bioRxiv Science⌕ Search

Biology subjects

Becerra, C.

Publications and source records attributed to Becerra, C..

2 recordsLinked to original sources

Genomic and Functional Characterization of Priestia megaterium MOD5IV isolated from the rhizosphere of Caesalina spinosa (Mol.): Enhancing Phytoremediation Potential in Multi-Metal Contaminated Soils

AimsMetal contamination poses a global threat due to its widespread occurrence and the high toxicity of these elements. Phytoremediation has emerged as a preferred approach for the bioremediation of metal-contaminated soils. The search for microorganisms facilitating phytoremediation, especially plant-growth-promoting bacteria (PGPB), has become critical to advance ecosystem remediation efforts. This research aimed to characterize in-depth a Priestia megaterium strain isolated from multimetal contaminated soils located at the Atacama Desert, showing potential for bacteria-assisted phytoremediation. Methods and ResultsThe strain MOD5IV exhibited notable PGPB features: phosphate and potassium solubilization, nitrogen fixation, phytohormone production, and growth promotion of Arabidopsis thaliana. Genomic analysis revealed a 5,254,635 bp chromosome plus nine plasmids, hosting over 6,000 genes. Functional annotation identified genes associated with resistance to copper, cadmium, lead, mercury, zinc, and cobalt. Also, genes linked to PGPB capabilities as siderophore-production, nutrient-solubilization, IAA-synthesis, and nitrogen-fixation. Accordingly, MOD5IV exhibited robust tolerance to multiple metals and enhanced the phytoremediation potential of Caesalpinia Spinosa (Mol.) in laboratory trials. ConclusionsMOD5IV proved to have promising traits for microbe-assisted phytoremediation of metal-contaminated soils. Impact StatementThis study contributed to the characterization of new native multi-metal-resistant PGPR bacteria for phytoremediation of metal-contaminated soils. Increasing the evidence of the Atacama Desert as a source of microbiological solutions for climate adaptation and environmental remediation.

microbiology↗

Sub-nucleosomal organization in urine cell-free DNA

Cell-free DNA (cfDNA) in urine is a promising analyte for noninvasive diagnostics. However, urine cfDNA is highly fragmented and whether characteristics of these fragments reflect underlying genomic architecture is unknown. Here, we perform comprehensive characterization of fragmentation patterns in urine cfDNA. We show modal size and genome-wide distribution of urine cfDNA fragments are consistent with transient protection from degradation by stable intermediates of nucleosome disassembly. Genome-wide nucleosome occupancy and fragment sizes in urine cfDNA are informative of cell of origin and renal epithelial cells are amongst the highest contributors in urine. Compared to a nucleosome occupancy map based on control urine samples, we observe a higher fraction of fragments with aberrant ends in cancer patients, distinguishing cancer samples with an area under the curve of 0.89. Our results demonstrate sub-nucleosomal organization in urine cfDNA and are proof-of-principle that genome-wide fragmentation analysis of urine cfDNA can enable cancer diagnostics.

genomics↗