Biology subjects

Lopez-Garcia, P.

Publications and source records attributed to Lopez-Garcia, P..

At least 19 recordsLinked to original sources

bioRxiv2026

Re-evaluating the eukaryotic Tree of Life with independent phylogenomic data

Understanding the phylogenetic relationships among eukaryotic lineages is essential for tracing the evolution of key phenotypic traits and inferring the nature of the Last Eukaryotic Common Ancestor. While phylogenomic analyses have clustered eukaryotic taxa into several well-supported major supergroups, the relationships among them remain largely uncertain. Phylogenetic signal erosion over deep time and limited available taxon sampling are among the possible causes. However, most previous studies rely on variations of the same core protein dataset, hence containing the same potential systematic biases. Here, we reconstructed the eukaryotic Tree of Life using a largely independent, marker-rich dataset derived from highly conserved Benchmarking Universal Single-Copy Orthologs. Unlike previous collections, our 277-marker supermatrix minimizes ribosomal protein representation and shares less than 25% overlap with previous datasets. State-of-the-art analyses of this dataset confirm most eukaryotic supergroups previously observed, but suggest different positions for some lineages. Notably, Telonemia clusters with Haptophyta rather than SAR (Stramenopiles-Alveolata-Rhizaria), and Ancyromonadida and Malawimonadida form a monophyletic group at the base of the Opimoda. Our results highlight the importance of analyzing independent phylogenomic datasets and support the hypothesis that extant eukaryotic diversity encompasses a small number of high-rank, supergroup lineages.

evolutionary biology↗

bioRxiv2026

Redox distribution of Asgard archaea and co-occurring taxa in microbial mats from an early Proterozoic ecosystem analog

Increasing evidence supports that eukaryotes originated from the symbiosis of an Asgard archaeon, the alphaproteobacterial ancestor of mitochondria, and possibly additional bacterial contributions. Eukaryogenesis likely occurred in redox-transition environments such as microbial mats or shallow sediments [~]2 billion years ago, when atmospheric oxygen was far lower than today, and oceans were euxinic. We investigated Asgardarchaeota-enriched microbial mats from the low-oxygen, sulfidic Catherine volcano lake (Afar region, Ethiopia), mimicking early Proterozoic conditions. 16S rRNA gene metabarcoding, metagenomics, and metagenome-assembled genome (MAG) analyses across redox-stratified layers of in situ and mesocosm-maintained mats revealed that Asgardarchaeota thrived in the sulfate-reduction zone, mainly co-occurring with Desulfurobacterota and Myxococcota, among others. Lokiarchaeia and Thorarchaeia were more abundant in deeper, anoxic layers. Within Heimdallarchaeia, Heimdallarchaeales were enriched in upper layers, correlating with oxygen-tolerant hydrogenase and sulfate-reduction genes, whereas Hodarchaeales were more relatively abundant in anoxic layers, correlating with methanogenesis. Although reactive-oxygen-species defense mechanisms were widespread in Asgardarchaeota MAGs, they lacked genes for aerobic respiration. These results support the hypothesis that Asgard archaea engaged primarily in syntrophic interactions with sulfate-reducers under conditions prevailing on the early Earth at the onset of eukaryogenesis.

microbiology↗

bioRxiv2025

Intracellular amorphous calcium carbonate biomineralization in methanotrophic gammaproteobacteria was acquired by horizontal gene transfer from cyanobacteria

Some bacteria genetically control the biomineralization of intracellular amorphous calcium carbonates (iACC) with potential implications for microbial physiology, evolution, bioremediation and biogeochemical cycling. Until now, this capacity has been documented in Cyanobacteria, the giant gammaproteobacterium Achromatium and a few magnetotactic Pseudomonadota and Nitrospirota. Here, we report the discovery of iACC biomineralization in members of the Methylococcaceae, a family of aerobic methanotrophic Gammaproteobacteria. A homolog of the ccyA gene, previously considered a diagnostic marker for iACC formation in Cyanobacteria, was identified in several Methylococcaceae genomes, based on a search of the conserved C-terminal (GlyZip)3 domain of the encoded calcyanin protein, with a sequence coverage higher than 60% and an E-value lower than 1e-20. Moreover, two cultivated strains, Methylococcus geothermalis and Methylococcus mesophilus, whose genomes contained the ccyA gene, were consistently shown to form iACC granules. The ccyA genes of Methylococcaceae and Microcystis share higher sequence similarity (47%) than with other Cyanobacteria (around 30%) within their common (GlyZip)3 domain, suggesting horizontal gene transfer (HGT) from an ancestral Microcystis-like cyanobacterium to Methylococcaceae. This finding extends the known taxonomic distribution of ccyA and suggests that the capability to biomineralize iACC was acquired by HGT, possibly in environments such as those close to the oxyclines of lakes, where Cyanobacteria and Methylococcaceae commonly co-exist. The discovery of iACC in methane-oxidizing Methylococcaceae highlights a previously unrecognized coupling between calcium carbonate biomineralization and methane cycling in aquatic environments, suggesting that iACC formation may play an overlooked role in microbial carbon storage and local geochemical regulation.

microbiology↗

bioRxiv2025

TDP-43 loss of function drives aberrant splicing in Parkinson's disease

Introductory paragraphWhile mRNA splicing dysregulation is a well-established contributor to neurodegeneration in disorders such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), its role in Parkinsons disease (PD) remains underexplored. Here, we analyse transcriptomic data from >500 post-mortem human brain samples from individuals with and without PD to show that splicing alterations are frequently detected. Differentially spliced genes were significantly more enriched for those causally-implicated in both PD and ALS than genes that were differentially expressed. Furthermore, we observed a strong association between these splicing alterations and dysfunction of the RNA-binding protein (RBP), TAR DNA-binding protein 43 (TDP-43). Strikingly, genes and exon junctions affected by TDP-43 knockdown overlapped significantly with those dysregulated across brain regions in PD. In brains from individuals with the LRRK2 c.6055G>A (p.G2019S) mutation, the most common genetic cause of PD, we also observed significant enrichment of TDP-43-dependent splicing changes. This finding was corroborated in human pluripotent stem cell-derived midbrain dopaminergic neurons and a LRRK2 p.G2019S knock-in mouse model, where reduced nuclear TDP-43 levels evidenced the well-recognised loss-of-function mechanism contributing to splicing dysregulation. By leveraging our RNA-based analyses we predicted TDP-43-dependent novel peptide sequences and validated their existence within human LRRK2 mutation mDNs, while also demonstrating an overall loss of protein and mRNA expression in mis-spliced genes. Collectively, our findings reveal that PD is marked by extensive splicing dysregulation dependent on TDP-43, making TDP-43 a promising new therapeutic target in PD.

neuroscience↗

bioRxiv2025

Microglial activation and alpha-synuclein oligomers drive the early inflammatory phase of Parkinson's disease

Parkinsons disease (PD) is characterised by insoluble -synuclein (Syn) aggregates in Lewy bodies (LBs) within the substantia nigra, with cortical pathology appearing as the disease progresses. Late-stage LB deposition, cellular stress, and neuronal loss obscure disease-driving events, we therefore performed multi-regional transcriptomic and aggregate profiling in early-midstage PD brains (Braak 3-4), where cortical regions are pathologically unaffected. We report neuroimmune activation as an early PD feature, characterised by the expansion of a high-SNCA-expressing microglial state. This robust immune signature occurs prior to LB formation, but is associated with oligomeric Syn within cortical microglia. In hiPSC-derived microglia, both endogenous Syn oligomerisation, and exogenous oligomer uptake, trigger transcriptional reprogramming, characterised by interferon-driven inflammation, antigen presentation, and mitochondrial suppression, closely mirroring the early PD brain. These findings describe mechanisms by which Syn oligomerisation potently initiates early neuroinflammation, highlighting a critical interplay between proteinopathy and immune activation at the earliest stages of disease.

neuroscience↗

bioRxiv2025

Molecular phylogeny of the SELMA translocation machinery recounts the evolution of complex photosynthetic eukaryotes.

Photosynthetic eukaryotes and their relatives are the result of an intricate evolutionary history involving a series of plastid acquisitions through endosymbiosis, multiple reversions to heterotrophy, and sometimes total plastid losses. Among these events, one of the most debated is the emergence and diversification of the CASH lineages (Cryptophyta, Alveolata, Stramenopiles and Haptophyta). Although they all include species bearing a complex plastid that derived from the endosymbiosis of a red alga, their phylogenetic relationships remain controversial, and the timing and number of plastid acquisitions are still undetermined. The inner metabolism of all plastids is mostly supported by nuclear-encoded proteins, and consequently, mechanisms allowing the relocation of those proteins have evolved or were recycled at each endosymbiotic event. Thus, the study of the composition and origins of those translocation machineries provides important clues for understanding how photosynthetic lineages have emerged and might be related. In CASH species, the SELMA complex, composed of about 20 proteins, is dedicated to the transport of pre-proteins across the periplastidial membrane, the second outermost membrane of secondary red plastids. In this work, we present the comprehensive genomic survey and phylogenetic analysis of the proteins composing the SELMA complex. We confirm the presence, homology and monophyletic origin of SELMA in the four CASH lineages and use these observations to infer a scenario for the serial transmission of secondary red plastids that differs from previous hypotheses and alters how the evolution of photosynthetic eukaryotes is envisioned.

evolutionary biology↗

bioRxiv2025

Nested parasitism in hypersaline environments: viruses and virus satellites of haloarchaea and their nanosized cellular symbionts

It is increasingly recognized that hyperparasitism, whereby a parasite exploits a host which itself is a parasite, is a common phenomenon across ecosystems and domains of life. Here, to explore hyperparasitism in Archaea, we focused on ultra-small archaea of the phylum Nanohaloarchaeota, a distinct lineage within the DPANN superphylum, which establish obligate symbiotic interactions with extreme halophiles of the class Halobacteria. We assembled five metagenomes originating from geothermally influenced salt lakes in the Danakil Depression, Ethiopia, and reconstructed the viromes associated with both haloarchaea and nanohaloarchaea. Both archaeal lineages were associated with viruses from four distinct groups, including head-tailed viruses (class Caudoviricetes), tailless icosahedral viruses, pleomorphic viruses and spindle-shaped viruses, which represent 12 previously undescribed families. The haloarchaeal viruses (HVs) and nanohaloarchaeal viruses (NHVs) are only distantly related, suggesting that viruses from the four groups co-evolved with their respective hosts for an extended period, likely since the divergence of the two archaeal lineages from their last common ancestor. Consistently, our results show that HVs and NHVs are well-adapted to replicate in their respective hosts and to thrive in hypersaline environments. No evidence of host switching between haloarchaea and nanohaloarchaea was obtained, but multiple horizontal transfers of genes implicated in virion structure and morphogenesis between HVs and NHVs were detected. We also identified several NHVs-encoded auxiliary metabolic genes implicated in nucleotide and amino acid metabolisms, which could enhance the metabolic capabilities of the nanohaloarchaeal hosts that have highly reduced genomes. Finally, in addition to HVs and NHVs, we describe plasmid-derived virus satellites that appear to have originated convergently to parasitize spindle-shaped viruses of both haloarchaea and nanohaloarchaea, uncovering an additional layer of parasitism. Collectively, our findings fill the knowledge gap on the diversity of HVs and NHVs, highlight the complexity of virus-host and virus-virus interactions in hypersaline environments, and open doors for further mining of the virosphere of the globally distributed DPANN archaea.

microbiology↗

bioRxiv2025

An anti-amyloidogenic approach to specifically block memory consolidation in mice for therapeutic intervention

Post-traumatic stress disorder (PTSD) is a mental health disorder triggered by the exposure to a traumatic event, which manifests with anguish, intrusive memories, and negative mood changes. So far, there is no efficient treatment for PTSD other than symptomatic palliative care. However, the cytoplasmic polyadenylation element binding protein-3 (CPEB3) has been recently associated to a potential risk gene for PTSD. Considering that CPEB3 protein is a functional amyloid whose importance for long-term memory consolidation in mammals is well established, we propose the active (amyloid) state of CPEB3 as a promising therapeutic target to block the consolidation of traumatic memories through by the anti-amyloidogenic polyglutamine binding peptide 1 (QBP1). Here we report a preclinical development in mice of this pharmacological treatment for PTSD based on the action of the QBP1 peptide. We first characterized the human CPEB3 (hCPEB3) protein in vitro, showing how its amyloid aggregation is inhibited by the active core of QBP1 (QBP1-M8) without affecting other self-assembly processes such as phase separation. Then, we generated and characterized a novel transgenic mouse that constitutively expresses QBP1 in tandem (TgQBP1). TgQBP1 mice have shown that the consolidation of simple learning is impaired after 24 h for both hippocampal-dependent and aversive memories and that it is limited to new learned memories and has no effect on short-term memory. Furthermore, fear induced anxiety was reduced in comparison to WT mice, suggesting that PTSD-like symptoms are also being ameliorated. Intriguingly, we found that aversive memories seem to be more strongly affected in younger mice. Finally, the analysis of CPEB3 amyloid presence in hippocampal extracted samples showed a correlative decrease in murine CPEB3 oligomerization in the TgQBP1 mice. Taking together, these results strongly suggest that the amyloidogenic blockage of CPEB3 by QBP1 peptide is a potential drug for the prevention and treatment of PTSD.

neuroscience↗

bioRxiv2024

Phylogenomics of neglected flagellated protists supports a revised eukaryotic tree of life

Eukaryotes evolved from prokaryotic predecessors in the early Proterozoic1,2 and radiated from their already complex last common ancestor3, diversifying into several supergroups with unresolved deep evolutionary connections4. They evolved extremely diverse lifestyles, playing crucial roles in the carbon cycle5,6. Heterotrophic flagellates are arguably the most diverse eukaryotes4,7-9 and often occupy basal positions in phylogenetic trees. However, many of them remain undersampled4,10 and/or incertae sedis4,11-18. Progressive improvement of phylogenomic methods and a wider protist sampling have reshaped and consolidated major clades in the eukaryotic tree13-19. This is illustrated by the Opimoda14, one of the largest eukaryotic supergroups (Amoebozoa, Ancyromonadida, Apusomonadida, Breviatea, CRuMs, Malawimonadida, and Opisthokonta -including animals and fungi-)4,14,19-22. However, their deepest evolutionary relationships still remain uncertain. Here, we sequenced transcriptomes of poorly studied flagellates23,24 (fourteen apusomonads25,26, seven ancyromonads27 and one cultured Mediterranean strain of Meteora sporadica17) and conducted comprehensive phylogenomics analyses with an expanded taxon sampling of early-branching protists. Our findings support the monophyly of Opimoda, with CRuMs being sister to the Amorphea (amoebozoans, breviates, apusomonads, and opisthokonts), and ancyromonads and malawimonads forming a moderately supported clade. By mapping key complex phenotypic traits onto this phylogenetic framework, we infer an opimodan biflagellate ancestor with an excavate-like feeding groove, which ancyromonads subsequently lost. While breviates and apusomonads retained the ancestral biflagellate state, some early-diverging Amorphea lost one or both flagella, facilitating the evolution of amoeboid morphologies, novel feeding modes, and palintomic cell division resulting in multinucleated cells. These innovations likely facilitated the subsequent evolution of fungal and metazoan multicellularity.

evolutionary biology↗

bioRxiv2024

Extremely acidic proteomes and metabolic flexibility in bacteria and highly diversified archaea thriving in geothermal chaotropic brines

Few described archaeal, and fewer bacterial, lineages thrive at salt-saturating conditions, such as solar saltern crystallizers (salinity above 30%-w/v). They accumulate molar K+ cytoplasmic concentrations to maintain osmotic balance ( salt-in strategy), and have proteins adaptively enriched in negatively charged, acidic amino acids. Here, we analyzed metagenomes and metagenome-assembled genomes (MAGs) from geothermally influenced hypersaline ecosystems with increasing chaotropicity in the Danakil Depression. Normalized abundances of universal single-copy genes confirmed that haloarchaea and Nanohaloarchaeota encompass 99% of microbial communities in the near life-limiting conditions of the Western-Canyon Lakes (WCLs). Danakil metagenome- and MAG-inferred proteomes, compared to those of freshwater, seawater and solar saltern ponds up to saturation (6-14-32% salinity), showed that WCL archaea encode the most acidic proteomes ever observed (median protein isoelectric points [≤]4.4). We identified previously undescribed Halobacteria families as well as an Aenigmatarchaeota family and a bacterial phylum independently adapted to extreme halophily. Despite phylum-level diversity decreasing with increasing salinity-chaotropicity, and unlike in solar salterns, adapted archaea exceedingly diversified in Danakil ecosystems, challenging the notion of decreasing diversity under extreme conditions. Metabolic flexibility to utilize multiple energy and carbon resources generated by local hydrothermalism along feast-and-famine strategies seemingly shape microbial diversity in these ecosystems near life limits.

microbiology↗

bioRxiv2024

Culture- and genome-based characterization of a tripartite interaction between patescibacterial epibionts, methylotrophic proteobacteria, and a jumbo phage in freshwater ecosystems

Patescibacteria form a very diverse and widely distributed phylum of small bacteria inferred to have an episymbiotic lifestyle. However, the prevalence of this lifestyle within the phylum and their host specificity remain poorly known due to the scarcity of cultured representatives. Here, we describe a complex system consisting of a patescibacterium, its gammaproteobacterial hosts, and their respective phages based on enrichment cultures and metagenomic data from two shallow, geographically close, freshwater ecosystems. The patescibacterium, Strigamonas methylophilicida sp. nov., defines a new genus within the family Absconditicoccaceae. It grows as epibiont on cells of methanotrophic species of the gammaproteobacterial family Methylophilaceae. Strigamonas cells grow tightly attached to the host, sometimes forming stacks that connect two host cells. Despite a surprisingly large genome (1.9 Mb) compared to many other Patescibacteria, S. methylophilicida lacks many essential biosynthetic pathways, including the complete biosynthesis of phospholipids, amino acids, and nucleic acids, implying a dependence on the host to obtain these molecules. We also identified and assembled the complete genomes of one patescibacterial phage that might represent a new virus family within the class Caudoviricetes, and two Methylophilaceae phages predicted to have head-tailed and filamentous virions, respectively. The patesciphage uses a modified genetic code similar to that of its host and encodes four tRNA genes, including the suppressor tRNA gene for the UGA stop codon, which is reassigned to glycine in many Patescibacteria. Our results confirm a prevalent episymbiotic lifestyle in Absconditicoccaceae and further suggest a clade-specific adaptation of this patescibacterial family for gammaproteobacterial hosts. IMPORTANCEPatescibacteria are ultra-small bacteria with reduced genomes that rely on symbiotic interactions with other prokaryotes, yet their host specificity and associated viral parasites remain poorly characterized due to limited cultured representatives. Here, we describe Strigamonas methylophilicida, a new patescibacterial species of the family Absconditicoccaceae that grows as an epibiont on various methylotrophic Gammaproteobacteria. This expands the host range for this family beyond previously documented photosynthetic partners. Using enrichment cultures and metagenomics, we retrieved complete genomes of novel phages infecting S. methylophilicida and its hosts, including one phage that uses a modified genetic code matching that of the patescibacterium. These findings reveal a previously unrecognized patescibacteria- methylotroph-phage tripartite interaction in freshwater environments, highlight the adaptations of patescibacterial phages, and shed light on the complex ecology and evolution of host-parasite-phage dynamics in understudied bacterial lineages.

microbiology↗

bioRxiv2024

Alpha-synuclein aggregates trigger anti-viral immune pathways and RNA editing in human astrocytes

RNA editing is a post transcriptional mechanism that targets changes in RNA transcripts to modulate innate immune responses. We report the role of astrocyte specific, ADAR1 mediated RNA editing in neuroinflammation in Parkinsons disease. We generated hiPSC-derived astrocytes, neurons and co-cultures and exposed them to small soluble alpha-synuclein aggregates. Oligomeric alpha-synuclein triggered an inflammatory glial state associated with TLR activation, viral responses, and cytokine secretion. This reactive state resulted in loss of neurosupportive functions, and the induction of neuronal toxicity. Notably, interferon response pathways were activated leading to upregulation, and isoform switching of the RNA deaminase enzyme, ADAR1. ADAR1 mediates A-to-I RNA editing, and increases in RNA editing were observed in inflammatory pathways in cells, as well as in post-mortem human PD brain. Aberrant, or dysregulated, ADAR1 responses and RNA editing may lead to sustained inflammatory reactive states in astrocytes triggered by alpha-synuclein aggregation, and this may drive the neuroinflammatory cascade in Parkinsons.

neuroscience↗

bioRxiv2023

Exploring the prokaryote-eukaryote interplay in microbial mats from an Andean athalassohaline wetland

Microbial community assembly results from the interaction between biotic and abiotic factors. However, environmental selection is thought to predominantly shape communities in extreme ecosystems. Salar de Huasco, situated in the high altitude Andean Altiplano, represents a poly-extreme ecosystem displaying spatial gradients of physicochemical conditions. To disentangle the influence of abiotic and biotic factors, we studied prokaryotic and eukaryotic communities from microbial mats and underlying sediments across contrasting areas of this athalassohaline ecosystem. The prokaryotic communities were primarily composed of bacteria, notably including a significant proportion of photosynthetic organisms like Cyanobacteria and anoxygenic photosynthetic members of Alpha- and Gammaproteobacteria and Chloroflexi. Additionally, Bacteroidetes, Verrucomicrobia, and Deltaproteobacteria were abundantly represented. Among eukaryotes, photosynthetic organisms (Ochrophyta, Archaeplastida) were predominant, alongside relatively abundant ciliates, cercozoans, and flagellated fungi. Salinity emerged as a key driver for the assembly of prokaryotic communities. Collectively, abiotic factors influenced both prokaryotic and eukaryotic communities, particularly those of algae. However, prokaryotic communities strongly correlated with photosynthetic eukaryotes, suggesting a pivotal role of biotic interactions in shaping these communities. Co-occurrence networks suggested potential interactions between different organisms, such as diatoms with specific photosynthetic and heterotrophic bacteria or with protist predators, indicating influences beyond environmental selection. While some associations may be explained by environmental preferences, the robust biotic correlations, alongside insights from other ecosystems and experimental studies, suggest that symbiotic and trophic interactions significantly shape microbial mat and sediment microbial communities in this athalassohaline ecosystem.

microbiology↗

bioRxiv2023

Several independent adaptations of archaea to hypersaline environments

Several archaeal lineages thrive in high, saturating salt concentrations. These extremely halophilic archaea, including Halobacteria, Nanohaloarchaeota, Methanonatronarchaeia, and Haloplasmatales, must maintain osmotic equilibrium with their environment. For this, they use a salt-in strategy, which involves pumping molar concentrations of potassium into the cells, which, in turn, has led to extensive proteome-wide modifications to prevent protein aggregation. However, the evolutionary history underlying these adaptations remains poorly understood. In particular, the number of times that these dramatic proteome-sweeping changes occurred is unclear due to the conflicting phylogenetic positions found for several of these lineages. Here, we present a resolved phylogeny of extremely halophilic archaea obtained using improved taxon sampling and state-of-the-art phylogenetic approaches designed to cope with the strong compositional biases of their proteomes. We describe two new uncultured lineages, Afararchaeaceae and Asboarchaeaceae, which break the long branches at the base of Haloarchaea and Nanohaloarchaeota, respectively. Our extensive phylogenomic analyses show that at least four independent adaptations to extreme halophily occurred during archaeal evolution. Finally, gene-tree/species-tree reconciliation suggests that gene duplication and horizontal gene transfer played an important role in this process, for example, by spreading key genes (such as those encoding potassium transporters) across the various extremely halophilic lineages.

evolutionary biology↗

bioRxiv2023

Molecular and morphological characterisation of four new ancyromonad genera and proposal for an updated taxonomy of the Ancyromonadida

Ancyromonads are small biflagellated protists with a bean-shaped morphology. They are cosmopolitan in marine, freshwater and soil environments, where they attach to surfaces while feeding on bacteria. These poorly known grazers stand out by their uncertain phylogenetic position in the tree of eukaryotes, forming a deep-branching orphan lineage that is considered key to better understanding the early evolution of eukaryotes. Despite their ecological and evolutionary interest, only limited knowledge exists about their true diversity. Here, we aimed to better characterise ancyromonads by integrating environmental surveys with behavioural observation and description of cell morphology, for which sample isolation and culturing is indispensable. We studied 18 ancyromonad strains, including 14 new isolates and 7 new species. Most of them belong to three new and genetically divergent genera: Caraotamonas, Nyramonas, and Olneymonas (encompassing 4 species). The remaining three new species belong to the already known genera Fabomonas and Ancyromonas. We also raised Striomonas, formerly a subgenus of Nutomonas, to full genus status, based on morphological and phylogenetic grounds. For all these new species, we studied their morphology under light and electron microscopy and carried out molecular phylogenetic analyses, including as well 18S rRNA gene sequences from several environmental surveys. Based on these analyses, we have updated the taxonomy of Ancyromonadida.

microbiology↗

bioRxiv2023

High quality genome and transcriptome data for two new species of Mantamonas, a deep-branching eukaryote clade

Mantamonads were long considered to represent an "orphan" lineage in the tree of eukaryotes, likely branching near the most frequently assumed position for the root of eukaryotes. Recent phylogenomic analyses have placed them as part of the "CRuMs" supergroup, along with collodictyonids and rigifilids. This supergroup appears to branch at the base of Amorphea, making it of special importance for understanding the deep evolutionary history of eukaryotes. However, the lack of representative species and complete genomic data associated with them has hampered the investigation of their biology and evolution. Here, we isolated and described two new species of mantamonads, Mantamonas vickermani sp. nov. and Mantamonas sphyraenae sp. nov., for each of which we generated transcriptomic sequence data, as well as a high-quality genome for the latter. The estimated size of the M. sphyraenae genome is 25 Mb; our de novo assembly appears to be highly contiguous and complete with 9,416 predicted protein-coding genes. This near-chromosome-scale genome assembly is the first described for the CRuMs supergroup.

genomics↗

bioRxiv2022

Expanding the molecular and morphological diversity of Apusomonadida, a deep-branching group of gliding bacterivorous protists

Apusomonads are cosmopolitan bacterivorous biflagellate protists usually gliding on freshwater and marine sediment or wet soils. These nanoflagellates form a sister lineage to opisthokonts and may have retained ancestral features helpful to understanding the early evolution of this large supergroup. Although molecular environmental analyses indicate that apusomonads are genetically diverse, few species have been described. Here, we morphologically characterize eleven new apusomonad strains. Based on molecular phylogenetic analyses of the rRNA gene operon, we describe four new strains of the known species Multimonas media, Podomonas capensis, Apusomonas proboscidea and Apusomonas australiensis, and rename Thecamonas oxoniensis as Mylnikovia oxoniensis n. gen., n. comb. Additionally, we describe four new genera and six new species: Catacumbia lutetiensis n. gen. n. sp., Cavaliersmithia chaoae n. gen. n. sp., Singekia montserratensis n. gen. n. sp., Singekia franciliensis n. gen. n. sp., Karpovia croatica n. gen. n. sp. and Chelonemonas dolani n. sp. Our comparative analysis suggests that apusomonad ancestor was a fusiform biflagellate with a dorsal pellicle, a plastic ventral surface and a sleeve covering the anterior flagellum, that thrived in marine, possibly oxygen-poor, environments. It likely had a complex cell cycle with dormant and multiple fission stages, and sex. Our results extend known apusomonad diversity, allow updating their taxonomy, and provide elements to understand early eukaryotic evolution.

microbiology↗

bioRxiv2022

Description of Gloeomargarita ahousahtiae sp. nov., a thermophilic member of the order Gloeomargaritales with intracellular carbonate inclusions

A unicellular cyanobacterium, strain VI4D9, was isolated from thermophilic microbial mats thriving in a hot spring of the Ahousaht territory of Vancouver Island, Canada. The cells were elongated rods (5.1 m in length and 1.2 m in width on average). Their UV-visible absorption spectra revealed that they contain chlorophyll a, phycocyanin, and carotenoids. Transmission electron microscopy showed the presence of thylakoids concentrated on one side of the cells. The strain grew within a temperature range of 37-50{degrees}C, with an optimum at 45{degrees}C. Its genome had a size of 3,049,282 bp and a DNA G+C content of 51.8 mol%. The cells contained numerous intracellular spherical granules easily visible under scanning electron microscopy. Energy-dispersive x-ray spectroscopy revealed that these granules were made of Ca-, Ba- and Sr-containing carbonates. A phylogenetic 16S rRNA gene tree robustly placed this strain as sister to several environmental sequences and the described species Gloeomargarita lithophora, also characterized by the possession of intracellular carbonate inclusions. We consider strain VI4D9 to represent a new Gloeomargarita species based on its marked phenotypic differences with G. lithophora, notably, its thermophilic nature and different thylakoid organization. We propose the name Gloeomargarita ahousahtiae sp. nov. for this newly isolated thermophilic cyanobacterium. The type strain is VI4D9 (Culture Collection of Algae and Protozoa strain 1472/1; Laboratorio de Algas Continentales Mexico strain LAC 140). G. ahousahtiae is the second species described within the recently discovered order Gloeomargaritales.

microbiology↗