Biology subjects

Banciu, H. L.

Publications and source records attributed to Banciu, H. L..

6 recordsLinked to original sources

bioRxiv2026

MEGAHIT k-mer range tuning trades computational efficiency for improved recovery of functional genes across cave sediment and wastewater metagenomes

Shotgun metagenomics is a powerful approach for profiling complex microbial ecosystems and discovering functional genes, including antimicrobial resistance genes (ARGs) and biosynthetic gene clusters (BGCs). De novo assembly with tools such as MEGAHIT commonly uses multiple k-mer lengths, but the effect of reduced k-mer sets on functional gene recovery has received limited attention. Here, we quantify the trade-off between assembly speed and functional-gene recovery using 17 cave sediment metagenomes and 10 wastewater metagenomes assembled under 19 MEGAHIT k-mer scenarios. In cave metagenomes, finer-grained k-mer ranges recovered more BGCs and, in several pairwise comparisons, more ARGs, but required longer runtimes. In wastewater metagenomes, finer-grained settings most clearly affected ARG recovery, whereas BGC counts did not differ significantly after Friedman testing. These results indicate that reduced k-mer sets can lower computational cost but may miss biologically relevant functional signal, depending on the dataset and downstream target. The study provides a quantitative basis for selecting MEGAHIT k-mer parameters according to whether computational efficiency or functional gene discovery is the primary aim.

bioinformatics↗

bioRxiv2025

Metagenomics reveal allopatric speciation and higher connectivity among coastal vs. inland hypersaline lakes and solar salterns

Hypersaline environments, due to their discrete and geographically isolated nature, constitute ideal systems for studying evolutionary patterns and microbial diversification, and especially here when contrasting coastal with inland systems. Based on metagenomic comparisons of 25 hypersaline sites across 11 countries, we explored the influence of environmental factors, ionic composition, and geographic distance on their microbial community structures and taxa diversification. Our results revealed that microbial communities from coastal environments were taxonomically and functionally more similar to each other than to those from inland sites. A distance-decay relationship in the genetic relatedness, significantly more pronounced for the coastal sites, was observed among reconstructed metagenome-assembled genomes (MAGs), clearer at distances below 400 km, but still detectable across global scales up to 20,000 km. The 484 MAGs recovered, representing 284 distinct species, revealed a striking global ubiquity, with 62.5% of the species showed cosmopolitanism as were detected across multiple sites. The higher taxonomic and genetic similarity of coastal environments over the inland sites seems to reflect an environmental connection that may be related to the ocean current dynamics. Most cosmopolitan species showed clear allopatric differentiation, although few cases of a single globally dominant genomovar (average nucleotide identity, ANI > 99.8%) were also observed, especially for some Haloquadratum species. The findings suggest that coastal hypersaline systems are loosely constrained by geographic isolation, with clear signals of allopatric speciation at the mesoscale (tenths to hundreds of kilometers) that become blurrier at larger scales.

microbiology↗

bioRxiv2025

Community-level physiological profiling of carbon substrate metabolization by microbial communities associated to sediments and water in karstic caves from Romania

Cave ecosystems comprise specialized microbial communities that play essential roles in biogeochemical cycles; yet their metabolic capabilities and ecological functions are not yet fully understood. As conventional cultivation techniques offer limited insights into the metabolic capabilities, methods based on direct functionality screening could provide more in-depth knowledge of cave microbial activity. In this study, we utilized the Community-Level Physiological Profiling (CLPP) based on Biolog(R) EcoPlate approach to assessing carbon substrate utilization by microbial communities associated with pool water, sediment, sediment (limon), and moonmilk from five caves in Romania. Principal Component Analysis (PCA) and Generalized Additive Models (GAMs) statistics were employed to infer the patterns of C-substrate metabolization and their environmental drivers. Environmental variables such as sodium (Na) and electrical conductivity (EC) significantly impacted C-utilization capabilities as indicated by both PCA and GAM. The latter analysis elucidated non-linear relationships between variables, such as EC, Na, and Mg, and microbial metabolic diversity indices. However, distinct C utilization patterns were detected among sampled sites and chemical types. Unlike moonmilk samples whose associated microbial communities appeared as exhibiting low C-substrate utilization, the highest activity was shown in cave pool water samples with the associated microbial communities extensively consuming D-galacturonic acid and Tween 80. Conversely, substrates like L-threonine and -ketobutyric acid showed limited utilization across all cave samples. Average Well Color Development (AWCD) and Shannon diversity indices indicated that microbial communities associated to samples from Closani and Muierilor caves demonstrated the highest metabolic diversity. Our findings suggested that metabolic profiling using Biolog(R)EcoPlates method combined with multivariate statistical methods might prove as suitable approach to effectively screen for cave microbial functionality and the probable environmental drivers. Besides, this work distinguishes from similar studies by relying on GAM analysis to predict the environmental factors governing the microbially-mediated organic carbon degradation in subterranean ecosystems.

microbiology↗

bioRxiv2022

Competition-cooperation in the chemoautotrophic ecosystem of Movile Cave - first metagenomic approach on sediments

BackgroundMovile Cave (Dobrogea, SE Romania) hosts a subterranean chemoautotrophically-based ecosystem supported by a sulfidic thermal aquifer analogous to the deep-sea hydrothermal ecosystems. Our current understanding of Movile Cave microbiology has been confined to the thermal water proximity (no more than 2 m distant), with most studies focusing on the water-floating mat, which likely acts as the primary production powerhouse in this sulfidic ecosystem. To gain more insightful information on the functioning of the sulfidic Movile Cave ecosystem, we employed a metagenomics-resolved approach to reveal the microbiome diversity, metabolic potential, and interactions and infer its roles within the food webs in the sediments beyond the sulfidic thermal waters. ResultsA customized bioinformatics pipeline led to the recovery of 106 high-quality metagenome-assembled genomes from 7 cave sediment metagenomes. Assemblies taxonomy spanned 19 bacterial and three archaeal phyla with Acidobacteriota, Chloroflexota, Proteobacteria, Planctomycetota, Ca. Patescibacteria, Thermoproteota, Methylomirabilota, and Ca. Zixibacteria as prevalent phyla. Functional gene analyses allowed prediction of CO2 fixation, methanotrophy, sulfur and ammonia oxidation as possibly occurring in the explored sediments. Species Metabolic Coupling Analysis of metagenome-scale metabolic models revealed the highest competition-cooperation interactions in the sediments collected at the farthest distance from the sulfidic water. As a result of simulated metabolic interactions, autotrophs and methanotrophs were hypothesized as major donors of exchanged metabolites in the sediment communities. Cross-feeding dependencies were assumed only towards currency molecules and inorganic compounds (O2, PO43-, H+, Fe2+, Cu2+) in the sediment nearby sulfidic water, whereas hydrogen sulfide and methanol are predictably traded exclusively among communities dwelling in the distant gallery. ConclusionsThese findings suggest that the primary production potential of the Movile Cave expands way beyond its hydrothermal waters, enhancing our understanding of ecological interactions inside chemolithoautotrophically based subterranean ecosystems and their functioning.

microbiology↗

bioRxiv2021

Intact rDNA arrays of Potentilla-origin detected in Erythronium nucleus suggest recent eudicot-to-monocot horizontal transfer

The occurrence of horizontal gene transfer (HGT) in Eukarya is increasingly gaining recognition. Nuclear-to-nuclear jump of DNA between plant species at high phylogenetic distance and devoid of intimate association (e.g., parasitism) is still scarcely reported. Within eukaryotes, components of ribosomal DNA (rDNA) multigene family have been found to be horizontally transferred in protists, fungi and grasses. However, in neither case HGT occurred between phylogenetic families, nor the transferred rDNA remained tandemly arrayed and transcriptionally active in the recipient organism. This study aimed to characterize an alien eudicot-type of 45S nuclear rDNA, assumingly transferred horizontally to the genome of monocot European Erythronium (Liliaceae). Genome skimming coupled by PacBio HiFi sequencing of a BAC clone were applied to determine DNA sequence of the alien rDNA. A clear phylogenetic signal traced the origin of the alien rDNA of Erythronium back to the Argentea clade of Potentilla (Rosaceae) and deemed the transfer to have occurred in the common ancestor of E. dens-canis and E. caucasicum. Though being discontinuous, transferred rDNA preserved its general tandemly arrayed feature in the host organism. Southern blotting, molecular cytogenetics, and sequencing of a BAC clone derived from flow-sorted nuclei indicated integration of the alien rDNA into the recipients nuclear genome. Unprecedently, dicot-type alien rDNA was found to be transcribed in the monocot Erythronium albeit much less efficiently than the native counterpart. This study adds a new example to the growing list of naturally transgenic plants while holding the scientific community continually in suspense about the mode of DNA transfer. Significance StatementRibosomal DNA is an essential component of all cellular genomes. In plants, accidental movement of rDNA via horizontal gene transfer has only been reported in sexually incompatible grasses (monocots) where it involved non-functional rDNA units. In this study, we propose that evolutionary trajectories of eudicots and monocots were bypassed by the jump of rDNA from a Potentilla species (Rosaceae) to a common ancestor of Erythronium dens-canis and E. caucasicum (Liliaceae). The alien eudicot-type rDNA appeared relatively well conserved in the examined host Erythronium genome, being able to be expressed while preserving its general tandemly repeated feature, evidences that have no match in earlier literature.

plant biology↗

bioRxiv2019

Visualization of Loki- and Heimdallarchaeia (Asgardarchaeota) by fluorescence in situ hybridization and catalyzed reporter deposition (CARD-FISH)

Metagenome-assembled genomes (MAGs) of Asgardarchaeota are starting to be recovered from a variety of habitats, broadening their environmental distribution and providing access to the genetic makeup of this archaeal lineage. Despite their singular phylogenetic position at the base of the eukaryotic tree of life, the morphology of these bewildering organisms remains a mystery. In order to visualize this elusive group, we applied a combination of CARD-FISH and epifluorescence microscopy on coastal hypersaline sediment samples, using specifically designed CARD-FISH probes for Heimdallarchaeia and Lokiarchaeia lineages and provide the first visual evidence for both these groups. Here, we show that while Heimdallarchaeia are characterized by a uniform cellular morphology typified by central DNA localization, Lokiarchaeia display a plethora of shapes and sizes that likely reflect their broad phylogenetic diversity and ecological distribution.

microbiology↗