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Bisaccia M, Berini F, Marinelli F, Binda E. Emerging Trends in Antimicrobial Resistance in Polar Aquatic Ecosystems. Antibiotics (Basel) 2025; 14:394. [PMID: 40298543 PMCID: PMC12024378 DOI: 10.3390/antibiotics14040394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2025] [Revised: 04/01/2025] [Accepted: 04/04/2025] [Indexed: 04/30/2025] Open
Abstract
The global spread of antimicrobial resistance (AMR) threatens to plummet society back to the pre-antibiotic era through a resurgence of common everyday infections' morbidity. Thus, studies investigating antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in urban, agricultural, and clinical settings, as well as in extreme environments, have become increasingly relevant in the One Health perspective. Since the Antarctic and Arctic regions are considered amongst the few remaining pristine environments on Earth, the characterization of their native resistome appears to be of the utmost importance to understand whether and how it is evolving as a result of anthropogenic activities and climate change. In the present review, we report on the phenotypic (e.g., disk diffusion test) and genotypic (e.g., PCR, metagenomics) approaches used to study AMR in the aquatic environment of polar regions, as water represents one of AMR main dissemination routes in nature. Their advantages and limits are described, and the emerging trends resulting from the analysis of ARB and ARGs diffusion in polar waters discussed. The resistome detected in these extreme environments appears to be mostly comparable to those from more anthropized areas, with the predominance of tetracycline, β-lactam, and sulfonamide resistance (and related ARGs). Indeed, AMR is, in all cases, more consistently highlighted in sites impacted by human and wildlife activities with respect to more pristine ones. Surprisingly, aminoglycoside and fluroquinolone determinants seem to have an even higher incidence in the Antarctic and Arctic aquatic environment compared to that from other areas of the world, corroborating the need for a more thorough AMR surveillance in these regions.
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Affiliation(s)
- Melissa Bisaccia
- Department of Biotechnology and Life Sciences (DBSV), University of Insubria, 21100 Varese, Italy; (M.B.); (F.B.); (E.B.)
| | - Francesca Berini
- Department of Biotechnology and Life Sciences (DBSV), University of Insubria, 21100 Varese, Italy; (M.B.); (F.B.); (E.B.)
- Climate Change Research Center (CCRC), University of Insubria, 22100 Como, Italy
| | - Flavia Marinelli
- Department of Biotechnology and Life Sciences (DBSV), University of Insubria, 21100 Varese, Italy; (M.B.); (F.B.); (E.B.)
- Climate Change Research Center (CCRC), University of Insubria, 22100 Como, Italy
| | - Elisa Binda
- Department of Biotechnology and Life Sciences (DBSV), University of Insubria, 21100 Varese, Italy; (M.B.); (F.B.); (E.B.)
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González D, Bruna P, Contreras MJ, Leal K, Urrutia CV, Núñez-Montero K, Barrientos L. Genome Mining of Pseudarthrobacter sp. So.54, a Rhizospheric Bacteria from Colobanthus quitensis Antarctic Plant. Biomolecules 2025; 15:534. [PMID: 40305262 PMCID: PMC12025171 DOI: 10.3390/biom15040534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2025] [Revised: 03/25/2025] [Accepted: 04/01/2025] [Indexed: 05/02/2025] Open
Abstract
Antarctic microorganisms have genomic characteristics and biological functions to ensure survival in complex habitats, potentially representing bioactive compounds of biotechnological interest. Pseudarthrobacter sp. So.54 is an Antarctic bacteria strain isolated from the rhizospheric soil of Colobanthus quitensis. Our work aimed to study its genomic characteristics and metabolic potential, linked to environmental adaptation and the production of secondary metabolites with possible biotechnological applications. Whole-genome sequencing, assembly, phylogenetic analysis, functional annotation, and genomic islands prediction were performed to determine the taxonomic affiliation and differential characteristics of the strain So.54. Additionally, Biosynthetic Gene Clusters (BGCs) responsible for secondary metabolites production were identified. The assembled genome of strain So.54 has 3,871,805 bp with 66.0% G + C content. Phylogenetic analysis confirmed that strain So.54 belongs to the Pseudarthrobacter genus; nevertheless, its nucleotide and amino acid identity values were below the species threshold. The main metabolic pathways and 64 genomic islands associated with stress defense and environmental adaptation, such as heavy metal resistance genes, were identified. AntiSMASH analysis predicted six BGCs with low or no similarity to known clusters, suggesting potential as novel natural products. These findings indicate that strain So.54 could be a novel Pseudarthrobacter species with significant environmental adaptation and biotechnological potential.
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Affiliation(s)
- Dayaimi González
- Programa de Doctorado en Ciencias Mención Biología Celular y Molecular Aplicada, Universidad de La Frontera, Temuco 4811230, Chile (C.V.U.)
- Centro de Excelencia en Medicina Traslacional (CEMT), Universidad de La Frontera, Avenida Alemania 0458, Temuco 4810296, Chile
| | - Pablo Bruna
- Programa de Doctorado en Ciencias Mención Biología Celular y Molecular Aplicada, Universidad de La Frontera, Temuco 4811230, Chile (C.V.U.)
- Núcleo Científico y Tecnológico en Biorecursos (BIOREN), Universidad de La Frontera, Avenida Francisco Salazar 01145, Temuco 4811230, Chile
| | - María J. Contreras
- Facultad de Ciencias de la Salud, Instituto de Ciencias Aplicadas, Universidad Autónoma de Chile, Avenida Alemania 1090, Temuco 4800000, Chile
| | - Karla Leal
- Facultad de Ciencias de la Salud, Instituto de Ciencias Aplicadas, Universidad Autónoma de Chile, Avenida Alemania 1090, Temuco 4800000, Chile
| | - Catherine V. Urrutia
- Programa de Doctorado en Ciencias Mención Biología Celular y Molecular Aplicada, Universidad de La Frontera, Temuco 4811230, Chile (C.V.U.)
- Centro de Excelencia en Medicina Traslacional (CEMT), Universidad de La Frontera, Avenida Alemania 0458, Temuco 4810296, Chile
| | - Kattia Núñez-Montero
- Facultad de Ingeniería, Instituto de Ciencias Aplicadas, Universidad Autónoma de Chile, Avenida Alemania 1090, Temuco 4800000, Chile
| | - Leticia Barrientos
- Facultad de Ingeniería, Instituto de Ciencias Aplicadas, Universidad Autónoma de Chile, Avenida Alemania 1090, Temuco 4800000, Chile
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Reiß F, Kiefer N, Reiß P, Kalkhof S, Noll M. Facade eluates affect active and total soil microbiome. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2025; 364:125242. [PMID: 39528135 DOI: 10.1016/j.envpol.2024.125242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2024] [Revised: 10/09/2024] [Accepted: 11/02/2024] [Indexed: 11/16/2024]
Abstract
The application of biocides in building materials has become a prevalent practice to mitigate the growth of microorganisms such as algae, fungi, and bacteria on the façades. These can leach out from the material and reach the nearby soil environment. This study aimed to characterize the effect of façade eluates generated within different leaching experiments on total and metabolic active soil microbial community composition and functions. Façade eluates were produced by immersion testing DIN EN 16105 and a natural weathering experiment. Afterward, soil microcosms were treated with the respective façade eluate and incubated for 29 days. Subsequently, the active and total soil microbial community compositions were investigated. Fungal internal transcribed spacer region gene and bacterial 16S rRNA gene were sequenced for active (bromodeoxyuridine labeled DNA) microbial community and total community. Façade eluates reduced total bacterial and fungal gene copy numbers. Overall, active bacterial and fungal richness was reduced and altered in community composition in comparison to the total richness and composition, respectively. Façade eluates retrieved of façade samples without biocides did alter the soil microbial communities to the same extent as façade eluates with biocides. Additionally, members of the active microbiome that benefit from the presence of façade eluates and omitted ones could be identified. Our result demonstrated that façade eluates affect active and total soil microbial community composition and function regardless of the leaching procedure and biocides addition.
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Affiliation(s)
- Fabienne Reiß
- Institute for Bioanalysis, Department of Applied Sciences, Coburg University of Applied Sciences and Arts, Coburg, Germany
| | - Nadine Kiefer
- Institute for Bioanalysis, Department of Applied Sciences, Coburg University of Applied Sciences and Arts, Coburg, Germany; Department of Preclinical Development and Validation, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Pascal Reiß
- Physical Chemistry IV, Department of Chemistry, University of Bayreuth, Bayreuth, Germany
| | - Stefan Kalkhof
- Institute for Bioanalysis, Department of Applied Sciences, Coburg University of Applied Sciences and Arts, Coburg, Germany; Department of Preclinical Development and Validation, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany; University of Leipzig, Institute for Analytical Chemistry, Leipzig, Germany
| | - Matthias Noll
- Institute for Bioanalysis, Department of Applied Sciences, Coburg University of Applied Sciences and Arts, Coburg, Germany; Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany.
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Otur Ç, Okay S, Konuksever Ö, Duyar O, Kaya Y, Kurt-Kızıldoğan A. Comprehensive characterization and resistome analysis of Antarctic Pseudomonas migulae strain CAS19. World J Microbiol Biotechnol 2024; 40:347. [PMID: 39397126 DOI: 10.1007/s11274-024-04153-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 09/30/2024] [Indexed: 10/15/2024]
Abstract
Although traditionally considered pristine, Antarctica faces an increasing threat of antibiotic resistance due to human intervention. Here, we obtained a bacterial isolate, the CAS19 strain, from a lake water sample from Ardley Island, Antarctica and characterized it comprehensively. The CAS19 was a psychrotrophic and neutrophilic/alkalitolerant bacterium thriving at temperatures from 15 to 33 °C and pH levels from 6.0 to 9.0. Besides the production of siderophore and indole acetic acid, it also exhibited proteolytic and lipolytic activities. It was identified as Pseudomonas migulae by multilocus (16S rRNA, gyrB, rpoB and rpoD) sequence analysis, and its genome was 6.5 Mbps in length, had 59% GC content, and contained 5,821 coding sequences. The CAS19 was resistant to several antibiotics, including trimethoprim, penicillin, vancomycin, and erythromycin, confirmed by RT-qPCR analysis, with a notable increase in dfr (63-fold), bla (461-fold), vanW (31.7-fold) and macA (24.7-fold) expressions upon antibiotic exposure. Additionally, CAS19 exhibited resistance to heavy metals with an order of Cr(III) = Cu(II) > Ni(II) > Zn(II) > Cd(II), and showed diesel fuel (5%) degradation capacity. Cold-related genes cspA_2 and cspD were overexpressed at 4 and 15 °C, consistent with the cold adaptation mechanism. In conclusion, for the first time an Antarctic P. migulae isolate has been characterized in detail, uncovering a rich resistome repertoir that might be associated with anthropogenic disturbances.
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Affiliation(s)
- Çiğdem Otur
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, Samsun, 55139, Türkiye
| | - Sezer Okay
- Department of Vaccine Technology, Vaccine Institute, Hacettepe University, Ankara, 06230, Türkiye.
| | - Ömer Konuksever
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, Samsun, 55139, Türkiye
| | - Oğuzhan Duyar
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, Samsun, 55139, Türkiye
| | - Yılmaz Kaya
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, Samsun, 55139, Türkiye
| | - Aslıhan Kurt-Kızıldoğan
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, Samsun, 55139, Türkiye.
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Ramasamy KP, Mahawar L, Rajasabapathy R, Rajeshwari K, Miceli C, Pucciarelli S. Comprehensive insights on environmental adaptation strategies in Antarctic bacteria and biotechnological applications of cold adapted molecules. Front Microbiol 2023; 14:1197797. [PMID: 37396361 PMCID: PMC10312091 DOI: 10.3389/fmicb.2023.1197797] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/31/2023] [Indexed: 07/04/2023] Open
Abstract
Climate change and the induced environmental disturbances is one of the major threats that have a strong impact on bacterial communities in the Antarctic environment. To cope with the persistent extreme environment and inhospitable conditions, psychrophilic bacteria are thriving and displaying striking adaptive characteristics towards severe external factors including freezing temperature, sea ice, high radiation and salinity which indicates their potential in regulating climate change's environmental impacts. The review illustrates the different adaptation strategies of Antarctic microbes to changing climate factors at the structural, physiological and molecular level. Moreover, we discuss the recent developments in "omics" approaches to reveal polar "blackbox" of psychrophiles in order to gain a comprehensive picture of bacterial communities. The psychrophilic bacteria synthesize distinctive cold-adapted enzymes and molecules that have many more industrial applications than mesophilic ones in biotechnological industries. Hence, the review also emphasizes on the biotechnological potential of psychrophilic enzymes in different sectors and suggests the machine learning approach to study cold-adapted bacteria and engineering the industrially important enzymes for sustainable bioeconomy.
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Affiliation(s)
| | - Lovely Mahawar
- Department of Plant Physiology, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture, Nitra, Slovakia
| | - Raju Rajasabapathy
- Department of Marine Science, Bharathidasan University, Tiruchirappalli, Tamilnadu, India
| | | | - Cristina Miceli
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Sandra Pucciarelli
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
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Fenibo EO, Selvarajan R, Abia ALK, Matambo T. Medium-chain alkane biodegradation and its link to some unifying attributes of alkB genes diversity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 877:162951. [PMID: 36948313 DOI: 10.1016/j.scitotenv.2023.162951] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 05/06/2023]
Abstract
Hydrocarbon footprints in the environment, via biosynthesis, natural seepage, anthropogenic activities and accidents, affect the ecosystem and induce a shift in the healthy biogeochemical equilibrium that drives needed ecological services. In addition, these imbalances cause human diseases and reduce animal and microorganism diversity. Microbial bioremediation, which capitalizes on functional genes, is a sustainable mitigation option for cleaning hydrocarbon-impacted environments. This review focuses on the bacterial alkB functional gene, which codes for a non-heme di‑iron monooxygenase (AlkB) with a di‑iron active site that catalyzes C8-C16 medium-chain alkane metabolism. These enzymes are ubiquitous and share common attributes such as being controlled by global transcriptional regulators, being a component of most super hydrocarbon degraders, and their distributions linked to horizontal gene transfer (HGT) events. The phylogenetic approach used in the HGT detection suggests that AlkB tree topology clusters bacteria functionally and that a preferential gradient dictates gene distribution. The alkB gene also acts as a biomarker for bioremediation, although it is found in pristine environments and absent in some hydrocarbon degraders. For instance, a quantitative molecular method has failed to link alkB copy number to contamination concentration levels. This limitation may be due to AlkB homologues, which have other functions besides n-alkane assimilation. Thus, this review, which focuses on Pseudomonas putida GPo1 alkB, shows that AlkB proteins are diverse but have some unifying trends around hydrocarbon-degrading bacteria; it is erroneous to rely on alkB detection alone as a monitoring parameter for hydrocarbon degradation, alkB gene distribution are preferentially distributed among bacteria, and the plausible explanation for AlkB affiliation to broad-spectrum metabolism of hydrocarbons in super-degraders hitherto reported. Overall, this review provides a broad perspective of the ecology of alkB-carrying bacteria and their directed biodegradation pathways.
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Affiliation(s)
- Emmanuel Oliver Fenibo
- World Bank Africa Centre of Excellence, Centre for Oilfield Chemical Research, University of Port Harcourt, Port Harcourt 500272, Nigeria
| | - Ramganesh Selvarajan
- Laboratory of Extraterrestrial Ocean Systems (LEOS), Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China; Department of Environmental Science, University of South Africa, Florida Campus, 1710, South Africa
| | - Akebe Luther King Abia
- Department of Environmental Science, University of South Africa, Florida Campus, 1710, South Africa; Environmental Research Foundation, Westville 3630, South Africa
| | - Tonderayi Matambo
- Institute for the Development of Energy for African Sustainability, University of South Africa, Roodepoort 1709, South Africa.
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