Biology subjects

Ionescu, D.

Publications and source records attributed to Ionescu, D..

11 recordsLinked to original sources

bioRxiv2026

Giant bacteria in gut microbiomes

The advent of sequencing-based omics has transformed our understanding of the gut microbiome, enabling microbial communities to be characterised at unprecedented scale and resolution. However, these approaches provide limited information about cellular traits such as size and morphology. Giant bacteria remain largely overlooked in gut microbiome research, despite their extraordinary cell size, extreme polyploidy and unusual reproductive strategies. Epulopiscium, one of the largest known heterotrophic bacteria, has been studied primarily as an intestinal symbiont of surgeonfish, leaving its broader host range unresolved. Here we show, by a large-scale analysis of publicly available 16S ribosomal RNA amplicon samples, alongside locally collected human samples, that Epulopiscium spp. occur across diverse hosts, including humans and a broad diversity of animals. Full-length 16S rRNA gene phylogenies resolved multiple Epulopiscium-related lineages with distinct host compositions. Among human samples, Epulopiscium sequences were most abundant during the first year of life. In adults, abundance varied across disease states, increasing in inflammatory bowel disease and colorectal cancer while decreasing in neurological conditions compared with a healthy adult baseline. Similar patterns were also observed in mouse models. Our study broadens the known host range of Epulopiscium and establishes giant bacteria as an overlooked component of gut microbiome diversity. These findings highlight the need to combine sequence-based studies with classical microbiological techniques to identify organisms with unique traits, otherwise hidden by taxonomy or phylogeny.

microbiology↗

bioRxiv2026

Polyploid Achromatium sp. expresses protein variants based on environmental cues

Achromatium spp. are giant bacteria harboring hundreds of non-clonal chromosomes per cell. The allelic divergence they exhibit could be a mechanism to enable fine-tuned responses to environmental changes, enabling this organism to broaden its ecological range. However, while ubiquitous in freshwater and marine environments, Achromatium has not been obtained in culture, leaving the role and functioning of its genomic and proteomic diversity poorly understood. Here, we incubated freshly collected freshwater Achromatium under three temperature conditions to conduct comparative mass spectrometry-based proteomics experiments. These were interpreted against an Achromatium-specific protein atlas developed from curated published and new assemblies from marine and freshwater environments. This de novo assembled atlas allowed a twenty-fold increase in the number of identified proteins compared to mass spectrometry data searches against the UniProt database. Predicted proteins from the Achromatium atlas were grouped into orthologs, 5% of which showed temperature-associated detection of distinct protein variants within the group. This provides the first indication that Achromatium uses distinct protein variants under different environmental conditions, enabling it to swiftly respond to environmental changes through differential expression from its cache of chromosomes.

microbiology↗

bioRxiv2026

Intracellular genomic variability driven by cellular compartmentalization in the giant bacterium Achromatium spp

Bacteria of the genus Achromatium harbor hundreds of chromosomes that were previously suggested to be genetically diverse. By sequencing multiple regions from individual cells, we demonstrate that chromosomes within a single cell differ in nucleotide and amino acid sequence, reaching levels of divergence well below accepted bacterial species boundaries and below the range associated with homologous recombination. Sequencing of dividing cells further revealed that daughter cells inherit distinct chromosome populations, a mode of inheritance previously associated with sexual reproduction in eukaryotes. Combining subcellular sequencing with high-resolution microscopy, we reconstruct the three-dimensional cellular architecture of Achromatium and show that extensive intracellular heterogeneity arises from the spatial segregation of chromosome populations by the cells internal structure, which limits genome-wide recombination. Our findings establish cellular architecture as a determinant of genome evolution in giant polyploid bacteria and identify spatial genome segregation as a mechanism enabling the maintenance and inheritance of divergent chromosome populations in bacteria.

microbiology↗

bioRxiv2026

Chemotaxis and motility of Achromatium oxaliferum in response to oxygen, sulfide, and nitrate

Bacteria of the genus Achromatium are known for their large cell sizes and intracellular calcium carbonate deposits. Achromatium inhabit freshwater, brackish, and marine sediments where they accumulate to high abundances at the oxic-anoxic interface. These bacteria alter their vertical position in the sediment along with daily fluctuations in oxygen concentrations. Yet, the mechanism behind their migration in the sediment remains unknown. In this study, we used chemotaxis assays and time-lapse microphotography to analyze the motility and chemotactic behavior of Achromatium oxaliferum. Microscopic observations revealed that rolling and gliding were the main forms of locomotion exhibited by Achromatium. In absence of any stimulant, the movement appeared to be mostly random and changes in direction frequently occurred. Chemotaxis assays showed a negative chemotaxis of Achromatium to oxygen, sulfide, and nitrate, as evidenced by the change from undirected to directed locomotion against the respective chemical gradient. For periods of more than 1 hour, Achromatium cells moved continuously towards regions of low concentration. We further investigated whether the genetic repertoire of Achromatium corresponds to our observations. Based on lab experiments and bioinformatic analyses we conclude that Achomatium motility is propelled by type IV pili guided by a plethora of chemo- and photoreceptors. We conclude that Achromatium uses negative chemo- and phototaxis to confine their distribution in aquatic sediments between opposing oxygen and sulfide gradients. This allows Achromatium to dynamically adjust its position in redox gradients, and thus is likely to have a major contribution to its success in the global colonization of diverse aquatic sediments.

microbiology↗

bioRxiv2025

A food chain of ribozymes built on an ancestral strand

Molecular life forms in the prebiotic earth were capable of self-reproduction from basic building blocks. However, scarcity of building blocks likely led to the evolution of heterotrophic, predatory species. In this work we reconstruct a simple model of such interactions between RNA molecules, based on RNA strands found in sinkhole mineral pools in the Dead Sea. These RNA strands exhibited significant stability in this divergent chemical environment, and contained sequence motifs reminiscent of two ribozyme species, suggesting they could be ancestral to both. We built a system in which a single ancestral RNA strand serves as a limiting resource forming two different species of ribozymes that compete over it. One of these species is capable of metabolizing the other in order to free more of this resource, driving the assembly of additional copies of itself. This interaction resembles a rudimentary food chain, the dynamics of which is sensitive to environmental factors such as temperature and magnesium concentrations, with competitive advantage shifting between the species. Taken together, these findings highlight a hypothetical feature of prebiotic life, and hint at the possibility that heterotrophic RNA is a phenomenon that might still occur today in some unique geochemical niches, and even in the overlooked background of modern biological systems.

biophysics↗

bioRxiv2024

Phenotypic variability between closely related Trichodesmium strains as a means to making the most out of heterogeneous microenvironments

The cynobacteria Trichodesmium spp., play an important role in oceanic carbon and nitrogen cycles. Forming colonies that host diverse microorganisms likely enhances Trichodesmiums metabolic flexibility and resilience. Combining single-colony metagenomics and metatranscriptomics with a novel bioinformatic approach we investigated the community composition and transcriptional activity of 69 individual Trichodesmium thiebautii colonies collected from the northern Red Sea, Israel. Three Trichodesmium strains were detected in all colonies, each with a heterogenous yet distinct transcriptional-activity profile. N-fixation, superoxide dismutase, and ATPase activities were similar among colonies, while P and Fe uptake, as well as photosynthesis, were high in only few colonies. Colonies had no core microbiome with >70% dissimilarity in the associated microbial communities, yet, the abundance of some species was correlated with the activity of specific Trichodesmium strains. We propose Trichodesmium occupies heterogeneous microenvironments with which it deals through inter-strain phenotypic variability further fine-tuned through interactions with beneficial, non-fixed, heterotrophic colonizers.

microbiology↗

bioRxiv2022

From microbes to mammals: pond biodiversity homogenization across different land-use types in an agricultural landscape

Local biodiversity patterns are expected to strongly reflect variation in topography, land use, dispersal boundaries, nutrient supplies, contaminant spread, management practices and other anthropogenic influences. In contrast, studies focusing on specific taxa revealed a biodiversity homogenization effect in areas subjected to long-term intensive industrial agriculture. We investigated whether land use affects biodiversity and metacommunity structure in 67 kettle holes (KH) representing small aquatic islands embedded in the patchwork matrix of a largely agricultural landscape comprising grassland, forest, and arable fields. These KH, similar to millions of standing water bodies of glacial origin, spread across northern Europe, Asia, and North America, are physico-chemically diverse, differ in the degree of coupling with their surroundings. We assessed biodiversity patterns of eukaryotes, Bacteria and Archaea in relation to environmental features of the KH, using deep-amplicon-sequencing of eDNA. First, we asked whether deep sequencing of eDNA provides a representative picture of KH biodiversity across the three domains of life. Second, we investigated if and to what extent KH biodiversity is influenced by the surrounding land-use. Our data shows that deep eDNA amplicon sequencing is useful for in-depth assessments of cross-domain biodiversity comprising both micro- and macro-organisms, but, has limitations with respect to single-taxa conservation studies. Using this broad method, we show that sediment eDNA, integrating several years to decades, depicts the history of agricultural land-use intensification. The latter, coupled with landscape wide nutrient enrichment (including by atmospheric deposition), groundwater connectivity between KH and organismal movement in the tight network of ponds, resulted in a biodiversity homogenization in the KH water, levelling off todays detectable differences in KH biodiversity between land-use types.

ecology↗

bioRxiv2020

Genomic and morphologic characterization of a planktonic Thiovulum (Campylobacterota) dominating the surface waters of the sulfidic Movile Cave, Romania

Life in Movile Cave (Romania) relies entirely on carbon fixation by bacteria. The microbial community in the surface water of Movile Caves hypoxic air bells is dominated by large spherical-ovoid bacteria we identified as Thiovulum sp. (Campylobacterota). These form a separate phylogenetic cluster within the Thiovulaceae, consisting mostly of freshwater cave bacteria. We compared the closed genome of this Thiovulum to that of the marine strain Thiovulum ES, and to a genome we assembled from public data from the sulfidic Frasassi caves. The Movile and Frasassi Thiovulum were very similar, differing greatly from the marine strain. Based on their genomes, cave Thiovulum can switch between aerobic and anaerobic sulfide oxidation using O2 and NO3- as electron acceptors, respectively. NO3-, is likely reduced to NH3 via dissimilatory nitrate reduction to ammonia using periplasmic nitrate reductase (Nap) and hydroxylamine oxidoreductase. Thus, Thiovulum, is likely important to both S and N cycles in sulfidic subterranean aquatic ecosystems. Additionally, we suggest that the short peritrichous flagella-like structures typical of Thiovulum are type IV pili, for which genes were found in all Thiovulum genomes. These pili may play a role in veil formation, connecting adjacent cells and the exceptionally fast swimming of these bacteria.

microbiology↗

bioRxiv2020

Heterozygous, polyploid, giant bacterium, Achromatium, possesses an identical functional inventory worldwide across drastically different ecosystems

Achromatium is large, hyperpolyploid and the only known heterozygous bacterium. Single cells contain ca. 300 different chromosomes with allelic diversity typical of entire bacterial communities. Surveying all publicly available sediment sequence archives, we show Achromatia are common worldwide, spanning temperature, salinity, pH, and depth ranges normally resulting in bacterial speciation. Nevertheless, Achromatia display no ecotypic phylogenetic signal and contain a, globally identical, complete functional inventory. Achromatia cells from differing ecosystems (e.g. freshwater vs. saline) are, unexpectedly, equally functionally equipped but differ in gene expression patterns by transcribing only relevant genes. We suggest environmental adaptation occurs by increasing the copy number of relevant genes across the cells hundreds of chromosomes, without losing irrelevant ones, thus maintaining the ability to survive in any ecosystem type. The functional versatility of Achromatium, and its genomic features, reveal alternative genetic and evolutionary mechanisms, expanding our understanding of the role and evolution of polyploidy in bacteria while challenging the bacterial species concept and drivers of bacterial speciation.

microbiology↗

bioRxiv2018

Widespread formation of methane by Cyanobacteria in aquatic and terrestrial environments

Evidence is accumulating to challenge the paradigm that biogenic methanogenesis, traditionally considered a strictly anerobic process, is exclusive to Archaea. Here we demonstrate that Cyanobacteria living in marine, freshwater and terrestrial environments produce methane at substantial rates under light and dark oxic and anoxic conditions, forming a link between light driven primary productivity and methane production in globally relevant group of phototrophs. Biogenic methane production was enhanced during oxygenic photosynthesis and directly attributed to the cyanobacteria by applying stable isotope labelling techniques. We suggest that formation of methane by Cyanobacteria may contribute to methane accumulation in oxygen-saturated surface waters of marine and freshwater ecosystems. Moreover, in these environments, cyanobacterial blooms already do, and might further occur more frequently during future global warming and thus have a direct feedback on climate change. We further highlight that cyanobacterial methane production not only affects recent and future global methane budgets, but also has implications for inferences on Earths methane budget for the last 3.5 billion years, when this phylum is thought to have first evolved.

microbiology↗

bioRxiv2017

Recovering genomic clusters of secondary metabolites from lakes: a Metagenomics 2.0 approach

BackgroundMetagenomic approaches became increasingly popular in the past decades due to decreasing costs of DNA sequencing and bioinformatics development. So far, however, the recovery of long genes coding for secondary metabolism still represents a big challenge. Often, the quality of metagenome assemblies is poor, especially in environments with a high microbial diversity where sequence coverage is low and complexity of natural communities high. Recently, new and improved algorithms for binning environmental reads and contigs have been developed to overcome such limitations. Some of these algorithms use a similarity detection approach to classify the obtained reads into taxonomical units and to assemble draft genomes. This approach, however, is quite limited since it can classify exclusively sequences similar to those available (and well classified) in the databases.\n\nIn this work, we used draft genomes from Lake Stechlin, north-eastern Germany, recovered by MetaBat, an efficient binning tool that integrates empirical probabilistic distances of genome abundance, and tetranucleotide frequency for accurate metagenome binning. These genomes were screened for secondary metabolism genes, such as polyketide synthases (PKS) and non-ribosomal peptide synthases (NRPS), using the Anti-SMASH and NAPDOS workflows.\n\nResultsWith this approach we were able to identify 243 secondary metabolite clusters from 121 genomes recovered from the lake samples. A total of 18 NRPS, 19 PKS and 3 hybrid PKS/NRPS clusters were found. In addition, it was possible to predict the partial structure of several secondary metabolite clusters allowing for taxonomical classifications and phylogenetic inferences.\n\nConclusionsOur approach revealed a great potential to recover and study secondary metabolites genes from any aquatic ecosystem.

bioinformatics↗