0.1% RA) groups remained small portion during the field surveys. Taxonomic novelty (at < 90% sequence identity) was high in the Amoebozoa, Cryptista, Haptista, Rhizaria, and Stramenopila groups (69.8% of all novel OTUs), suggesting the presence of a large number of hidden species in hypersaline environments. Remarkably, the high-abundance groups had little overlap with the other groups, implying the weakness of rare-to-prevalent community dynamics. The low-abundance Discoba group alone temporarily became the high-abundance group, suggesting that it is an opportunistic group. Overall, the composition and diversity of the eukaryotic community in hypersaline environments may be persistently stabilized, despite diverse disturbance events.

Accumulation patterns of intracellular salts in a new halophilic amoeboflagellate, Euplaesiobystra salpumilio sp. nov., (Heterolobosea; Discoba) under hypersaline conditions

Halophilic microbial eukaryotes are present in many eukaryotic lineages and major groups; however, our knowledge of their diversity is still limited. Furthermore, almost nothing is known about the intracellular accumulation of salts in most halophilic eukaryotes. Here, we isolate a novel halophilic microbial eukaryote from hypersaline water of 134 practical salinity units (PSU) in a solar saltern. This species is an amoeboflagellate (capable of the amoeba-flagellate-cyst transformation) in the heterolobosean group and belongs to the genus Euplaesiobystra based on morphological data and 18S rDNA sequences. However, the isolate is distinct from any of the described Euplaesiobystra species. Especially, it is the smallest Euplaesiobystra to date, has a distinct cytostome, and grows optimally at 75–100 PSU. Furthermore, the phylogenetic tree of the 18S rDNA sequences demonstrates that the isolate forms a strongly supported group, sister to Euplaesiobystra hypersalinica. Thus, we propose that the isolate, Euplaesiobystra salpumilio, is a novel species. E. salpumilio displays a significantly increased influx of the intracellular Na⁺ and K⁺ at 50, 100, and 150 PSU, compared to freshwater species. However, the intracellular retention of the Na⁺ and K⁺ at 150 PSU does not significantly differ from 100 PSU, suggesting that E. salpumilio can extrude the Na⁺ and K⁺ from cells under high-salinity conditions. Interestingly, actively growing E. salpumilio at 100 and 150 PSU may require more intracellular accumulation of Na⁺ than the no-growth but-viable state at 50 PSU. It seems that our isolate displays two salt metabolisms depending on the tested salinities. E. salpumilio shows a salt-in strategy for Na⁺ at lower salinity of 100 PSU, while it displays a salt-out strategy for Na⁺ at higher salinity of 150 PSU. Our results suggest that the novel halophilic E. salpumilio fundamentally uses a salt-out strategy at higher salinities, and the accumulation patterns of intracellular salts in this species are different from those in other halophilic microbial eukaryotes.

Morphology and Ecology of Two New Amoebae, Isolated From a Thalassohaline Lake, Dziani Dzaha

Dziani Dzaha is a hypersaline lake (Mayotte island), whose microbial community is dominated by photosynthetic microorganisms. Here, we describe two new free-living heteroloboseans. One belonging to the Pharyngomonas genus and the other, whose 18S rRNA gene sequence shares only 85% homology to its closest relatives Euplaesiobystra hypersalinica, was proposed as a new species of this genus being called Euplaesiobystra dzianiensis. Both strains were salt tolerant to 75‰ and grew between 25 and 37°C. Their distribution patterns varied seasonally and depended also on depth. Noticeably, both free-living amoebae isolates were able to graze on Arthrospira filaments, which are found within the same water layer. In conclusion, we document for the first time the presence and ecology of free-living amoebae in the thalassohaline lake Dziani Dzaha, and describe a new species of the Euplaesiobystra genus.

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, 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‰ to 280‰, 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 rRNA gene divergences (up to 42.4%). Some strains grow best at salinities from 75 to 125‰ and represent halophiles. All but one of these belong to two geographically heterogeneous clusters that form 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 rRNA gene phylogenies, unlike most previous analyses based on two sequences.

A New Halophilic Heterolobosean Flagellate, Aurem hypersalina gen. n. et sp. n., Closely Related to the Pleurostomum-Tulamoeba Clade: Implications for Adaptive Radiation of Halophilic Eukaryotes

Halophilic protozoa are independently scattered across the molecular phylogeny of eukaryotes; most of which are assigned to Heterolobosea. Here, we isolated a biflagellate from a hypersaline water of 342‰ salinity. This isolate shared several morphological features with typical halophilic heterolobosean flagellates. In addition, molecular phylogenetic trees of the 18S rRNA gene sequences clearly indicated flagellate is a heterolobosean species closely related to the halophilic Tulamoebidae. However, the flagellate was not accommodated to any described genus. Cells were ovoid-shaped, and no amoebae were observed. The two unequal flagella beat heterodynamically. An ear-like bulge at the margin of a cytostomal groove was observed. Flagellates could grow at 100-200‰ salinity, suggesting an obligately halophilic species. Currently, it appears that the new halophilic Aurem hypersalina forms a strong clade with Tulamoebidae, and is sister to the Tulamoebidae, indicating that this new clade is composed almost entirely of obligate halophilic taxa. Thus, A. hypersalina and the Tulamoebidae clade currently represent a unique adaptive radiation of halophilic eukaryotes.

Dactylomonas gen. nov., a Novel Lineage of Heterolobosean Flagellates with Unique Ultrastructure, Closely Related to the Amoeba Selenaion koniopes Park, De Jonckheere & Simpson, 2012

We report the discovery of a new genus of heterolobosean flagellates, Dactylomonas gen. nov., with two species, D. venusta sp. nov. and D. crassa sp. nov. Phylogenetic analysis of the SSU rRNA gene showed that Dactylomonas is closely related to the amoeba Selenaion, the deepest-branching lineage of Tetramitia. Dactylomonads possess two flagella, and ultrastructural studies revealed an unexpected organization of the flagellar apparatus, which resembled Pharyngomonada (the second lineage of Heterolobosea) instead of Tetramitia: basal bodies were orthogonal to each other and a putative root R1 was present in the mastigont. On the other hand, Dactylomonas displayed several features uncommon in Heterolobosea: a microtubular corset, a distinctive rostrum supported by the main part of the right microtubular root, a finger-like projection on the proximal part of the recurrent flagellum, and absence of a ventral groove. In addition, Dactylomonas is anaerobic and seems to have lost mitochondrial cristae. Dactylomonas and Selenaion are accommodated in the family Selenaionidae fam. nov. and order Selenionida ord. nov. The taxonomy of Tetramitia is partially revised, and the family Neovahlkampfiidae fam. nov. is established.

Recent Advances in Halophilic Protozoa Research

Most research on microorganisms adapted to hypersaline habitats has focused on Archaea and Bacteria, with microbial eukaryotes receiving much less attention. Over the past 15 yr, our knowledge of phagotrophic microbial eukaryotes, i.e. protozoa, from hypersaline habitats has greatly improved through combinations of microscopy, molecular phylogenetics, environmental sequencing, transcriptomics and growth experiments. High salinity waters from salterns, other landlocked water masses and deep hypersaline anoxic basins contain unique and diverse halophilic protozoan assemblages. These have the potential to exert substantial grazing pressure on prokaryotes and other eukaryotes. They represent many separate evolutionary lineages; species of Heterolobosea, Bicosoecida, and Ciliophora have been most intensively characterized, with several proven to be extreme (or borderline extreme) halophiles. Transcriptomic examinations of the bicosoecid Halocafeteria (and the heteroloboseid Pharyngomonas) indicate that high-salt adaptation is associated with a subtle shift in protein amino acid composition, and involves the differential expression of genes participating in ion homeostasis, signal transduction, stress management, and lipid remodeling. Instances of gene duplication and lateral transfer possibly conferring adaptation have been documented. Indirect evidence suggests that these protozoa use "salt-out" osmoadaptive strategies.

Neovahlkampfia nana n. sp. Reinforcing an Underrepresented Subclade of Tetramitia, Heterolobosea

The study provides robust genetic evidence that a newly isolated naked ameba with morphological and ultrastructural features indicative of Heterolobosea is a new species. Neovahlkampfia nana n. sp. associates with the yet underrepresented subclade of Tetramitia I. Considerable differences found in 18S rRNA gene sequences of individual molecular clones derived from DNA of five clonal cultures, using a low fidelity DNA polymerase, raised the issue of intragenomic sequence variation, a phenomenon that has not been previously studied in Heterolobosea. However, as proved using a higher fidelity DNA polymerase, the sequence variability observed was introduced by PCR mediated by the low fidelity polymerase and fixed by molecular cloning. This points to the potentially dubious validity of some current nominal species of Heterolobosea that differ from one another in just one or two base positions.