1
|
Marchetti A, Orlando M, Bombardi L, Fusco S, Mangiagalli M, Lotti M. Evolutionary history and activity towards oligosaccharides and polysaccharides of GH3 glycosidases from an Antarctic marine bacterium. Int J Biol Macromol 2024; 275:133449. [PMID: 38944065 DOI: 10.1016/j.ijbiomac.2024.133449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 05/30/2024] [Accepted: 06/24/2024] [Indexed: 07/01/2024]
Abstract
Glycoside hydrolases (GHs) are pivotal in the hydrolysis of the glycosidic bonds of sugars, which are the main carbon and energy sources. The genome of Marinomonas sp. ef1, an Antarctic bacterium, contains three GHs belonging to family 3. These enzymes have distinct architectures and low sequence identity, suggesting that they originated from separate horizontal gene transfer events. M-GH3_A and M-GH3_B, were found to differ in cold adaptation and substrate specificity. M-GH3_A is a bona fide cold-active enzyme since it retains 20 % activity at 10 °C and exhibits poor long-term thermal stability. On the other hand, M-GH3_B shows mesophilic traits with very low activity at 10 °C (< 5 %) and higher long-term thermal stability. Substrate specificity assays highlight that M-GH3_A is a promiscuous β-glucosidase mainly active on cellobiose and cellotetraose, whereas M-GH3_B is a β-xylosidase active on xylan and arabinoxylan. Structural analysis suggests that such functional differences are due to their differently shaped active sites. The active site of M-GH3_A is wider but has a narrower entrance compared to that of M-GH3_B. Genome-based prediction of metabolic pathways suggests that Marinomonas sp. ef1 can use monosaccharides derived from the GH3-catalyzed hydrolysis of oligosaccharides either as a carbon source or for producing osmolytes.
Collapse
Affiliation(s)
- Alessandro Marchetti
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza 2, Milano 20126, Italy
| | - Marco Orlando
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza 2, Milano 20126, Italy
| | - Luca Bombardi
- Biochemistry and Industrial Biotechnology (BIB) Laboratory, Department of Biotechnology, University of Verona, Verona, Italy
| | - Salvatore Fusco
- Biochemistry and Industrial Biotechnology (BIB) Laboratory, Department of Biotechnology, University of Verona, Verona, Italy
| | - Marco Mangiagalli
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza 2, Milano 20126, Italy.
| | - Marina Lotti
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza 2, Milano 20126, Italy
| |
Collapse
|
2
|
Okoye AU, Selvarajan R, Chikere CB, Okpokwasili GC, Mearns K. Characterization and identification of long-chain hydrocarbon-degrading bacterial communities in long-term chronically polluted soil in Ogoniland: an integrated approach using culture-dependent and independent methods. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:30867-30885. [PMID: 38622422 PMCID: PMC11096258 DOI: 10.1007/s11356-024-33326-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 04/11/2024] [Indexed: 04/17/2024]
Abstract
Escalating oil consumption has resulted in an increase in accidental spills of petroleum hydrocarbons, causing severe environmental degradation, notably in vulnerable regions like the Niger Delta. Complex mixture of these hydrocarbons particularly long-chain alkanes presents unique challenges in restoration of polluted environment due to their chemical properties. This study aimed to investigate the long-chain hydrocarbon-degrading bacterial communities within long-term chronically polluted soil in Ogoniland, by utilizing both traditional cultivation methods and modern culture-independent techniques. Results revealed that surface-polluted soil (SPS) and subsurface soil (SPSS) exhibit significantly higher total organic carbon (TOC) ranging from 5.64 to 5.06% and total petroleum hydrocarbons (TPH) levels ranging from 36,775 ppm to 14,087 ppm, compared to unpolluted soil (UPS) with 1.97% TOC and 479 ppm TPH, respectively. Analysis of carbon chain lengths reveals the prevalence of longer-chain alkanes (C20-28) in the surface soil. Culture-dependent methods, utilizing crude oil enrichment (COE) and paraffin wax enrichment (PWE), yield 47 bacterial isolates subjected to a long-chain alkane degradation assay. Twelve bacterial strains demonstrate significant degradation abilities across all enriched media. Three bacterial members, namely Pseudomonas sp. (almA), Marinomonas sp. (almA), and Alteromonas (ladA), exhibit genes responsible for long-chain alkane degradation, demonstrating efficiency between 50 and 80%. Culture-independent analysis reveals that surface SPS samples exhibit greater species richness and diversity compared to subsurface SPSS samples. Proteobacteria dominates as the phylum in both soil sample types, ranging from 22.23 to 82.61%, with Firmicutes (0.2-2.22%), Actinobacteria (0.4-3.02%), and Acidobacteria (0.1-3.53%) also prevalent. Bacterial profiles at genus level revealed that distinct variations among bacterial populations between SPS and SPSS samples comprising number of hydrocarbon degraders and the functional predictions also highlight the presence of potential catabolic genes (nahAa, adh2, and cpnA) in the polluted soil. However, culture-dependent analysis only captured a few of the dominant members found in culture-independent analysis, implying that more specialized media or environments are needed to isolate more bacterial members. The findings from this study contribute valuable information to ecological and biotechnological aspects, aiding in the development of more effective bioremediation applications for restoring oil-contaminated environments.
Collapse
Affiliation(s)
- Amara Ukamaka Okoye
- Department of Microbiology, Faculty of Science, University of Port Harcourt, Port Harcourt, 500272, Nigeria
| | - Ramganesh Selvarajan
- Department of Environmental Science, Florida Campus, University of South Africa, Roodepoort, 1709, South Africa.
- Laboratory of Extraterrestrial Ocean Systems (LEOS), Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China.
| | - Chioma Blaise Chikere
- Department of Microbiology, Faculty of Science, University of Port Harcourt, Port Harcourt, 500272, Nigeria
- Department of Environmental Science, Florida Campus, University of South Africa, Roodepoort, 1709, South Africa
| | | | - Kevin Mearns
- Department of Environmental Science, Florida Campus, University of South Africa, Roodepoort, 1709, South Africa
| |
Collapse
|
3
|
Nagoth JA, John MS, Ramasamy KP, Mancini A, Zannotti M, Piras S, Giovannetti R, Rathnam L, Miceli C, Biondini MC, Pucciarelli S. Synthesis of Bioactive Nickel Nanoparticles Using Bacterial Strains from an Antarctic Consortium. Mar Drugs 2024; 22:89. [PMID: 38393060 PMCID: PMC10890439 DOI: 10.3390/md22020089] [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: 01/26/2024] [Revised: 02/11/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
Marine microorganisms have been demonstrated to be an important source for bioactive molecules. In this paper we report the synthesis of Ni nanoparticles (NiSNPs) used as reducing and capping agents for five bacterial strains isolated from an Antarctic marine consortium: Marinomonas sp. ef1, Rhodococcus sp. ef1, Pseudomonas sp. ef1, Brevundimonas sp. ef1, and Bacillus sp. ef1. The NiSNPs were characterized by Ultraviolet-visible (UV-vis) spectroscopy, Dynamic Light Scattering (DLS), Transmission Electron Microscopy (TEM), X-ray diffraction (XRD) and Fourier Transform Infrared (FTIR) spectroscopic analysis. The maximum absorbances in the UV-Vis spectra were in the range of 374 nm to 422 nm, corresponding to the Surface plasmon resonance (SPR) of Nickel. DLS revealed NiSNPs with sizes between 40 and 45 nm. All NiSNPs were polycrystalline with a face-centered cubic lattice, as revealed by XRD analyses. The NiSNPs zeta potential values were highly negative. TEM analysis showed that the NiSNPs were either spherical or rod shaped, well segregated, and with a size between 20 and 50 nm. The FTIR spectra revealed peaks of amino acid and protein binding to the NiSNPs. Finally, all the NiSNPs possess significant antimicrobial activity, which may play an important role in the management of infectious diseases affecting human health.
Collapse
Affiliation(s)
- Joseph Amruthraj Nagoth
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy; (J.A.N.); (M.S.J.); (K.P.R.); (A.M.); (C.M.); (M.C.B.)
| | - Maria Sindhura John
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy; (J.A.N.); (M.S.J.); (K.P.R.); (A.M.); (C.M.); (M.C.B.)
- Department of Dermatology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kesava Priyan Ramasamy
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy; (J.A.N.); (M.S.J.); (K.P.R.); (A.M.); (C.M.); (M.C.B.)
- Department of Ecology and Environmental Science, Umeå University, 90187 Umeå, Sweden
| | - Alessio Mancini
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy; (J.A.N.); (M.S.J.); (K.P.R.); (A.M.); (C.M.); (M.C.B.)
| | - Marco Zannotti
- Chemistry Interdisciplinary Project (ChIP), Chemistry Division, School of Science and Technology, University of Camerino, 62032 Camerino, Italy; (M.Z.); (S.P.); (R.G.)
| | - Sara Piras
- Chemistry Interdisciplinary Project (ChIP), Chemistry Division, School of Science and Technology, University of Camerino, 62032 Camerino, Italy; (M.Z.); (S.P.); (R.G.)
| | - Rita Giovannetti
- Chemistry Interdisciplinary Project (ChIP), Chemistry Division, School of Science and Technology, University of Camerino, 62032 Camerino, Italy; (M.Z.); (S.P.); (R.G.)
| | - Lydia Rathnam
- Department of Physics, Pondicherry University, Puducherry 605014, India;
| | - Cristina Miceli
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy; (J.A.N.); (M.S.J.); (K.P.R.); (A.M.); (C.M.); (M.C.B.)
| | - Maria Chiara Biondini
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy; (J.A.N.); (M.S.J.); (K.P.R.); (A.M.); (C.M.); (M.C.B.)
| | - Sandra Pucciarelli
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy; (J.A.N.); (M.S.J.); (K.P.R.); (A.M.); (C.M.); (M.C.B.)
| |
Collapse
|