Biology subjects

Bagi, A.

Publications and source records attributed to Bagi, A..

3 recordsLinked to original sources

bioRxiv2026

Taxonomic vs. Functional Diversity for the Impact Assessment of Offshore Oil & Gas Activities: An Exploratory Study on Benthic Prokaryotes

Improving environmental management in the offshore Oil & Gas sector requires approaches that capture the ecosystem services (ES) provided by marine sediments, particularly their roles in carbon and nutrient cycling. Microbial communities are central to these processes, and molecular tools offer new opportunities to assess their functional diversity. To explore how different sequencing approaches inform environmental impact assessment, we compared taxonomic and functional prediction based on 16S metabarcoding, shotgun metagenomics and messenger RNA-based metatranscriptomics, targeting prokaryotic communities. Our aims were to evaluate the ability of each approach to detect impact and to determine how well they captured functions relevant to ES. All approaches revealed clear differences in community composition between impacted and non-impacted sediments at both taxonomic and functional levels, with impact significantly associated with hydrocarbon and barium content. Functional inventories showed substantial overlap across the three approaches, and 48-55 ES-related processes were detectable in all datasets. While metagenomics provided the strongest statistical discrimination between impact groups, metatranscriptomics resolved the actively expressed pathways underpinning ES, yielding the most biologically meaningful functional profiles despite its lower statistical power. All approaches indicated that Oil & Gas activity drives shift towards anaerobic, hydrocarbon-degrading, and sulfur-respiring microbial communities, with hydrocarbon degradation, sulfur cycling, and metal detoxification being the dominant ES processes in impacted sediments. Metabarcoding was confirmed as a cost-effective option for impact assessment when focused on taxonomic composition. However, functional prediction from metabarcoding data proved less reliable, as several ES showed contrasting associations to impact category between metabarcoding and shotgun sequencing approaches.

microbiology↗

bioRxiv2021

Distinct stress-dependent signatures of cellular and extracellular tRNA-derived small RNAs (tDRs)

The cellular response to stress is an important determinant of disease pathogenesis. Uncovering the molecular fingerprints of distinct stress responses may yield novel biomarkers for different diseases, and potentially identify key signaling pathways important for disease progression. tRNAs and tRNA-derived small RNAs (tDRs) comprise one of the most abundant RNA species in cells and have been associated with cellular stress responses. The presence of RNA modifications on tDRs has been an obstacle for accurately identifying tDRs with conventional small RNA sequencing. Here, we use AlkB-facilitated methylation sequencing (ARM-seq) to uncover a comprehensive landscape of cellular and extracellular tDR expression in a variety of human and rat cells during common stress responses, including nutritional deprivation, hypoxia, and oxidative stress. We found that extracellular tDRs have a distinct fragmentation signature with a predominant length of 31-33 nts and a highly specific termination position when compared with intracellular tDRs. Importantly, we found these signatures are better discriminators of different cellular stress responses compared to extracellular miRNAs. Distinct extracellular tDR signatures for each profiled stressor are elucidated in four different types of cells. This distinct extracellular tDR fragmentation pattern is also noted in plasma extracellular RNAs from patients on cardiopulmonary bypass. The observed overlap of these patient tDR signatures with the signatures of nutritional deprivation and oxidative stress in our cellular models provides preliminary in vivo corroboration of our findings and demonstrates the potential to establish novel extracellular tDR biomarkers in human disease models.

cell biology↗

bioRxiv2019

Discovery of functional gene markers of bacteria for monitoring hydrocarbon pollution in the marine environment - a metatranscriptomics approach

The use of natural marine bacteria as "oil sensors" for the detection of pollution events can be suggested as a novel way of monitoring oil occurrence at sea. Nucleic acid-based devices generically called genosensors are emerging as potentially promising tools for in situ detection of specific microbial marker genes suited for that purpose. Functional marker genes are particularly interesting as targets for oil-related genosensing but their identification remains a challenge. Here, seawater samples, collected in tanks with oil addition mimicking a realistic oil spill scenario, were filtered and archived by the Environmental Sample Processor (ESP), a fully robotized genosensor, and the samples were then used for post-retrieval metatranscriptomic analysis. After extraction, RNA from ESP-archived samples at start, day 4 and day 7 of the experiment was used for sequencing. Metatranscriptomics revealed that several KEGG pathways were significantly enriched in samples exposed to oil. However, these pathways were highly expressed also in the non-oil-exposed water samples, most likely as a result of the release of natural organic matter from decaying phytoplankton. Temporary peaks of aliphatic alcohol and aldehyde dehydrogenases and monoaromatic ring-degrading enzymes (e.g. ben, box, and dmp clusters) were observed on day 4 in both control and oil tanks. Few alkane 1-monooxygenase genes were upregulated on oil, mostly transcribed by families Porticoccaceae and Rhodobacteraceae, together with aromatic ring-hydroxylating dioxygenases, mostly transcribed by Rhodobacteraceae. Few transcripts from obligate hydrocarbonoclastic genera of Alcanivorax, Oleispira and Cycloclasticus, were significantly enriched in the oil-treated tank in comparison to control, and these were mostly transporters and genes involved in nitrogen and phosphorous acquisition. This study highlights the importance of seasonality, i.e., phytoplankton occurrence and senescence leading to organic compound release which can be used preferentially by bacteria over oil compounds, delaying the latter process. As a result, such seasonal effect can reduce the sensitivity of genosensing tools employing bacterial functional genes to sense oil. A better understanding of the use of natural organic matter by bacteria involved in oil-biodegradation is needed to develop an array of functional markers enabling the rapid and specific in situ detection of anthropogenic pollution.

microbiology↗