Trends in biotechnology, Journal Year: 2024, Volume and Issue: unknown
Published: Nov. 1, 2024
Language: Английский
Microorganisms, Journal Year: 2024, Volume and Issue: 12(3), P. 444 - 444
Published: Feb. 22, 2024
Plastics in the ocean create "plastisphere", a diverse habitat hosting various life forms. Other than pollution induced by plastics, co-occurrence of primary producers, symbiotic organisms, decomposers, and pathogens within plastisphere raises questions about how they influence dynamics marine ecosystems. Here, we used shotgun DNA-sequencing approach to describe species thriving on floating plastics collected two Mediterranean sites. Our findings revealed many bacteria, eukaryotes, viruses, archaea each plastic. Proteobacteria was dominant (70% reads entire dataset), with other groups such as Ascomycota fungi (11%) Bacteroidetes (9%) also being represented. The community structure not affected polymeric composition or plastic shape. Notably, pathogenic Vibrio species, including V. campbelli, alginolyticus, coralliilyticus, were among most abundant species. Viruses, despite showing lower relative abundances, occurred all samples, especially Herpesvirales, Caudovirales, Poxviridae groups. A significant finding presence White Spot Syndrome virus (WSSV). This pathogen, responsible for devastating outbreaks aquaculture systems, had been previously reported plastisphere. study emphasizes need further investigation into ecological economic impacts organisms ocean.
Language: Английский
Citations
6
PLoS ONE, Journal Year: 2024, Volume and Issue: 19(4), P. e0300503 - e0300503
Published: April 5, 2024
Plastic materials, including microplastics, accumulate in all types of ecosystems, even remote and cold environments such as the European Alps. This pollution poses a risk for environment humans needs to be addressed. Using shotgun DNA metagenomics soils collected eastern Swiss Alps at about 3,000 m a.s.l., we identified genes their proteins that potentially can degrade plastics. We screened metagenomes plastisphere bulk soil with differential abundance analysis, conducted similarity-based screening specific databases dedicated putative plastic-degrading genes, selected those high probability signal peptides extracellular export confidence functional domains. procedure resulted final list nine candidate genes. The lengths predicted were between 425 845 amino acids, genera producing these belonged mainly Caballeronia Bradyrhizobium . applied validation, using heterologous expression followed by enzymatic assays supernatant. Five tested showed significantly increased activities when used an esterase assay, one five from hydrolase-type esterase, clearly had highest activity, more than double. performed fluorescence plastic degradation BI-OPL ecovio ® only positively active but like negative controls, did not show any activity. In contrast, activity positive control, which contained PLA-degrading gene insert known literature, was 20 times higher controls. These findings suggest silico validation is suitable finding new enzymes. Although found enzyme, our approach has potential type plastics various ecosystems search rapidly efficiently
Language: Английский
Citations
4
PROTEOMICS, Journal Year: 2025, Volume and Issue: unknown
Published: Jan. 6, 2025
Marine plastispheres represent dynamic microhabitats where microorganisms colonise plastic debris and interact. Metaproteomics has provided novel insights into the metabolic processes within these communities; however, early interactions driving plastisphere formation remain unclear. This study utilised metaproteomic metagenomic approaches to explore on low-density polyethylene (LDPE) over 3 (D3) 7 (D7) days, focusing microbial diversity, activity biofilm development. In total, 2948 proteins were analysed, revealing dominant proteomes from Pseudomonas Marinomonas, with near-complete metagenome-assembled genomes (MAGs). dominated at D3, whilst D7, along Acinetobacter, Vibrio other genera became more prevalent. Marinomonas showed high expression of reactive oxygen species (ROS) suppression proteins, associated oxidative stress regulation, granule formation, alternative carbon utilisation enzymes, also indicated nutrient limitations. Interestingly, 13 alkanes xenobiotic degradation enzymes expressed by five genera. The toxins, several type VI secretion system (TVISS) their competitive advantage against taxa. Upregulated pathways relating substrate transport suggested enhanced cross-feeding diverse community. These enhance our understanding ecology its potential for biotechnological applications.
Language: Английский
Citations
0
Biofilm, Journal Year: 2025, Volume and Issue: unknown, P. 100271 - 100271
Published: March 1, 2025
Language: Английский
Citations
0
Biotechnology Advances, Journal Year: 2025, Volume and Issue: 82, P. 108590 - 108590
Published: April 28, 2025
Language: Английский
Citations
0
iMeta, Journal Year: 2025, Volume and Issue: unknown
Published: May 6, 2025
Abstract Metaproteomics is an emerging approach for studying microbiomes, offering the ability to characterize proteins that underpin microbial functionality within diverse ecosystems. As primary catalytic and structural components of provide unique insights into active processes ecological roles communities. By integrating metaproteomics with other omics disciplines, researchers can gain a comprehensive understanding ecology, interactions, functional dynamics. This review, developed by Initiative ( www.metaproteomics.org ), serves as practical guide both microbiome proteomics researchers, presenting key principles, state‐of‐the‐art methodologies, analytical workflows essential metaproteomics. Topics covered include experimental design, sample preparation, mass spectrometry techniques, data analysis strategies, statistical approaches.
Language: Английский
Citations
0
Environmental Science & Technology, Journal Year: 2024, Volume and Issue: 58(32), P. 14496 - 14505
Published: July 24, 2024
Although massive studies have investigated the spatiotemporally occurring marine plastisphere, a new microbial ecosystem colonizing surfaces of plastics, resulting biofragmentation process and impacts plastics on biogeochemical cycles remain largely unknown. Here, we leverage synchrotron-based Fourier transform infrared spectromicroscopy (FTIR mapping) metagenomic sequencing to explore independent microcosms amended with petroleum-based polyethylene (PE) biobased polyhydroxybutyrate (PHB) plastic films. FTIR mapping results demonstrate unequal fragmentation scenarios by which PE rarely releases oxidized fragments while PHB disintegrates quickly, gradually forming composed extracellular polymeric substances resembling Metagenomic analysis shows critical role hydrocarbonoclastic lineages in biodegradation two fatty acid degradation pathway, where host different trajectories between plastisphere (dominated
Language: Английский
Citations
3
Environmental Pollution, Journal Year: 2024, Volume and Issue: 358, P. 124479 - 124479
Published: July 2, 2024
The taxonomy of marine plastisphere communities has been extensively studied, demonstrating the ubiquity hydrocarbonoclastic bacteria potential biotechnological significance. However, prokaryotic functioning on plastic surfaces received limited attention, and question whether these microorganisms are active expressing specific molecular mechanisms underpinning colonisation remains to be addressed. aim this study was investigate process, identify taxa involved in biofilm formation used initiate colonisation. To achieve this, a characterised by genera as inoculum for short-term microcosm experiment using virgin low-density polyethylene sole carbon source. Following incubation 1 2 weeks (representing early late colonisation, respectively), taxonomic comparative metaproteomic approach revealed significant shift diversity composition, yet highlighted stability predominance Proteobacteria spanning 16 genera, including Marinomonas, Pseudomonas, Pseudoalteromonas. Relative quantification 1762 proteins shared between initial inoculum, planktonic cells surrounding artificial seawater, provided insights into differential regulation associated with formation. This included upregulation mediating cellular attachment plastisphere, example flagellin expressed Cobetia, Pseudoalteromonas, curli Cobetia. In addition energy metabolism Psychrobacter, Pseudomonas Cobetia within relative seawater. Further, we identified amino acid transport, glutamine hydrolysis glutamate Marinomonas unclassified Halomonadaceae, potentially coupled ammonia availability oxidative stress experienced plastisphere. Our provides novel dynamics function, highlighting targets regulating growth enhance bioremediation processes.
Language: Английский
Citations
1
Environmental Science and Pollution Research, Journal Year: 2024, Volume and Issue: unknown
Published: Aug. 1, 2024
Language: Английский
Citations
1
Journal of Proteome Research, Journal Year: 2024, Volume and Issue: unknown
Published: Oct. 25, 2024
In metaproteomics studies, constructing a reference protein sequence database that is both comprehensive and not overly large critical for the peptide identification step. Therefore, availability of well-curated databases tools custom construction essential to enhance performance analyses. this review, we first provide an overview by presenting concise historical background, outlining typical experimental bioinformatics workflow, emphasizing crucial step metaproteomics. We then delve into current available building such databases, highlighting their individual approaches, utility, advantages limitations. Next, examine existing detailing scope relevance in research. Then, practical recommendations metaproteomics, along with challenges area. conclude discussion anticipated advancements, emerging trends, future directions
Language: Английский
Citations
0